Daniel Tartakovsky

All Publications

• Non-equilibrium thermal models of lithium batteries JOURNAL OF POWER SOURCES Yang, X., Li, W., Um, K., Tartakovsky, D. M. 2024; 623

  View details for DOI 10.1016/j.jpowsour.2024.235428

  View details for Web of Science ID 001317626700001

• Dynamic mode decomposition of GRACE satellite data ADVANCES IN WATER RESOURCES Libero, G., Ciriello, V., Tartakovsky, D. M. 2024; 193

  View details for DOI 10.1016/j.advwatres.2024.104834

  View details for Web of Science ID 001339939400001

• High-order Lagrangian algorithms for Liouville models of particle-laden flows JOURNAL OF COMPUTATIONAL PHYSICS Dominguez-Vazquez, D., Castiblanco-Ballesteros, S. A., Jacobs, G. B., Tartakovsky, D. M. 2024; 515

  View details for DOI 10.1016/j.jcp.2024.113281

  View details for Web of Science ID 001278946600001

• Design of Stable Hollow Particles for Silicon Anodes ACS ENERGY LETTERS Joshi, S. A., Tchelepi, H. A., Tartakovsky, D. M. 2024

  View details for DOI 10.1021/acsenergylett.4c01873

  View details for Web of Science ID 001312747000001

• A meshless stochastic method for Poisson-Nernst-Planck equations. The Journal of chemical physics Monteiro, H. B., Tartakovsky, D. M. 2024; 161 (5)

  Abstract

  A plethora of biological, physical, and chemical phenomena involve transport of charged particles (ions). Its continuum-scale description relies on the Poisson-Nernst-Planck (PNP) system, which encapsulates the conservation of mass and charge. The numerical solution of these coupled partial differential equations is challenging and suffers from both the curse of dimensionality and difficulty in efficiently parallelizing. We present a novel particle-based framework to solve the full PNP system by simulating a drift-diffusion process with time- and space-varying drift. We leverage Green's functions, kernel-independent fast multipole methods, and kernel density estimation to solve the PNP system in a meshless manner, capable of handling discontinuous initial states. The method is embarrassingly parallel, and the computational cost scales linearly with the number of particles and dimension. We use a series of numerical experiments to demonstrate both the method's convergence with respect to the number of particles and computational cost vis-à-vis a traditional partial differential equation solver.

  View details for DOI 10.1063/5.0223018

  View details for PubMedID 39087897

• Data-driven models of nonautonomous systems JOURNAL OF COMPUTATIONAL PHYSICS Lu, H., Tartakovsky, D. M. 2024; 507

  View details for DOI 10.1016/j.jcp.2024.112976

  View details for Web of Science ID 001223076700001

• Efficient quadratures for high-dimensional Bayesian data assimilation JOURNAL OF COMPUTATIONAL PHYSICS Cheng, M., Wang, P., Tartakovsky, D. M. 2024; 506

  View details for DOI 10.1016/j.jcp.2024.112945

  View details for Web of Science ID 001222686900001

• Liouville models of particle-laden flow PHYSICS OF FLUIDS Dominguez-Vazquez, D., Jacobs, G. B., Tartakovsky, D. M. 2024; 36 (6)

  View details for DOI 10.1063/5.0207403

  View details for Web of Science ID 001239083900012

• Extended dynamic mode decomposition for model reduction in fluid dynamics simulations PHYSICS OF FLUIDS Libero, G., Chiofalo, A., Ciriello, V., Tartakovsky, D. M. 2024; 36 (6)

  View details for DOI 10.1063/5.0207957

  View details for Web of Science ID 001250829100011

• Polynomial chaos enhanced by dynamic mode decomposition for order-reduction of dynamic models ADVANCES IN WATER RESOURCES Libero, G., Tartakovsky, D. M., Ciriello, V. 2024; 186

  View details for DOI 10.1016/j.advwatres.2024.104677

  View details for Web of Science ID 001221490300001

• Neural Oscillators for Generalization of Physics-Informed Machine Learning Kapoor, T., Chandra, A., Tartakovsky, D. M., Wang, H., Nunez, A., Dollevoet, R., Wooldridge, M., Dy, J., Natarajan, S. ASSOC ADVANCEMENT ARTIFICIAL INTELLIGENCE. 2024: 13059-13067

  View details for Web of Science ID 001241515300010

• Surrogate models of heat transfer in fractured rock and their use in parameter estimation COMPUTERS & GEOSCIENCES Song, G., Roubinet, D., Wang, X., Li, G., Song, X., Tartakovsky, D. M. 2024; 183

  View details for DOI 10.1016/j.cageo.2023.105509

  View details for Web of Science ID 001137346900001

• Feature-informed data assimilation JOURNAL OF COMPUTATIONAL PHYSICS Srivastava, A., Kang, W., Tartakovsky, D. M. 2023; 494

  View details for DOI 10.1016/j.jcp.2023.112499

  View details for Web of Science ID 001099272000001

• DRIPS: A framework for dimension reduction and interpolation in parameter space JOURNAL OF COMPUTATIONAL PHYSICS Lu, H., Tartakovsky, D. M. 2023; 493

  View details for DOI 10.1016/j.jcp.2023.112455

  View details for Web of Science ID 001073628700001

• Parsimonious models of in-host viral dynamics and immune response APPLIED MATHEMATICS LETTERS Lu, H., Giannino, F., Tartakovsky, D. M. 2023; 145

  View details for DOI 10.1016/j.aml.2023.108781

  View details for Web of Science ID 001044515300001

• Hypertonic treatment of acute respiratory distress syndrome. Frontiers in bioengineering and biotechnology Li, W., Martini, J., Intaglietta, M., Tartakovsky, D. M. 2023; 11: 1250312

  Abstract

  Many viral infections, including the COVID-19 infection, are associated with the hindrance of blood oxygenation due to the accumulation of fluid, inflammatory cells, and cell debris in the lung alveoli. This condition is similar to Acute Respiratory Distress Syndrome (ARDS). Mechanical positive-pressure ventilation is often used to treat this condition, even though it might collapse pulmonary capillaries, trapping red blood cells and lowering the lung's functional capillary density. We posit that the hyperosmotic-hyperoncotic infusion should be explored as a supportive treatment for ARDS. As a first step in verifying the feasibility of this ARDS treatment, we model the dynamics of alveolar fluid extraction by osmotic effects. These are induced by increasing blood plasma osmotic pressure in response to the increase of blood NaCl concentration. Our analysis of fluid drainage from a plasma-filled pulmonary alveolus, in response to the intravenous infusion of 100 ml of 1.28 molar NaCl solution, shows that alveoli empty of fluid in approximately 15 min. These modeling results are in accordance with available experimental and clinical data; no new data were collected. They are used to calculate the temporal change of blood oxygenation, as oxygen diffusion hindrance decreases upon absorption of the alveolar fluid into the pulmonary circulation. Our study suggests the extraordinary speed with which beneficial effects of the proposed ARDS treatment are obtained and highlight its practicality, cost-efficiency, and avoidance of side effects of mechanical origin.

  View details for DOI 10.3389/fbioe.2023.1250312

  View details for PubMedID 37936822

  View details for PubMedCentralID PMC10627238

• Effective Models of Heat Conduction in Composite Electrodes JOURNAL OF THE ELECTROCHEMICAL SOCIETY Li, W., Tartakovsky, D. M. 2023; 170 (10)

  View details for DOI 10.1149/1945-7111/acfdd4

  View details for Web of Science ID 001078589100001

• Uncertain characterization of reservoir fluids due to brittleness of equation of state regression GEOENERGY SCIENCE AND ENGINEERING Fulchignoni, L., Tartakovsky, D. M. 2023; 228

  View details for DOI 10.1016/j.geoen.2023.211985

  View details for Web of Science ID 001056385500001

• Probabilistic forecasting of cumulative production of reservoir fluid with uncertain properties GEOENERGY SCIENCE AND ENGINEERING Fulchignoni, L., Santim, C., Tartakovsky, D. M. 2023; 227

  View details for DOI 10.1016/j.geoen.2023.211819

  View details for Web of Science ID 001053100000001

• Discovery of sparse hysteresis models for piezoelectric materials APPLIED PHYSICS LETTERS Chandra, A., Daniels, B., Curti, M., Tiels, K., Lomonova, E. A., Tartakovsky, D. M. 2023; 122 (21)

  View details for DOI 10.1063/5.0146134

  View details for Web of Science ID 000993581000012

• Screening of Electrolyte-Anode Buffers to Suppress Lithium Dendrite Growth in All-Solid-State Batteries JOURNAL OF THE ELECTROCHEMICAL SOCIETY Li, W., Tchelepi, H. A., Tartakovsky, D. M. 2023; 170 (5)

  View details for DOI 10.1149/1945-7111/acd0da

  View details for Web of Science ID 000981779500001

• Fast and Accurate Estimation of Evapotranspiration for Smart Agriculture WATER RESOURCES RESEARCH Li, W., Tartakovsky, D. M. 2023; 59 (4)

  View details for DOI 10.1029/2023WR034535

  View details for Web of Science ID 000977206200001

• Method of Distributions for Two-Phase Flow in Heterogeneous Porous Media WATER RESOURCES RESEARCH Yang, H., Tchelepi, H. A., Tartakovsky, D. M. 2022; 58 (12)

  View details for DOI 10.1029/2022WR032607

  View details for Web of Science ID 000929780100001

• Information geometry of physics-informed statistical manifolds and its use in data assimilation JOURNAL OF COMPUTATIONAL PHYSICS Boso, F., Tartakovsky, D. M. 2022; 467

  View details for DOI 10.1016/j.jcp.2022.111438

  View details for Web of Science ID 000917225500012

• Deep Learning for Simultaneous Inference of Hydraulic and Transport Properties WATER RESOURCES RESEARCH Zhou, Z., Zabaras, N., Tartakovsky, D. M. 2022; 58 (10)

  View details for DOI 10.1029/2021WR031438

  View details for Web of Science ID 000863034200001

• Impact of Carbon Binder Domain on the Performance of Lithium-metal Batteries JOURNAL OF THE ELECTROCHEMICAL SOCIETY Boso, F., Li, W., Um, K., Tartakovsky, D. M. 2022; 169 (10)

  View details for DOI 10.1149/1945-7111/ac9a82

  View details for Web of Science ID 000877314400001

• Autonomous learning of nonlocal stochastic neuron dynamics. Cognitive neurodynamics Maltba, T. E., Zhao, H., Tartakovsky, D. M. 2022; 16 (3): 683-705

  Abstract

  Neuronal dynamics is driven by externally imposed or internally generated random excitations/noise, and is often described by systems of random or stochastic ordinary differential equations. Such systems admit a distribution of solutions, which is (partially) characterized by the single-time joint probability density function (PDF) of system states. It can be used to calculate such information-theoretic quantities as the mutual information between the stochastic stimulus and various internal states of the neuron (e.g., membrane potential), as well as various spiking statistics. When random excitations are modeled as Gaussian white noise, the joint PDF of neuron states satisfies exactly a Fokker-Planck equation. However, most biologically plausible noise sources are correlated (colored). In this case, the resulting PDF equations require a closure approximation. We propose two methods for closing such equations: a modified nonlocal large-eddy-diffusivity closure and a data-driven closure relying on sparse regression to learn relevant features. The closures are tested for the stochastic non-spiking leaky integrate-and-fire and FitzHugh-Nagumo (FHN) neurons driven by sine-Wiener noise. Mutual information and total correlation between the random stimulus and the internal states of the neuron are calculated for the FHN neuron.

  View details for DOI 10.1007/s11571-021-09731-9

  View details for PubMedID 35603048

  View details for PubMedCentralID PMC9120337

• Stability-Guided Strategies to Mitigate Dendritic Growth in Lithium-Metal Batteries JOURNAL OF THE ELECTROCHEMICAL SOCIETY Li, W., Tchelepi, H. A., Ju, Y., Tartakovsky, D. M. 2022; 169 (6)

  View details for DOI 10.1149/1945-7111/ac7978

  View details for Web of Science ID 000816869500001

• Effective Representation of Active Material and Carbon Binder in Porous Electrodes JOURNAL OF THE ELECTROCHEMICAL SOCIETY Li, W., Tartakovsky, D. M. 2022; 169 (4)

  View details for DOI 10.1149/1945-7111/ac6832

  View details for Web of Science ID 000788713900001

• From Fluid Flow to Coupled Processes in Fractured Rock: Recent Advances and New Frontiers REVIEWS OF GEOPHYSICS Viswanathan, H. S., Ajo-Franklin, J., Birkholzer, J. T., Carey, J. W., Guglielmi, Y., Hyman, J. D., Karra, S., Pyrak-Nolte, L. J., Rajaram, H., Srinivasan, G., Tartakovsky, D. M. 2022; 60 (1)

  View details for DOI 10.1029/2021RG000744

  View details for Web of Science ID 000777485900006

• POLYNOMIAL CHAOS EXPANSIONS FOR STIFF RANDOM ODEs SIAM JOURNAL ON SCIENTIFIC COMPUTING Shi, W., Tartakovsky, D. M. 2022; 44 (3): A1021-A1046

  View details for DOI 10.1137/21M1432545

  View details for Web of Science ID 000830284700001

• Physics-informed neural networks for modelling anisotropic and bi-anisotropic electromagnetic constitutive laws through indirect data Chandra, A., Curti, M., Tiels, K., Lomonova, E. A., Tartakovsky, D. M., Ishibuchi, H., Kwoh, C. K., Tan, A. H., Srinivasan, D., Miao, C., Trivedi, A., Crockett, K. IEEE. 2022: 1451-1459

  View details for DOI 10.1109/SSCI51031.2022.10022292

  View details for Web of Science ID 000971973800195

• Data-driven sparse discovery of hysteresis models for piezoelectric actuators Chandra, A., Curti, M., Tiels, K., Lomonova, E. A., Tartakovsky, D. M., IEEE IEEE. 2022

  View details for DOI 10.1109/CEFC55061.2022.9940793

  View details for Web of Science ID 000942521800146

• Thermal Experiments for Fractured Rock Characterization: Theoretical Analysis and Inverse Modeling WATER RESOURCES RESEARCH Zhou, Z., Roubinet, D., Tartakovsky, D. M. 2021; 57 (12)

  View details for DOI 10.1029/2021WR030608

  View details for Web of Science ID 000735901700060

• Autonomous learning of nonlocal stochastic neuron dynamics COGNITIVE NEURODYNAMICS Maltba, T. E., Zhao, H., Tartakovsky, D. M. 2021

  View details for DOI 10.1007/s11571-021-09731-9

  View details for Web of Science ID 000714299600001

• Mutual information for explainable deep learning of multiscale systems JOURNAL OF COMPUTATIONAL PHYSICS Taverniers, S., Hall, E. J., Katsoulakis, M. A., Tartakovsky, D. M. 2021; 444

  View details for DOI 10.1016/j.jcp.2021.110551

  View details for Web of Science ID 000722626200011

• Estimation of Evapotranspiration Rates and Root Water Uptake Profiles From Soil Moisture Sensor Array Data WATER RESOURCES RESEARCH Li, W., Wainwright, H. M., Yan, Q., Zhou, H., Dafflon, B., Wu, Y., Versteeg, R., Tartakovsky, D. M. 2021; 57 (11)

  View details for DOI 10.1029/2021WR030747

  View details for Web of Science ID 000723106900056

• Extended dynamic mode decomposition for inhomogeneous problems JOURNAL OF COMPUTATIONAL PHYSICS Lu, H., Tartakovsky, D. M. 2021; 444

  View details for DOI 10.1016/j.jcp.2021.110550

  View details for Web of Science ID 000722626200007

• A model of anemic tissue perfusion after blood transfusion shows critical role of endothelial response to shear stress stimuli. Journal of applied physiology (Bethesda, Md. : 1985) Li, W., Tsai, A. G., Intaglietta, M., Tartakovsky, D. M. 2021

  Abstract

  -- -Although some of the cardiovascular responses to changes in hematocrit (Hct) are not fully quantified experimentally, available information is sufficient to build a mathematical model of the consequences of treating anemia by introducing RBCs into the circulation via blood transfusion. We present such a model, which describes how the treatment of normovolemic anemia with blood transfusion impacts oxygen (O2) delivery (DO2, the product of blood O2 content and arterial blood flow) by the microcirculation. Our analysis accounts for the differential response of the endothelium to the wall shear stress (WSS) stimulus, changes in nitric oxide (NO) production due to modification of blood viscosity caused by alterations of both hematocrit (Hct) and cell free layer thickness, as well as for their combined effects on microvascular blood flow and DO2. Our model shows that transfusions of 1- and 2-unit of blood have a minimal effect on DO2 if the microcirculation is unresponsive to the WSS stimulus for NO production that causes vasodilatation increasing blood flow and DO2. Conversely, in a fully WSS responsive organism, blood transfusion significantly enhances blood flow and DO2, because increased viscosity stimulates endothelial NO production causing vasodilatation. This finding suggests that evaluation of a patients' pre-transfusion endothelial WSS responsiveness should be beneficial in determining the optimal transfusion requirements for treating anemic patients.

  View details for DOI 10.1152/japplphysiol.00524.2021

  View details for PubMedID 34647829

• Consensus Equilibrium for Subsurface Delineation WATER RESOURCES RESEARCH Yang, H., Lin, Y., Wohlberg, B., Tartakovsky, D. M. 2021; 57 (10)

  View details for DOI 10.1029/2021WR030151

  View details for Web of Science ID 000711970600003

• Exponential time differencing for problems without natural stiffness separation COMPUTATIONAL GEOSCIENCES Dendumrongsup, N., Tartakovsky, D. M. 2021

  View details for DOI 10.1007/s10596-021-10067-w

  View details for Web of Science ID 000666850800002

• Data-driven discovery of coarse-grained equations JOURNAL OF COMPUTATIONAL PHYSICS Bakarji, J., Tartakovsky, D. M. 2021; 434

  View details for DOI 10.1016/j.jcp.2021.110219

  View details for Web of Science ID 000637748800007

• GINNs: Graph-Informed Neural Networks for multiscale physics JOURNAL OF COMPUTATIONAL PHYSICS Hall, E. J., Taverniers, S., Katsoulakis, M. A., Tartakovsky, D. M. 2021; 433

  View details for DOI 10.1016/j.jcp.2021.110192

  View details for Web of Science ID 000635603100008

• Probabilistic Reconstruction of Hydrofacies With Support Vector Machines WATER RESOURCES RESEARCH Dendumrongsup, N., Tartakovsky, D. M. 2021; 57 (5)

  View details for DOI 10.1029/2021WR029622

  View details for Web of Science ID 000654464300061

• Hybrid models of chemotaxis with application to leukocyte migration. Journal of mathematical biology Lu, H., Um, K., Tartakovsky, D. M. 2021; 82 (4): 23

  Abstract

  Many chemical and biological systems involve reacting species with vastly different numbers of molecules/agents. Hybrid simulations model such phenomena by combining discrete (e.g., agent-based) and continuous (e.g., partial differential equation- or PDE-based) descriptors of the dynamics of reactants with small and large numbers of molecules/agents, respectively. We present a stochastic hybrid algorithm to model a stage of the immune response to inflammation, during which leukocytes reach a pathogen via chemotaxis. While large numbers of chemoattractant molecules justify the use of a PDE-based model to describe the spatiotemporal evolution of its concentration, relatively small numbers of leukocytes and bacteria involved in the process undermine the veracity of their continuum treatment by masking the effects of stochasticity and have to be treated discretely. Motility and interactions between leukocytes and bacteria are modeled via random walk and a stochastic simulation algorithm, respectively. Since the latter assumes the reacting species to be well mixed, the discrete component of our hybrid algorithm deploys stochastic operator splitting, in which the sequence of the diffusion and reaction operations is determined autonomously during each simulation step. We conduct a series of numerical experiments to ascertain the accuracy and computational efficiency of our hybrid simulations and, then, to demonstrate the importance of randomness for predicting leukocyte migration and fate during the immune response to inflammation.

  View details for DOI 10.1007/s00285-021-01581-7

  View details for PubMedID 33646399

• Lagrangian models of particle-laden flows with stochastic forcing: Monte Carlo, moment equations, and method of distributions analyses PHYSICS OF FLUIDS Dominguez-Vazquez, D., Jacobs, G. B., Tartakovsky, D. M. 2021; 33 (3)

  View details for DOI 10.1063/5.0039787

  View details for Web of Science ID 000635658600001

• Temperature estimation from current and voltage measurements in lithium-ion battery systems JOURNAL OF ENERGY STORAGE Wang, P., Yang, L., Wang, H., Tartakovsky, D. M., Onori, S. 2021; 34

  View details for DOI 10.1016/j.est.2020.102133

  View details for Web of Science ID 000641252300004

• METHOD OF DISTRIBUTIONS FOR SYSTEMS WITH STOCHASTIC FORCING INTERNATIONAL JOURNAL FOR UNCERTAINTY QUANTIFICATION Rutjens, R. L., Jacobs, G. B., Tartakovsky, D. M. 2021; 11 (2): 83–104

  View details for DOI 10.1615/Int.J.UncertaintyQuantification.2020031940

  View details for Web of Science ID 000628530200005

• DYNAMICS OF DATA-DRIVEN AMBIGUITY SETS FOR HYPERBOLIC CONSERVATION LAWS WITH UNCERTAIN INPUTS SIAM JOURNAL ON SCIENTIFIC COMPUTING Boso, F., Boskos, D., Cortes, J., Martinez, S., Tartakovsky, D. M. 2021; 43 (3): A2102-A2129

  View details for DOI 10.1137/20M1325034

  View details for Web of Science ID 000674142500015

• Tensor methods for the Boltzmann-BGK equation JOURNAL OF COMPUTATIONAL PHYSICS Boelens, A. P., Venturi, D., Tartakovsky, D. M. 2020; 421

  View details for DOI 10.1016/j.jcp.2020.109744

  View details for Web of Science ID 000579455000009

• Solute dispersion in bifurcating networks JOURNAL OF FLUID MECHANICS Zimmerman, R. A., Tartakovsky, D. M. 2020; 901

  View details for DOI 10.1017/jfm.2020.573

  View details for Web of Science ID 000563033700001

• Markov chain Monte Carlo with neural network surrogates: application to contaminant source identification STOCHASTIC ENVIRONMENTAL RESEARCH AND RISK ASSESSMENT Zhou, Z., Tartakovsky, D. M. 2020

  View details for DOI 10.1007/s00477-020-01888-9

  View details for Web of Science ID 000577850300001

• Estimation of distributions via multilevel Monte Carlo with stratified sampling JOURNAL OF COMPUTATIONAL PHYSICS Taverniers, S., Tartakovsky, D. M. 2020; 419

  View details for DOI 10.1016/j.jcp.2020.109572

  View details for Web of Science ID 000629857800004

• Accelerated Multilevel Monte Carlo With Kernel-Based Smoothing and Latinized Stratification WATER RESOURCES RESEARCH Taverniers, S., Bosma, S. M., Tartakovsky, D. M. 2020; 56 (9)

  View details for DOI 10.1029/2019WR026984

  View details for Web of Science ID 000578452200037

• Learning on dynamic statistical manifolds PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES Boso, F., Tartakovsky, D. M. 2020; 476 (2239): 20200213

  Abstract

  Hyperbolic balance laws with uncertain (random) parameters and inputs are ubiquitous in science and engineering. Quantification of uncertainty in predictions derived from such laws, and reduction of predictive uncertainty via data assimilation, remain an open challenge. That is due to nonlinearity of governing equations, whose solutions are highly non-Gaussian and often discontinuous. To ameliorate these issues in a computationally efficient way, we use the method of distributions, which here takes the form of a deterministic equation for spatio-temporal evolution of the cumulative distribution function (CDF) of the random system state, as a means of forward uncertainty propagation. Uncertainty reduction is achieved by recasting the standard loss function, i.e. discrepancy between observations and model predictions, in distributional terms. This step exploits the equivalence between minimization of the square error discrepancy and the Kullback-Leibler divergence. The loss function is regularized by adding a Lagrangian constraint enforcing fulfilment of the CDF equation. Minimization is performed sequentially, progressively updating the parameters of the CDF equation as more measurements are assimilated.

  View details for DOI 10.1098/rspa.2020.0213

  View details for Web of Science ID 000556904800010

  View details for PubMedID 32831613

  View details for PubMedCentralID PMC7426049

• Lagrangian dynamic mode decomposition for construction of reduced-order models of advection-dominated phenomena JOURNAL OF COMPUTATIONAL PHYSICS Lu, H., Tartakovsky, D. M. 2020; 407

  View details for DOI 10.1016/j.jcp.2020.109229

  View details for Web of Science ID 000519535500024

• Analytical model for gravity segregation of horizontal multiphase flow in porous media PHYSICS OF FLUIDS Rabinovich, A., Bedrikovetsky, P., Tartakovsky, D. M. 2020; 32 (4)

  View details for DOI 10.1063/5.0003325

  View details for Web of Science ID 000526582300001

• Modified immersed boundary method for flows over randomly rough surfaces JOURNAL OF COMPUTATIONAL PHYSICS Kwon, C., Tartakovsky, D. M. 2020; 406

  View details for DOI 10.1016/j.jcp.2019.109195

  View details for Web of Science ID 000514822600024

• Bayesian Update and Method of Distributions: Application to Leak Detection in Transmission Mains WATER RESOURCES RESEARCH Alawadhi, A., Tartakovsky, D. M. 2020; 56 (2)

  View details for DOI 10.1029/2019WR025879

  View details for Web of Science ID 000535672800071

• Data-Informed Method of Distributions for Hyperbolic Conservation Laws SIAM Journal on Scientific Computing Boso, F., Tartakovsky, D. M. 2020; 42 (1): 25

  View details for DOI 10.1137/19M1260773

• PREDICTION ACCURACY OF DYNAMIC MODE DECOMPOSITION SIAM JOURNAL ON SCIENTIFIC COMPUTING Lu, H., Tartakovsky, D. M. 2020; 42 (3): A1639–A1662

  View details for DOI 10.1137/19M1259948

  View details for Web of Science ID 000551255700016

• Resource-Constrained Model Selection for Uncertainty Propagation and Data Assimilation SIAM-ASA JOURNAL ON UNCERTAINTY QUANTIFICATION Yang, L., Wang, P., Tartakovsky, D. M. 2020; 8 (3): 1118–38

  View details for DOI 10.1137/19M1263376

  View details for Web of Science ID 000590148500010

• Method of distributions for quantification of geologic uncertainty in flow simulations Method of distributions for quantification of geologic uncertainty in flow simulations Yang, H. J., Boso, F., Tchelepi, H. A., Tartakovsky, D. M. 2020

  View details for DOI 10.1029/2020WR027643

• Stochastic self-tuning hybrid algorithm for reaction-diffusion systems JOURNAL OF CHEMICAL PHYSICS Ruiz-Martinez, A., Bartol, T. M., Sejnowski, T. J., Tartakovsky, D. M. 2019; 151 (24): 244117

  Abstract

  Many biochemical phenomena involve reactants with vastly different concentrations, some of which are amenable to continuum-level descriptions, while the others are not. We present a hybrid self-tuning algorithm to model such systems. The method combines microscopic (Brownian) dynamics for diffusion with mesoscopic (Gillespie-type) methods for reactions and remains efficient in a wide range of regimes and scenarios with large variations of concentrations. Its accuracy, robustness, and versatility are balanced by redefining propensities and optimizing the mesh size and time step. We use a bimolecular reaction to demonstrate the potential of our method in a broad spectrum of scenarios: from almost completely reaction-dominated systems to cases where reactions rarely occur or take place very slowly. The simulation results show that the number of particles present in the system does not degrade the performance of our method. This makes it an accurate and computationally efficient tool to model complex multireaction systems.

  View details for DOI 10.1063/1.5125022

  View details for Web of Science ID 000513160200023

  View details for PubMedID 31893874

  View details for PubMedCentralID PMC7341680

• Distribution-Based Global Sensitivity Analysis in Hydrology WATER RESOURCES RESEARCH Ciriello, V., Lauriola, I., Tartakovsky, D. M. 2019

  View details for DOI 10.1029/2019WR025844

  View details for Web of Science ID 000495174400001

• Probabilistic Forecast of Single-Phase Flow in Porous Media With Uncertain Properties WATER RESOURCES RESEARCH Yang, H., Boso, F., Tchelepi, H. A., Tartakovsky, D. M. 2019

  View details for DOI 10.1029/2019WR026090

  View details for Web of Science ID 000494648300001

• Efficient gHMC Reconstruction of Contaminant Release History FRONTIERS IN ENVIRONMENTAL SCIENCE Barajas-Solano, D. A., Alexander, F. J., Anghel, M., Tartakovsky, D. M. 2019; 7

  View details for DOI 10.3389/fenvs.2019.00149

  View details for Web of Science ID 000496942100001

• Diffusion in Porous Media: Phenomena and Mechanisms TRANSPORT IN POROUS MEDIA Tartakovsky, D. M., Dentz, M. 2019; 130 (1): 105–27

  View details for DOI 10.1007/s11242-019-01262-6

  View details for Web of Science ID 000509938900004

• Causality and Bayesian Network PDEs for multiscale representations of porous media JOURNAL OF COMPUTATIONAL PHYSICS Um, K., Hall, E. J., Katsoulakis, M. A., Tartakovsky, D. M. 2019; 394: 658–78

  View details for DOI 10.1016/j.jcp.2019.06.007

  View details for Web of Science ID 000478572700032

• Microstructural heterogeneity drives reaction initiation in granular materials APPLIED PHYSICS LETTERS Bakarji, J., Tartakovsky, D. M. 2019; 114 (25)

  View details for DOI 10.1063/1.5108902

  View details for Web of Science ID 000474433800038

• A Mechanistic Analysis of Possible Blood Transfusion Failure to Increase Circulatory Oxygen Delivery in Anemic Patients ANNALS OF BIOMEDICAL ENGINEERING Zimmerman, R. A., Tsai, A. G., Intaglietta, M., Tartakovsky, D. M. 2019; 47 (4): 1094–1105

  View details for DOI 10.1007/s10439-019-02200-9

  View details for Web of Science ID 000461026400015

• A Mechanistic Analysis of Possible Blood Transfusion Failure to Increase Circulatory Oxygen Delivery in Anemic Patients. Annals of biomedical engineering Zimmerman, R. A., Tsai, A. G., Intaglietta, M., Tartakovsky, D. M. 2019

  Abstract

  The effects of changing hematocrit (Hct) on the rate of circulatory oxygen ([Formula: see text]) delivery were modeled analytically to describe transfusion of 0.5-3.0 units of packed red blood cells (pRBC, 300 mL/unit, 60% Hct) to anemic patients. In our model, Hct affects [Formula: see text] delivery to the microcirculation by changing blood [Formula: see text] carrying capacity and blood viscosity, which in turn affects blood flow velocity and, therefore, [Formula: see text] delivery. Changing blood velocity impacts the [Formula: see text] delivery by affecting the oxygen diffusive losses as blood transits through the arteriolar vasculature. An increase in Hct has two opposite effects: it increases the blood [Formula: see text] carrying capacity and decreases the flow velocity. This suggests the existence of an optimal Hct that maximizes [Formula: see text] delivery. Our results show that maximal [Formula: see text] delivery occurs in the anemic range, where [Formula: see text]%. Optimal blood management is associated with transfusing enough units up to reaching maximal [Formula: see text] delivery. Although somewhat complex to implement, this practice would result in both substantial blood savings and improved [Formula: see text] delivery.

  View details for PubMedID 30659435

• Quantification of Predictive Uncertainty in Models of FtsZ ring assembly in Escherichia coli. Journal of theoretical biology Ye, Y. n., Ruiz-Martinez, A. n., Wang, P. n., Tartakovsky, D. M. 2019: 110006

  Abstract

  Quantitative predictions of FtsZ protein polymerization are essential for understanding the self-regulating mechanisms in biochemical systems. Due to structural complexity and parametric uncertainty, existing kinetic models remain incomplete and their predictions error-prone. To address such challenges, we perform probabilistic uncertainty quantification and global sensitivity analysis of the concentrations of various protein species predicted with a recent FtsZ protein polymerization model. Our results yield a ranked list of modeling shortcomings that can be improved in order to develop more accurate predictions and more realistic representations of key mechanisms of biochemical systems and their response to changes in internal or external conditions. Our conclusions and improvement recommendations can be extended to other kinetics models.

  View details for DOI 10.1016/j.jtbi.2019.110006

  View details for PubMedID 31539529

• Method of Distributions for Water Hammer Equations With Uncertain Parameters WATER RESOURCES RESEARCH Alawadhi, A., Boso, F., Tartakovsky, D. M. 2018; 54 (11): 9398–9411

  View details for DOI 10.1029/2018WR023383

  View details for Web of Science ID 000453369400046

• Nonlocal PDF methods for Langevin equations with colored noise JOURNAL OF COMPUTATIONAL PHYSICS Maltba, T., Gremaud, P. A., Tartakoysky, D. M. 2018; 367: 87–101

  View details for DOI 10.1016/j.jcp.2018.04.023

  View details for Web of Science ID 000432926800005

• Information-Theoretic Approach to Bidirectional Scaling WATER RESOURCES RESEARCH Boso, F., Tartakovsky, D. M. 2018; 54 (7): 4916–28

  View details for DOI 10.1029/2017WR021993

  View details for Web of Science ID 000442502100041

• Probabilistic Forecasting of Nitrogen Dynamics in Hyporheic Zone WATER RESOURCES RESEARCH Boso, F., Marzadri, A., Tartakovsky, D. M. 2018; 54 (7): 4417–31

  View details for DOI 10.1029/2018WR022525

  View details for Web of Science ID 000442502100014

• Interpretation of Heat-Pulse Tracer Tests for Characterization of Three-Dimensional Velocity Fields in Hyporheic Zone WATER RESOURCES RESEARCH Zlotnik, V., Tartakovsky, D. M. 2018; 54 (6): 4028–39

  View details for DOI 10.1029/2017WR022476

  View details for Web of Science ID 000440309900015

• Efficient models of polymerization applied to FtsZ ring assembly in Escherichia coli PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Ruiz-Martinez, A., Bartol, T. M., Sejnowski, T. J., Tartakovsky, D. M. 2018; 115 (19): 4933–38

  Abstract

  High protein concentrations complicate modeling of polymer assembly kinetics by introducing structural complexity and a large variety of protein forms. We present a modeling approach that achieves orders of magnitude speed-up by replacing distributions of lengths and widths with their average counterparts and by introducing a hierarchical classification of species and reactions into sets. We have used this model to study FtsZ ring assembly in Escherichia coli The model's prediction of key features of the ring formation, such as time to reach the steady state, total concentration of FtsZ species in the ring, total concentration of monomers, and average dimensions of filaments and bundles, are all in agreement with the experimentally observed values. Besides validating our model against the in vivo observations, this study fills some knowledge gaps by proposing a specific structure of the ring, describing the influence of the total concentration in short and long kinetics processes, determining some characteristic mechanisms in polymer assembly regulation, and providing insights about the role of ZapA proteins, critical components for both positioning and stability of the ring.

  View details for PubMedID 29686085

• The frequency domain approach to analyse field-scale miscible flow transport experiments in the soils BIOSYSTEMS ENGINEERING Severino, G., Toraldo, G., Tartakovsky, D. M. 2018; 168: 96–104

  View details for DOI 10.1016/j.biosystemseng.2016.10.002

  View details for Web of Science ID 000431932100009

• Hydrodynamic dispersion in a tube with diffusive losses through its walls JOURNAL OF FLUID MECHANICS Zimmerman, R. A., Severino, G., Tartakovsky, D. M. 2018; 837: 546-561

  View details for DOI 10.1017/jfm.2017.870

  View details for Web of Science ID 000419396900004

• Global sensitivity analysis of multiscale properties of porous materials JOURNAL OF APPLIED PHYSICS Um, K., Zhang, X., Katsoulakis, M., Plechac, P., Tartakovsky, D. M. 2018; 123 (7)

  View details for DOI 10.1063/1.5009691

  View details for Web of Science ID 000425807400014

• A Hybrid Multiscale Model of Miscible Reactive Fronts WATER RESOURCES RESEARCH Siuliukina, N., Tartakovsky, D. M. 2018; 54 (1): 61–71

  View details for DOI 10.1002/2017WR020867

  View details for Web of Science ID 000428474000004

• Parallel tensor methods for high-dimensional linear PDEs Journal of Computational Physics Boelens, A. M., Venturi, D., Tartakovsky, D. M. 2018; 375: 519 - 539

  View details for DOI 10.1016/j.jcp.2018.08.057

• Effects of Hydraulic Soil Properties on Vegetation Pattern Formation in Sloping Landscapes BULLETIN OF MATHEMATICAL BIOLOGY Severino, G., Giannino, F., Carteni, F., Mazzoleni, S., Tartakovsky, D. M. 2017; 79 (12): 2773–84

  View details for DOI 10.1007/s11538-017-0348-4

  View details for Web of Science ID 000416819300001

• Effects of Hydraulic Soil Properties on Vegetation Pattern Formation in Sloping Landscapes. Bulletin of mathematical biology Severino, G., Giannino, F., Cartení, F., Mazzoleni, S., Tartakovsky, D. M. 2017; 79 (12): 2773-2784

  Abstract

  Current models of vegetation pattern formation rely on a system of weakly nonlinear reaction-diffusion equations that are coupled by their source terms. While these equations, which are used to describe a spatiotemporal planar evolution of biomass and soil water, qualitatively capture the emergence of various types of vegetation patterns in arid environments, they are phenomenological and have a limited predictive power. We ameliorate these limitations by deriving the vertically averaged Richards' equation to describe flow (as opposed to "diffusion") of water in partially saturated soils. This establishes conditions under which this nonlinear equation reduces to its weakly nonlinear reaction-diffusion counterpart used in the previous models, thus relating their unphysical parameters (e.g., diffusion coefficient) to the measurable soil properties (e.g., hydraulic conductivity) used to parameterize the Richards equation. Our model is valid for both flat and sloping landscapes and can handle arbitrary topography and boundary conditions. The result is a model that relates the environmental conditions (e.g., precipitation rate, runoff and soil properties) to formation of multiple patterns observed in nature (such as stripes, labyrinth and spots).

  View details for DOI 10.1007/s11538-017-0348-4

  View details for PubMedID 29052101

• Impact of Hydrogeological Uncertainty on Estimation of Environmental Risks Posed by Hydrocarbon Transportation Networks WATER RESOURCES RESEARCH Ciriello, V., Lauriola, I., Bonvicini, S., Cozzani, V., Di Federico, V., Tartakovsky, D. M. 2017; 53 (11): 8686–97

  View details for DOI 10.1002/2017WR021368

  View details for Web of Science ID 000418736700003

• Estimation of Intrinsic Length Scales of Flow in Unsaturated Porous Media WATER RESOURCES RESEARCH Assouline, S., Ciriello, V., Tartakovsky, D. M. 2017; 53 (11): 9980–87

  View details for DOI 10.1002/2017WR021629

  View details for Web of Science ID 000418736700073

• Posttransfusion Increase of Hematocrit per se Does Not Improve Circulatory Oxygen Delivery due to Increased Blood Viscosity ANESTHESIA AND ANALGESIA Zimmerman, R., Tsai, A. G., Vazquez, B. Y., Cabrales, P., Hofmann, A., Meier, J., Shander, A., Spahn, D. R., Friedman, J. M., Tartakovsky, D. M., Intaglietta, M. 2017; 124 (5): 1547-1554

  Abstract

  Blood transfusion is used to treat acute anemia with the goal of increasing blood oxygen-carrying capacity as determined by hematocrit (Hct) and oxygen delivery (DO2). However, increasing Hct also increases blood viscosity, which may thus lower DO2 if the arterial circulation is a rigid hydraulic system as the resistance to blood flow will increase. The net effect of transfusion on DO2 in this system can be analyzed by using the relationship between Hct and systemic blood viscosity of circulating blood at the posttransfusion Hct to calculate DO2 and comparing this value with pretransfusion DO2. We hypothesized that increasing Hct would increase DO2 and tested our hypothesis by mathematically modeling DO2 in the circulation.Calculations were made assuming a normal cardiac output (5 L/min) with degrees of anemia ranging from 5% to 80% Hct deficit. We analyzed the effects of transfusing 0.5 or more units of 300 cc of packed red blood cells (PRBCs) at an Hct of 65% and calculated microcirculatory DO2 after accounting for increased blood viscosity and assuming no change in blood pressure. Our model accounts for O2 diffusion out of the circulation before blood arriving to the nutritional circulation and for changes in blood flow velocity. The immediate posttransfusion DO2 was also compared with DO2 after the transient increase in volume due to transfusion has subsided.Blood transfusion of up to 3 units of PRBCs increased DO2 when Hct (or hemoglobin) was 60% lower than normal, but did not increase DO2 when administered before this threshold.After accounting for the effect of increasing blood viscosity on blood flow owing to increasing Hct, we found in a mathematical simulation of DO2 that transfusion of up to 3 units of PRBCs does not increase DO2, unless anemia is the result of an Hct deficit greater than 60%. Observations that transfusions occasionally result in clinical improvement suggest that other mechanisms possibly related to increased blood viscosity may compensate for the absence of increase in DO2.

  View details for DOI 10.1213/ANE.0000000000002008

  View details for Web of Science ID 000400206800028

  View details for PubMedID 28328758

• Optimal design of nanoporous materials for electrochemical devices APPLIED PHYSICS LETTERS Zhang, X., Tartakovsky, D. M. 2017; 110 (14)

  View details for DOI 10.1063/1.4979466

  View details for Web of Science ID 000399162100043

• An analytical model for carrier-facilitated solute transport in weakly heterogeneous porous media APPLIED MATHEMATICAL MODELLING Severino, G., Campagna, R., Tartakovsky, D. M. 2017; 44: 261-273

  View details for DOI 10.1016/j.apm.2016.10.064

  View details for Web of Science ID 000401208500019

• On the use of reverse Brownian motion to accelerate hybrid simulations JOURNAL OF COMPUTATIONAL PHYSICS Bakarji, J., Tartakovsky, D. M. 2017; 334: 68-80

  View details for DOI 10.1016/j.jcp.2016.12.032

  View details for Web of Science ID 000395210500005

• A tightly-coupled domain-decomposition approach for highly nonlinear stochastic multiphysics systems JOURNAL OF COMPUTATIONAL PHYSICS Taverniers, S., Tartakovsky, D. M. 2017; 330: 884-901

  View details for DOI 10.1016/j.jcp.2016.10.052

  View details for Web of Science ID 000394408900046

• Doubly Penalized LASSO for Reconstruction of Biological Networks PROCEEDINGS OF THE IEEE Asadi, B., Maurya, M. R., Tartakovsky, D. M., Subramaniam, S. 2017; 105 (2): 319-329

  View details for DOI 10.1109/JPROC.2016.2535282

  View details for Web of Science ID 000394532000011

• Effective Ion Diffusion in Charged Nanoporous Materials JOURNAL OF THE ELECTROCHEMICAL SOCIETY Zhang, X., Tartakovsky, D. M. 2017; 164 (4): E53-E61

  View details for DOI 10.1149/2.0491704jes

  View details for Web of Science ID 000400958600116

• Role of glycocalyx in attenuation of shear stress on endothelial cells: from in vivo experiments to microfluidic circuits Battiato, I., Tartakovsky, D., Cabrales, P., Intaglietta, M., IEEE IEEE. 2017

  View details for Web of Science ID 000426983700057

• Noise-driven interfaces and their macroscopic representation PHYSICAL REVIEW E Dentz, M., Neuweiler, I., Meheust, Y., Tartakovsky, D. M. 2016; 94 (5)

  Abstract

  We study the macroscopic representation of noise-driven interfaces in stochastic interface growth models in (1+1) dimensions. The interface is characterized macroscopically by saturation, which represents the fluctuating sharp interface by a smoothly varying phase field with values between 0 and 1. We determine the one-point interface height statistics for the Edwards-Wilkinson (EW) and Kadar-Paris-Zhang (KPZ) models in order to determine explicit deterministic equations for the phase saturation for each of them. While we obtain exact results for the EW model, we develop a Gaussian closure approximation for the KPZ model. We identify an interface compression term, which is related to mass transfer perpendicular to the growth direction, and a diffusion term that tends to increase the interface width. The interface compression rate depends on the mesoscopic mass transfer process along the interface and in this sense provides a relation between meso- and macroscopic interface dynamics. These results shed light on the relation between mesoscale and macroscale interface models, and provide a systematic framework for the upscaling of stochastic interface dynamics.

  View details for DOI 10.1103/PhysRevE.94.052802

  View details for Web of Science ID 000387394600006

• Particle Methods for Heat Transfer in Fractured Media TRANSPORT IN POROUS MEDIA Gisladottir, V. R., Roubinet, D., Tartakovsky, D. M. 2016; 115 (2): 311-326

  View details for DOI 10.1007/s11242-016-0755-2

  View details for Web of Science ID 000387411000006

• Noise-driven interfaces and their macroscopic representation. Physical review. E Dentz, M., Neuweiler, I., Méheust, Y., Tartakovsky, D. M. 2016; 94 (5-1): 052802-?

  Abstract

  We study the macroscopic representation of noise-driven interfaces in stochastic interface growth models in (1+1) dimensions. The interface is characterized macroscopically by saturation, which represents the fluctuating sharp interface by a smoothly varying phase field with values between 0 and 1. We determine the one-point interface height statistics for the Edwards-Wilkinson (EW) and Kadar-Paris-Zhang (KPZ) models in order to determine explicit deterministic equations for the phase saturation for each of them. While we obtain exact results for the EW model, we develop a Gaussian closure approximation for the KPZ model. We identify an interface compression term, which is related to mass transfer perpendicular to the growth direction, and a diffusion term that tends to increase the interface width. The interface compression rate depends on the mesoscopic mass transfer process along the interface and in this sense provides a relation between meso- and macroscopic interface dynamics. These results shed light on the relation between mesoscale and macroscale interface models, and provide a systematic framework for the upscaling of stochastic interface dynamics.

  View details for PubMedID 27967189

• Analytical models of axisymmetric reaction-diffusion phenomena in composite media INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER Zimmerman, R. A., Jankowski, T. A., Tartakovsky, D. M. 2016; 99: 425-431

  View details for DOI 10.1016/j.ijheatmasstransfer.2016.02.088

  View details for Web of Science ID 000384779300040

• Efficient Multiscale Models of Polymer Assembly BIOPHYSICAL JOURNAL Ruiz-Martinez, A., Bartol, T. M., Sejnowski, T. J., Tartakovsky, D. M. 2016; 111 (1): 185-196

  Abstract

  Protein polymerization and bundling play a central role in cell physiology. Predictive modeling of these processes remains an open challenge, especially when the proteins involved become large and their concentrations high. We present an effective kinetics model of filament formation, bundling, and depolymerization after GTP hydrolysis, which involves a relatively small number of species and reactions, and remains robust over a wide range of concentrations and timescales. We apply this general model to study assembly of FtsZ protein, a basic element in the division process of prokaryotic cells such as Escherichia coli, Bacillus subtilis, or Caulobacter crescentus. This analysis demonstrates that our model outperforms its counterparts in terms of both accuracy and computational efficiency. Because our model comprises only 17 ordinary differential equations, its computational cost is orders-of-magnitude smaller than the current alternatives consisting of up to 1000 ordinary differential equations. It also provides, to our knowledge, a new insight into the characteristics and functioning of FtsZ proteins at high concentrations. The simplicity and versatility of our model render it a powerful computational tool, which can be used either as a standalone descriptor of other biopolymers' assembly or as a component in more complete kinetic models.

  View details for DOI 10.1016/j.bpj.2016.05.022

  View details for Web of Science ID 000380371400021

  View details for PubMedID 27410746

  View details for PubMedCentralID PMC4944489

• Shear-Induced Nitric Oxide Production by Endothelial Cells BIOPHYSICAL JOURNAL Sriram, K., Laughlin, J. G., Rangamani, P., Tartakovsky, D. M. 2016; 111 (1): 208-221

  Abstract

  We present a biochemical model of the wall shear stress-induced activation of endothelial nitric oxide synthase (eNOS) in an endothelial cell. The model includes three key mechanotransducers: mechanosensing ion channels, integrins, and G protein-coupled receptors. The reaction cascade consists of two interconnected parts. The first is rapid activation of calcium, which results in formation of calcium-calmodulin complexes, followed by recruitment of eNOS from caveolae. The second is phosphorylation of eNOS by protein kinases PKC and AKT. The model also includes a negative feedback loop due to inhibition of calcium influx into the cell by cyclic guanosine monophosphate (cGMP). In this feedback, increased nitric oxide (NO) levels cause an increase in cGMP levels, so that cGMP inhibition of calcium influx can limit NO production. The model was used to predict the dynamics of NO production by an endothelial cell subjected to a step increase of wall shear stress from zero to a finite physiologically relevant value. Among several experimentally observed features, the model predicts a highly nonlinear, biphasic transient behavior of eNOS activation and NO production: a rapid initial activation due to the very rapid influx of calcium into the cytosol (occurring within 1-5 min) is followed by a sustained period of activation due to protein kinases.

  View details for DOI 10.1016/j.bpj.2016.05.034

  View details for Web of Science ID 000380371400023

  View details for PubMedID 27410748

  View details for PubMedCentralID PMC4944664

• The method of distributions for dispersive transport in porous media with uncertain hydraulic properties WATER RESOURCES RESEARCH Boso, F., Tartakovsky, D. M. 2016; 52 (6): 4700-4712

  View details for DOI 10.1002/2016WR018745

  View details for Web of Science ID 000380100200026

• Conservative tightly-coupled simulations of stochastic multiscale systems JOURNAL OF COMPUTATIONAL PHYSICS Taverniers, S., Pigarov, A. Y., Tartakovsky, D. M. 2016; 313: 400-414

  View details for DOI 10.1016/j.jcp.2016.02.047

  View details for Web of Science ID 000373615500021

• Simulating social-ecological systems: the Island Digital Ecosystem Avatars (IDEA) consortium GIGASCIENCE Davies, N., Field, D., Gavaghan, D., Holbrook, S. J., Planes, S., Troyer, M., Bonsall, M., Claudet, J., Roderick, G., Schmitt, R. J., Zettler, L. A., Berteaux, V., Bossin, H. C., Cabasse, C., Collin, A., Deck, J., Dell, T., Dunne, J., Gates, R., Harfoot, M., Hench, J. L., Hopuare, M., Kirch, P., Kotoulas, G., Kosenkov, A., Kusenko, A., Leichter, J. J., Lenihan, H., Magoulas, A., Martinez, N., Meyer, C., Stoll, B., Swalla, B., Tartakovsky, D. M., Murphy, H. T., Turyshev, S., Valdvinos, F., Williams, R., Wood, S. 2016; 5

  Abstract

  Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine-terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions.

  View details for DOI 10.1186/s13742-016-0118-5

  View details for Web of Science ID 000372428100001

  View details for PubMedID 26998258

  View details for PubMedCentralID PMC4797119

• Stochastic Collocation Methods for Nonlinear Parabolic Equations with Random Coefficients SIAM-ASA JOURNAL ON UNCERTAINTY QUANTIFICATION Barajas-Solano, D. A., Tartakovsky, D. M. 2016; 4 (1): 475–94

  View details for DOI 10.1137/130930108

  View details for Web of Science ID 000407996700020

• Temperature fields induced by geothermal devices ENERGY Ciriello, V., Bottarelli, M., Di Federico, V., Tartakovsky, D. M. 2015; 93: 1896-1903

  View details for DOI 10.1016/j.energy.2015.10.052

  View details for Web of Science ID 000367409500062

• Data-driven models of groundwater salinization in coastal plains JOURNAL OF HYDROLOGY Felisa, G., Ciriello, V., Antonellini, M., Di Federico, V., Tartakovsky, D. M. 2015; 531: 187-197

  View details for DOI 10.1016/j.jhydrol.2015.07.045

  View details for Web of Science ID 000366769200017

• Coexistence of short- and long-range ferromagnetic order in nanocrystalline Fe2Mn1-xCuxAl (x=0.0, 0.1 and 0.3) synthesized by high-energy ball milling JOURNAL OF MAGNETISM AND MAGNETIC MATERIALS Tran Dang Thanh, T. D., Nanto, D., Ngo Thi Uyen Tuyen, N. T., Nan, W., Yu, Y., Tartakovsky, D. M., Yu, S. C. 2015; 394: 37-43

  View details for DOI 10.1016/j.jmmm.2015.06.036

  View details for Web of Science ID 000360025800007

• Critical Behavior in Double-Exchange Ferromagnets of Pr0.6Sr0.4MnO3 Nanoparticles IEEE TRANSACTIONS ON MAGNETICS Tran Dang Thanh, T. D., YiKyung, Y., Ho, T. A., Manh, T. V., The Long Phan, T. L., Tartakovsky, D. M., Yu, S. C. 2015; 51 (11)

  View details for DOI 10.1109/TMAG.2015.2424978

  View details for Web of Science ID 000364770500159

• Impact of stochastic fluctuations in the cell free layer on nitric oxide bioavailability FRONTIERS IN COMPUTATIONAL NEUROSCIENCE Park, S., Intaglietta, M., Tartakovsky, D. M. 2015; 9

  Abstract

  A plasma stratum (cell free layer or CFL) generated by flowing blood interposed between the red blood cell (RBC) core and the endothelium affects generation, consumption, and transport of nitric oxide (NO) in the microcirculation. CFL width is a principal factor modulating NO diffusion and vessel wall shears stress development, thus significantly affecting NO bioavailability. Since the CFL is bounded by the surface formed by the chaotically moving RBCs and the stationary but spatially non-uniform endothelial surface, its width fluctuates randomly in time and space. We analyze how these stochastic fluctuations affect NO transport in the CFL and NO bioavailability. We show that effects due to random boundaries do not average to zero and lead to an increase of NO bioavailability. Since endothelial production of NO is significantly enhanced by temporal variability of wall shear stress, we posit that stochastic shear stress stimulation of the endothelium yields the baseline continual production of NO by the endothelium. The proposed stochastic formulation captures the natural continuous and microscopic variability, whose amplitude is measurable and is of the scale of cellular dimensions. It provides a realistic model of NO generation and regulation.

  View details for DOI 10.3389/fncom.2015.00131

  View details for Web of Science ID 000364958600001

  View details for PubMedID 26578944

  View details for PubMedCentralID PMC4621848

• Design of nanoporous materials with optimal sorption capacity JOURNAL OF APPLIED PHYSICS Zhang, X., Urita, K., Moriguchi, I., Tartakovsky, D. M. 2015; 117 (24)

  View details for DOI 10.1063/1.4923057

  View details for Web of Science ID 000357613900029

• A boundary-layer solution for flow at the soil-root interface JOURNAL OF MATHEMATICAL BIOLOGY Severino, G., Tartakovsky, D. M. 2015; 70 (7): 1645-1668

  Abstract

  Transpiration, a process by which plants extract water from soil and transmit it to the atmosphere, is a vital (yet least quantified) component of the hydrological cycle. We propose a root-scale model of water uptake, which is based on first principles, i.e. employs the generally accepted Richards equation to describe water flow in partially saturated porous media (both in a root and the ambient soil) and makes no assumptions about the kinematic structure of flow in a root-soil continuum. Using the Gardner (exponential) constitutive relation to represent the relative hydraulic conductivities in the Richards equations and treating the root as a cylinder, we use a matched asymptotic expansion technique to derive approximate solutions for transpiration rate and the size of a plant capture zone. These solutions are valid for roots whose size is larger than the macroscopic capillary length of a host soil. For given hydraulic properties, the perturbation parameter used in our analysis relates a root's size to the macroscopic capillary length of the ambient soil. This parameter determines the width of a boundary layer surrounding the soil-root interface, within which flow is strictly horizontal (perpendicular to the root). Our analysis provides a theoretical justification for the standard root-scale cylindrical flow model of plant transpiration that imposes a number of kinematic constraints on water flow in a root-soil continuum.

  View details for DOI 10.1007/s00285-014-0813-8

  View details for Web of Science ID 000354196800006

  View details for PubMedID 25008964

• Linear functional minimization for inverse modeling WATER RESOURCES RESEARCH Barajas-Solano, D. A., WOHLBERG, B. E., Vesselinov, V. V., Tartakovsky, D. M. 2015; 51 (6): 4516-4531

  View details for DOI 10.1002/2014WR016179

  View details for Web of Science ID 000358301200034

• Critical behavior and magnetocaloric effect of Pr1-xCaxMnO3 JOURNAL OF APPLIED PHYSICS Ho, T. A., Thanh, T. D., Yu, Y., Tartakovsky, D. M., Ho, T. O., Thang, P. D., Anh-Tuan Le, A. T., The-Long Phan, T. L., Yu, S. C. 2015; 117 (17)

  View details for DOI 10.1063/1.4914537

  View details for Web of Science ID 000354984100345

• Impact of Data Assimilation on Cost-Accuracy Tradeoff in Multifidelity Models SIAM-ASA JOURNAL ON UNCERTAINTY QUANTIFICATION Sinsbeck, M., Tartakovsky, D. M. 2015; 3 (1): 954–68

  View details for DOI 10.1137/141001743

  View details for Web of Science ID 000421348400039

• Hematocrit dispersion in asymmetrically bifurcating vascular networks AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY Sriram, K., Intaglietta, M., Tartakovsky, D. M. 2014; 307 (11): H1576-H1586

  Abstract

  Quantitative modeling of physiological processes in vasculatures requires an accurate representation of network topology, including vessel branching. We propose a new approach for reconstruction of vascular network, which determines how vessel bifurcations distribute red blood cells (RBC) in the microcirculation. Our method follows the foundational premise of Murray's law in postulating the existence of functional optimality of such networks. It accounts for the non-Newtonian behavior of blood by allowing the apparent blood viscosity to vary with discharge hematocrit and vessel radius. The optimality criterion adopted in our approach is the physiological cost of supplying oxygen to the tissue surrounding a blood vessel. Bifurcation asymmetry is expressed in terms of the amount of oxygen consumption associated with the respective tissue volumes being supplied by each daughter vessel. The vascular networks constructed with our approach capture a number of physiological characteristics observed in in vivo studies. These include the nonuniformity of wall shear stress in the microcirculation, the significant increase in pressure gradients in the terminal sections of the network, the nonuniformity of both the hematocrit partitioning at vessel bifurcations and hematocrit across the capillary bed, and the linear relationship between the RBC flux fraction and the blood flow fraction at bifurcations.

  View details for DOI 10.1152/ajpheart.00283.2014

  View details for Web of Science ID 000346019900005

  View details for PubMedID 25217657

  View details for PubMedCentralID PMC4255010

• Identifying Transport Behavior of Single-Molecule Trajectories BIOPHYSICAL JOURNAL Regner, B. M., Tartakovsky, D. M., Sejnowski, T. J. 2014; 107 (10): 2345-2351

  Abstract

  Models of biological diffusion-reaction systems require accurate classification of the underlying diffusive dynamics (e.g., Fickian, subdiffusive, or superdiffusive). We use a renormalization group operator to identify the anomalous (non-Fickian) diffusion behavior from a short trajectory of a single molecule. The method provides quantitative information about the underlying stochastic process, including its anomalous scaling exponent. The classification algorithm is first validated on simulated trajectories of known scaling. Then it is applied to experimental trajectories of microspheres diffusing in cytoplasm, revealing heterogeneous diffusive dynamics. The simplicity and robustness of this classification algorithm makes it an effective tool for analysis of rare stochastic events that occur in complex biological systems.

  View details for DOI 10.1016/j.bpj.2014.10.005

  View details for Web of Science ID 000345195700006

  View details for PubMedID 25418303

  View details for PubMedCentralID PMC4241458

• Vegetation Pattern Formation Due to Interactions Between Water Availability and Toxicity in Plant-Soil Feedback BULLETIN OF MATHEMATICAL BIOLOGY Marasco, A., Iuorio, A., Carteni, F., Bonanomi, G., Tartakovsky, D. M., Mazzoleni, S., Giannino, F. 2014; 76 (11): 2866-2883

  Abstract

  Development of a comprehensive theory of the formation of vegetation patterns is still in progress. A prevailing view is to treat water availability as the main causal factor for the emergence of vegetation patterns. While successful in capturing the occurrence of multiple vegetation patterns in arid and semiarid regions, this hypothesis fails to explain the presence of vegetation patterns in humid environments. We explore the rich structure of a toxicity-mediated model of the vegetation pattern formation. This model consists of three PDEs accounting for a dynamic balance between biomass, water, and toxic compounds. Different (ecologically feasible) regions of the model's parameter space give rise to stable spatial vegetation patterns in Turing and non-Turing regimes. Strong negative feedback gives rise to dynamic spatial patterns that continuously move in space while retaining their stable topology.

  View details for DOI 10.1007/s11538-014-0036-6

  View details for Web of Science ID 000345138900007

  View details for PubMedID 25338554

• Replacing the Transfusion of 1-2 Units of Blood with Plasma Expanders that Increase Oxygen Delivery Capacity: Evidence from Experimental Studies. Journal of functional biomaterials Tsai, A. G., Salazar Vázquez, B. Y., Cabrales, P., Kistler, E. B., Tartakovsky, D. M., Subramaniam, S., Acharya, S. A., Intaglietta, M. 2014; 5 (4): 232-245

  Abstract

  At least a third of the blood supply in the world is used to transfuse 1-2 units of packed red blood cells for each intervention and most clinical trials of blood substitutes have been carried out at this level of oxygen carrying capacity (OCC) restoration. However, the increase of oxygenation achieved is marginal or none at all for molecular hemoglobin (Hb) products, due to their lingering vasoactivity. This has provided the impetus for the development of "oxygen therapeutics" using Hb-based molecules that have high oxygen affinity and target delivery of oxygen to anoxic areas. However it is still unclear how these oxygen carriers counteract or mitigate the functional effects of anemia due to obstruction, vasoconstriction and under-perfusion. Indeed, they are administered as a low dosage/low volume therapeutic Hb (subsequently further diluted in the circulatory pool) and hence induce extremely small OCC changes. Hyperviscous plasma expanders provide an alternative to oxygen therapeutics by increasing the oxygen delivery capacity (ODC); in anemia they induce supra-perfusion and increase tissue perfusion (flow) by as much as 50%. Polyethylene glycol conjugate albumin (PEG-Alb) accomplishes this by enhancing the shear thinning behavior of diluted blood, which increases microvascular endothelial shear stress, causes vasodilation and lowering peripheral vascular resistance thus facilitating cardiac function. Induction of supra-perfusion takes advantage of the fact that ODC is the product of OCC and blood flow and hence can be maintained by increasing either or both. Animal studies suggest that this approach may save a considerable fraction of the blood supply. It has an additional benefit of enhancing tissue clearance of toxic metabolites.

  View details for DOI 10.3390/jfb5040232

  View details for PubMedID 25350267

  View details for PubMedCentralID PMC4285404

• Non-Newtonian Flow of Blood in Arterioles: Consequences for Wall Shear Stress Measurements MICROCIRCULATION Sriram, K., Intaglietta, M., Tartakovsky, D. M. 2014; 21 (7): 628-639

  Abstract

  Our primary goal is to investigate the effects of non-Newtonian blood properties on wall shear stress in microvessels. The secondary goal is to derive a correction factor for the Poiseuille-law-based indirect measurements of wall shear stress.The flow is assumed to exhibit two distinct, immiscible and homogeneous fluid layers: an inner region densely packed with RBCs, and an outer cell-free layer whose thickness depends on discharge hematocrit. The cell-free layer is assumed to be Newtonian, while rheology of the RBC-rich core is modeled using the Quemada constitutive law.Our model provides a realistic description of experimentally observed blood velocity profiles, tube hematocrit, core hematocrit, and apparent viscosity over a wide range of vessel radii and discharge hematocrits.Our analysis reveals the importance of incorporating this complex blood rheology into estimates of WSS in microvessels. The latter is accomplished by specifying a correction factor, which accounts for the deviation of blood flow from the Poiseuille law.

  View details for DOI 10.1111/micc.12141

  View details for Web of Science ID 000343818400007

  View details for PubMedID 24703006

  View details for PubMedCentralID PMC4185264

• Information theoretic approach to complex biological network reconstruction: application to cytokine release in RAW 264.7 macrophages BMC SYSTEMS BIOLOGY Farhangmehr, F., Maurya, M. R., Tartakovsky, D. M., Subramaniam, S. 2014; 8

  Abstract

  High-throughput methods for biological measurements generate vast amounts of quantitative data, which necessitate the development of advanced approaches to data analysis to help understand the underlying mechanisms and networks. Reconstruction of biological networks from measured data of different components is a significant challenge in systems biology.We use an information theoretic approach to reconstruct phosphoprotein-cytokine networks in RAW 264.7 macrophage cells. Cytokines are secreted upon activation of a wide range of regulatory signals transduced by the phosphoprotein network. Identifying these components can help identify regulatory modules responsible for the inflammatory phenotype. The information theoretic approach is based on estimation of mutual information of interactions by using kernel density estimators. Mutual information provides a measure of statistical dependencies between interacting components. Using the topology of the network derived, we develop a data-driven parsimonious input-output model of the phosphoprotein-cytokine network.We demonstrate the applicability of our information theoretic approach to reconstruction of biological networks. For the phosphoprotein-cytokine network, this approach not only captures most of the known signaling components involved in cytokine release but also predicts new signaling components involved in the release of cytokines. The results of this study are important for gaining a clear understanding of macrophage activation during the inflammation process.

  View details for DOI 10.1186/1752-0509-8-77

  View details for Web of Science ID 000338890900001

  View details for PubMedID 24964861

  View details for PubMedCentralID PMC4094931

• Cumulative distribution function solutions of advection-reaction equations with uncertain parameters PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES Boso, F., Broyda, S. V., Tartakovsky, D. M. 2014; 470 (2166)

  Abstract

  We derive deterministic cumulative distribution function (CDF) equations that govern the evolution of CDFs of state variables whose dynamics are described by the first-order hyperbolic conservation laws with uncertain coefficients that parametrize the advective flux and reactive terms. The CDF equations are subjected to uniquely specified boundary conditions in the phase space, thus obviating one of the major challenges encountered by more commonly used probability density function equations. The computational burden of solving CDF equations is insensitive to the magnitude of the correlation lengths of random input parameters. This is in contrast to both Monte Carlo simulations (MCSs) and direct numerical algorithms, whose computational cost increases as correlation lengths of the input parameters decrease. The CDF equations are, however, not exact because they require a closure approximation. To verify the accuracy and robustness of the large-eddy-diffusivity closure, we conduct a set of numerical experiments which compare the CDFs computed with the CDF equations with those obtained via MCSs. This comparison demonstrates that the CDF equations remain accurate over a wide range of statistical properties of the two input parameters, such as their correlation lengths and variance of the coefficient that parametrizes the advective flux.

  View details for DOI 10.1098/rspa.2014.0189

  View details for Web of Science ID 000335326400021

  View details for PubMedID 24910529

  View details for PubMedCentralID PMC4042727

• Noise propagation in hybrid models of nonlinear systems: The Ginzburg-Landau equation JOURNAL OF COMPUTATIONAL PHYSICS Taverniers, S., Alexander, F. J., Tartakovsky, D. M. 2014; 262: 313-324

  View details for DOI 10.1016/j.jcp.2014.01.015

  View details for Web of Science ID 000330955200017

• Analytical models of heat conduction in fractured rocks JOURNAL OF GEOPHYSICAL RESEARCH-SOLID EARTH Martinez, A. R., Roubinet, D., Tartakovsky, D. M. 2014; 119 (1): 83-98

  View details for DOI 10.1002/2012JB010016

  View details for Web of Science ID 000333033400006

• Hybrid modeling of heterogeneous geochemical reactions in fractured porous media WATER RESOURCES RESEARCH Roubinet, D., Tartakovsky, D. M. 2013; 49 (12): 7945-7956

  View details for DOI 10.1002/2013WR013999

  View details for Web of Science ID 000329929100009

• Stochastic smoothed profile method for modeling random roughness in flow problems COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING Zayernouri, M., Park, S., Tartakovsky, D. M., Karniadakis, G. E. 2013; 263: 99-112

  View details for DOI 10.1016/j.cma.2013.05.007

  View details for Web of Science ID 000322557600009

• Exact PDF equations and closure approximations for advective-reactive transport JOURNAL OF COMPUTATIONAL PHYSICS Venturi, D., Tartakovsky, D. M., Tartakovsky, A. M., Karniadakis, G. E. 2013; 243: 323-343

  View details for DOI 10.1016/j.jcp.2013.03.001

  View details for Web of Science ID 000319050800021

• Anomalous Diffusion of Single Particles in Cytoplasm BIOPHYSICAL JOURNAL Regner, B. M., Vucinic, D., Domnisoru, C., Bartol, T. M., Hetzer, M. W., Tartakovsky, D. M., Sejnowski, T. J. 2013; 104 (8): 1652-1660

  Abstract

  The crowded intracellular environment poses a formidable challenge to experimental and theoretical analyses of intracellular transport mechanisms. Our measurements of single-particle trajectories in cytoplasm and their random-walk interpretations elucidate two of these mechanisms: molecular diffusion in crowded environments and cytoskeletal transport along microtubules. We employed acousto-optic deflector microscopy to map out the three-dimensional trajectories of microspheres migrating in the cytosolic fraction of a cellular extract. Classical Brownian motion (BM), continuous time random walk, and fractional BM were alternatively used to represent these trajectories. The comparison of the experimental and numerical data demonstrates that cytoskeletal transport along microtubules and diffusion in the cytosolic fraction exhibit anomalous (nonFickian) behavior and posses statistically distinct signatures. Among the three random-walk models used, continuous time random walk provides the best representation of diffusion, whereas microtubular transport is accurately modeled with fractional BM.

  View details for DOI 10.1016/j.bpj.2013.01.049

  View details for Web of Science ID 000318262300006

  View details for PubMedID 23601312

  View details for PubMedCentralID PMC3627875

• Probability Density Function Method for Langevin Equations with Colored Noise PHYSICAL REVIEW LETTERS Wang, P., Tartakovsky, A. M., Tartakovsky, D. M. 2013; 110 (14)

  Abstract

  Understanding the mesoscopic behavior of dynamical systems described by Langevin equations with colored noise is a fundamental challenge in a variety of fields. We propose a new approach to derive closed-form equations for joint and marginal probability density functions of state variables. This approach is based on a so-called large-eddy-diffusivity closure and can be used to model a wide class of non-Markovian processes described by the noise with an arbitrary correlation function. We demonstrate the accuracy of the proposed probability density function method for several linear and nonlinear Langevin equations.

  View details for DOI 10.1103/PhysRevLett.110.140602

  View details for Web of Science ID 000316959200005

  View details for PubMedID 25166972

• Assessment and management of risk in subsurface hydrology: A review and perspective ADVANCES IN WATER RESOURCES Tartakovsky, D. M. 2013; 51: 247-260

  View details for DOI 10.1016/j.advwatres.2012.04.007

  View details for Web of Science ID 000314105900013

• CDF SOLUTIONS OF BUCKLEY-LEVERETT EQUATION WITH UNCERTAIN PARAMETERS MULTISCALE MODELING & SIMULATION Wang, P., Tartakovsky, D. M., Jarman, K. D., Tartakovsky, A. M. 2013; 11 (1): 118-133

  View details for DOI 10.1137/120865574

  View details for Web of Science ID 000316861400005

• COMPUTING GREEN'S FUNCTIONS FOR FLOW IN HETEROGENEOUS COMPOSITE MEDIA INTERNATIONAL JOURNAL FOR UNCERTAINTY QUANTIFICATION Barajas-Solano, D. A., Tartakovsky, D. M. 2013; 3 (1): 39-46

  View details for DOI 10.1615/Int.J.UncertaintyQuantification.2012003671

  View details for Web of Science ID 000343414300003

• Particle-tracking simulations of anomalous transport in hierarchically fractured rocks COMPUTERS & GEOSCIENCES Roubinet, D., de Dreuzy, J., Tartakovsky, D. M. 2013; 50: 52-58

  View details for DOI 10.1016/j.cageo.2012.07.032

  View details for Web of Science ID 000313611100007

• An Information-theoretic Algorithm to Data-driven Genetic Pathway Interaction Network Reconstruction of Dynamic Systems 2013 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (BIBM) Farhangmehr, F., Tartakovsky, D. M., Sadatmousavi, P., Maurya, M. R., Subramaniam, S. 2013

  View details for Web of Science ID 000348252400045

• A NEW PHYSIOLOGICAL BOUNDARY CONDITION FOR HEMODYNAMICS SIAM JOURNAL ON APPLIED MATHEMATICS Cousins, W., Gremaud, P. A., Tartakovsky, D. M. 2013; 73 (3): 1203-1223

  View details for DOI 10.1137/120895470

  View details for Web of Science ID 000321040600006

• Stochastic operator-splitting method for reaction-diffusion systems JOURNAL OF CHEMICAL PHYSICS Choi, T., Maurya, M. R., Tartakovsky, D. M., Subramaniam, S. 2012; 137 (18)

  Abstract

  Many biochemical processes at the sub-cellular level involve a small number of molecules. The local numbers of these molecules vary in space and time, and exhibit random fluctuations that can only be captured with stochastic simulations. We present a novel stochastic operator-splitting algorithm to model such reaction-diffusion phenomena. The reaction and diffusion steps employ stochastic simulation algorithms and Brownian dynamics, respectively. Through theoretical analysis, we have developed an algorithm to identify if the system is reaction-controlled, diffusion-controlled or is in an intermediate regime. The time-step size is chosen accordingly at each step of the simulation. We have used three examples to demonstrate the accuracy and robustness of the proposed algorithm. The first example deals with diffusion of two chemical species undergoing an irreversible bimolecular reaction. It is used to validate our algorithm by comparing its results with the solution obtained from a corresponding deterministic partial differential equation at low and high number of molecules. In this example, we also compare the results from our method to those obtained using a Gillespie multi-particle (GMP) method. The second example, which models simplified RNA synthesis, is used to study the performance of our algorithm in reaction- and diffusion-controlled regimes and to investigate the effects of local inhomogeneity. The third example models reaction-diffusion of CheY molecules through the cytoplasm of Escherichia coli during chemotaxis. It is used to compare the algorithm's performance against the GMP method. Our analysis demonstrates that the proposed algorithm enables accurate simulation of the kinetics of complex and spatially heterogeneous systems. It is also computationally more efficient than commonly used alternatives, such as the GMP method.

  View details for DOI 10.1063/1.4764108

  View details for Web of Science ID 000311317800003

  View details for PubMedID 23163359

  View details for PubMedCentralID PMC3505198

• Autoregulation and mechanotransduction control the arteriolar response to small changes in hematocrit AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY Sriram, K., Vazquez, B. Y., Tsai, A. G., Cabrales, P., Intaglietta, M., Tartakovsky, D. M. 2012; 303 (9): H1096-H1106

  Abstract

  Here, we present an analytic model of arteriolar mechanics that accounts for key autoregulation mechanisms, including the myogenic response and the vasodilatory effects of nitric oxide (NO) in the vasculature. It couples the fluid mechanics of blood flow in arterioles with solid mechanics of the vessel wall and includes the effects of wall shear stress- and stretch-induced endothelial NO production. The model can be used to describe the regulation of blood flow and NO transport under small changes in hematocrit and to analyze the regulatory response of arterioles to small changes in hematocrit. Our analysis revealed that the experimentally observed paradoxical increase in cardiac output with small increases in hematocrit results from the combination of increased NO production and the effects of a strong myogenic response modulated by elevated levels of WSS. Our findings support the hypothesis that vascular resistance varies inversely with blood viscosity for small changes in hematocrit in a healthy circulation that responds to shear stress stimuli. They also suggest beneficial effects independent of changes in O(2) carrying capacity associated with the postsurgical transfusion of one or two units of blood.

  View details for DOI 10.1152/ajpheart.00438.2012

  View details for Web of Science ID 000310650300002

  View details for PubMedID 22923620

  View details for PubMedCentralID PMC3517642

• Uncertainty quantification in kinematic-wave models JOURNAL OF COMPUTATIONAL PHYSICS Wang, P., Tartakovsky, D. M. 2012; 231 (23): 7868-7880

  View details for DOI 10.1016/j.jcp.2012.07.030

  View details for Web of Science ID 000308726600010

• Comparison of statistical and optimisation-based methods for data-driven network reconstruction of biochemical systems IET SYSTEMS BIOLOGY Asadi, B., Maurya, M. R., Tartakovsky, D. M., Subramaniam, S. 2012; 6 (5): 155-U53

  Abstract

  Data-driven reconstruction of biological networks is a crucial step towards making sense of large volumes of biological data. Although several methods have been developed recently to reconstruct biological networks, there are few systematic and comprehensive studies that compare different methods in terms of their ability to handle incomplete datasets, high data dimensions and noisy data. The authors use experimentally measured and synthetic datasets to compare three popular methods - principal component regression (PCR), linear matrix inequalities (LMI) and least absolute shrinkage and selection operator (LASSO) - in terms of root-mean-squared error (RMSE), average fractional error in the value of the coefficients, accuracy, sensitivity, specificity and the geometric mean of sensitivity and specificity. This comparison enables the authors to establish criteria for selection of an appropriate approach for network reconstruction based on a priori properties of experimental data. For instance, although PCR is the fastest method, LASSO and LMI perform better in terms of accuracy, sensitivity and specificity. Both PCR and LASSO are better than LMI in terms of fractional error in the values of the computed coefficients. Trade-offs such as these suggest that more than one aspect of each method needs to be taken into account when designing strategies for network reconstruction.

  View details for DOI 10.1049/iet-syb.2011.0052

  View details for Web of Science ID 000310434300001

  View details for PubMedID 23101870

• PEG-albumin supraplasma expansion is due to increased vessel wall shear stress induced by blood viscosity shear thinning AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY Sriram, K., Tsai, A. G., Cabrales, P., Meng, F., Acharya, S. A., Tartakovsky, D. M., Intaglietta, M. 2012; 302 (12): H2489-H2497

  Abstract

  We studied the extreme hemodilution to a hematocrit of 11% induced by three plasma expanders: polyethylene glycol (PEG)-conjugated albumin (PEG-Alb), 6% 70-kDa dextran, and 6% 500-kDa dextran. The experimental component of our study relied on microelectrodes and cardiac output to measure both the rheological properties of plasma-expander blood mixtures and nitric oxide (NO) bioavailability in vessel walls. The modeling component consisted of an analysis of the distribution of wall shear stress (WSS) in the microvessels. Our experiments demonstrated that plasma expansion with PEG-Alb caused a state of supraperfusion with cardiac output 40% above baseline, significantly increased NO vessel wall bioavailability, and lowered peripheral vascular resistance. We attributed this behavior to the shear thinning nature of blood and PEG-Alb mixtures. To substantiate this hypothesis, we developed a mathematical model of non-Newtonian blood flow in a vessel. Our model used the Quemada rheological constitutive relationship to express blood viscosity in terms of both hematocrit and shear rate. The model revealed that the net effect of the hemodilution induced by relatively low-viscosity shear thinning PEG-Alb plasma expanders is to reduce overall blood viscosity and to increase the WSS, thus intensifying endothelial NO production. These changes act synergistically, significantly increasing cardiac output and perfusion due to lowered overall peripheral vascular resistance.

  View details for DOI 10.1152/ajpheart.01090.2011

  View details for Web of Science ID 000305430100004

  View details for PubMedID 22505638

  View details for PubMedCentralID PMC3378262

• Impact of endothelium roughness on blood flow JOURNAL OF THEORETICAL BIOLOGY Park, S. W., Intaglietta, M., Tartakovsky, D. M. 2012; 300: 152-160

  Abstract

  Cell free layer (CFL), a plasma layer bounded by the red blood cell (RBC) core and the endothelium, plays an important physiological role. Its width affects the effective blood viscosity as well as the scavenging and production of nitric oxide (NO). Measurements of the CFL and its spatio-temporal variability are highly uncertain, exhibiting random fluctuations. Yet traditional models of blood flow and NO scavenging treat the CFL's bounding surfaces as deterministic and smooth. We investigate the effects of the endothelium roughness and uncertain (random) spatial variability on blood flow and the estimates of effective blood viscosity.

  View details for DOI 10.1016/j.jtbi.2012.01.017

  View details for Web of Science ID 000302113100016

  View details for PubMedID 22300799

  View details for PubMedCentralID PMC3307844

• Lagrangian models of reactive transport in heterogeneous porous media with uncertain properties PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES Severino, G., Tartakovsky, D. M., Srinivasan, G., Viswanathan, H. 2012; 468 (2140): 1154-1174

  View details for DOI 10.1098/rspa.2011.0375

  View details for Web of Science ID 000300820800013

• A Bayesian approach to integrate temporal data into probabilistic risk analysis of monitored NAPL remediation ADVANCES IN WATER RESOURCES Fernandez-Garcia, D., Bolster, D., Sanchez-Vila, X., Tartakovsky, D. M. 2012; 36: 108-120

  View details for DOI 10.1016/j.advwatres.2011.07.001

  View details for Web of Science ID 000299971900011

• Introduction to the special issue on uncertainty quantification and risk assessment ADVANCES IN WATER RESOURCES Tartakovsky, D. M., Nowak, W., Bolster, D. 2012; 36: 1-2

  View details for DOI 10.1016/j.advwatres.2011.12.010

  View details for Web of Science ID 000299971900001

• Probabilistic analysis of maintenance and operation of artificial recharge ponds ADVANCES IN WATER RESOURCES Pedretti, D., Barahona-Palomo, M., Bolster, D., Fernandez-Garcia, D., Sanchez-Vila, X., Tartakovsky, D. M. 2012; 36: 23-35

  View details for DOI 10.1016/j.advwatres.2011.07.008

  View details for Web of Science ID 000299971900004

• Semi-analytical solutions for solute transport and exchange in fractured porous media WATER RESOURCES RESEARCH Roubinet, D., de Dreuzy, J., Tartakovsky, D. M. 2012; 48

  View details for DOI 10.1029/2011WR011168

  View details for Web of Science ID 000299702600003

• Probabilistic analysis of groundwater-related risks at subsurface excavation sites ENGINEERING GEOLOGY Jurado, A., De Gaspari, F., Vilarrasa, V., Bolster, D., Sanchez-Vila, X., Fernandez-Garcia, D., Tartakovsky, D. M. 2012; 125: 35-44

  View details for DOI 10.1016/j.enggeo.2011.10.015

  View details for Web of Science ID 000301617700004

• Hybrid models of reactive transport in porous and fractured media ADVANCES IN WATER RESOURCES Battiato, I., Tartakovsky, D. M., Tartakovsky, A. M., Scheibe, T. D. 2011; 34 (9): 1140-1150

  View details for DOI 10.1016/j.advwatres.2011.01.012

  View details for Web of Science ID 000295653700007

• Mean arterial pressure nonlinearity in an elastic circulatory system subjected to different hematocrits BIOMECHANICS AND MODELING IN MECHANOBIOLOGY Branigan, T., Bolster, D., Salazar Vazquez, B. Y., Intaglietta, M., Tartakovsky, D. M. 2011; 10 (4): 591-598

  Abstract

  The level of hematocrit (Hct) is known to affect mean arterial pressure (MAP) by influencing blood viscosity. In the healthy population, an increase in Hct (and corresponding increase in viscosity) tends to raise MAP. However, data from a clinical study of type 2 diabetic patients indicate that this relationship is not universal. Instead, individuals in the lower levels of Hct range display a decrease in MAP for a given rise in Hct. After reaching a minimum, this trend is reversed, so that further increases in Hct lead to increases in MAP. We hypothesize that this anomalous behavior occurs due to changes in the circulatory autoregulation mechanism. To substantiate this hypothesis, we develop a physically based mathematical model that incorporates autoregulation mechanisms. Our model replicates the anomalous U-shaped relationship between MAP and Hct found in diabetic patients in the same range of Hct variability.

  View details for DOI 10.1007/s10237-010-0258-y

  View details for Web of Science ID 000292040600014

  View details for PubMedID 20878440

• Integration of cardiovascular regulation by the blood/endothelium cell-free layer WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE Hightower, C. M., Vazquez, B. Y., Park, S. W., Sriram, K., Martini, J., Yalcin, O., Tsai, A. G., Cabrales, P., Tartakovsky, D. M., Johnson, P. C., Intaglietta, M. 2011; 3 (4): 458-470

  Abstract

  The cell-free layer (CFL) width separating red blood cells in flowing blood from the endothelial cell membrane is shown to be a regulator of the balance between nitric oxide (NO) production by the endothelium and NO scavenging by blood hemoglobin. The CFL width is determined by hematocrit (Hct) and the vessel wall flow velocity gradient. These factors and blood and plasma viscosity determine vessel wall shear stress which regulates the production of NO in the vascular wall. Mathematical modeling and experimental findings show that vessel wall NO concentration is a strong nonlinear function of Hct and that small Hct variations have comparatively large effects on blood pressure regulation. Furthermore, NO concentration is a regulator of inflammation and oxygen metabolism. Therefore, small, sustained perturbations of Hct may have long-term effects that can promote pro-hypertensive and pro-inflammatory conditions. In this context, Hct and its variability are directly related to vascular tone, peripheral vascular resistance, oxygen transport and delivery, and inflammation. These effects are relevant to the analysis and understanding of blood pressure regulation, as NO bioavailability regulates the contractile state of blood vessels. Furthermore, regulation of the CFL is a direct function of blood composition therefore understanding of its physiology relates to the design and management of fluid resuscitation fluids. From a medical perspective, these studies propose that it should be of clinical interest to note small variations in patient's Hct levels given their importance in modulating the CFL width and therefore NO bioavailability. WIREs Syst Biol Med 2011 3 458-470 DOI: 10.1002/wsbm.150

  View details for DOI 10.1002/wsbm.150

  View details for Web of Science ID 000291821300006

  View details for PubMedID 21523919

• PDF equations for advective-reactive transport in heterogeneous porous media with uncertain properties JOURNAL OF CONTAMINANT HYDROLOGY Tartakovsky, D. M., Broyda, S. 2011; 120-21: 129-140

  Abstract

  We consider advective-reactive solute transport in porous media whose hydraulic and transport properties are uncertain. These properties are treated as random fields, which renders nonlinear advection-reaction transport equations stochastic. We derive a deterministic equation for the probability density function (PDF) of the concentration of a solute that undergoes heterogeneous reactions, e.g., precipitation or dissolution. The derivation treats exactly (without linearization) a reactive term in the transport equation which accounts for uncertainty (randomness) in both flow velocity and kinetic rate constants but requires a closure, such as a Large-Eddy-Diffusivity (LED) approximation used in the present analysis. No closure is required when reaction rates are the only source of uncertainty. We use exact concentration PDFs obtained for this setting to analyze the accuracy of our general, LED-based PDF equations.

  View details for DOI 10.1016/j.jconhyd.2010.08.009

  View details for Web of Science ID 000287889100010

• Applicability regimes for macroscopic models of reactive transport in porous media JOURNAL OF CONTAMINANT HYDROLOGY BATTIATO, I., Tartakovsky, D. M. 2011; 120-21: 18-26

  Abstract

  We consider transport of a solute that undergoes a nonlinear heterogeneous reaction: after reaching a threshold concentration value, it precipitates on the solid matrix to form a crystalline solid. The relative importance of three key pore-scale transport mechanisms (advection, molecular diffusion, and reaction) is quantified by the Péclet (Pe) and Damköhler (Da) numbers. We use multiple-scale expansions to upscale a pore-scale advection-diffusion equation with reactions entering through a boundary condition on the fluid-solid interface, and to establish sufficient conditions under which macroscopic advection-dispersion-reaction equations provide an accurate description of the pore-scale processes. These conditions are summarized by a phase diagram in the (Pe, Da)-space, parameterized with a scale-separation parameter that is defined as the ratio of characteristic lengths associated with the pore- and macro-scales.

  View details for DOI 10.1016/j.jconhyd.2010.05.005

  View details for Web of Science ID 000287889100002

• PDF equations for advective-reactive transport in heterogeneous porous media with uncertain properties. Journal of contaminant hydrology Tartakovsky, D. M., Broyda, S. 2011; 120-121: 129-140

  Abstract

  We consider advective-reactive solute transport in porous media whose hydraulic and transport properties are uncertain. These properties are treated as random fields, which renders nonlinear advection-reaction transport equations stochastic. We derive a deterministic equation for the probability density function (PDF) of the concentration of a solute that undergoes heterogeneous reactions, e.g., precipitation or dissolution. The derivation treats exactly (without linearization) a reactive term in the transport equation which accounts for uncertainty (randomness) in both flow velocity and kinetic rate constants but requires a closure, such as a Large-Eddy-Diffusivity (LED) approximation used in the present analysis. No closure is required when reaction rates are the only source of uncertainty. We use exact concentration PDFs obtained for this setting to analyze the accuracy of our general, LED-based PDF equations.

  View details for DOI 10.1016/j.jconhyd.2010.08.009

  View details for PubMedID 20926156

• Applicability regimes for macroscopic models of reactive transport in porous media. Journal of contaminant hydrology BATTIATO, I., Tartakovsky, D. M. 2011; 120-121: 18-26

  Abstract

  We consider transport of a solute that undergoes a nonlinear heterogeneous reaction: after reaching a threshold concentration value, it precipitates on the solid matrix to form a crystalline solid. The relative importance of three key pore-scale transport mechanisms (advection, molecular diffusion, and reaction) is quantified by the Péclet (Pe) and Damköhler (Da) numbers. We use multiple-scale expansions to upscale a pore-scale advection-diffusion equation with reactions entering through a boundary condition on the fluid-solid interface, and to establish sufficient conditions under which macroscopic advection-dispersion-reaction equations provide an accurate description of the pore-scale processes. These conditions are summarized by a phase diagram in the (Pe, Da)-space, parameterized with a scale-separation parameter that is defined as the ratio of characteristic lengths associated with the pore- and macro-scales.

  View details for DOI 10.1016/j.jconhyd.2010.05.005

  View details for PubMedID 20598771

• Reduced complexity models for probabilistic forecasting of infiltration rates ADVANCES IN WATER RESOURCES Wang, P., Tartakovsky, D. M. 2011; 34 (3): 375-382

  View details for DOI 10.1016/j.advwatres.2010.12.007

  View details for Web of Science ID 000287946600005

• The Effect of Small Changes in Hematocrit on Nitric Oxide Transport in Arterioles ANTIOXIDANTS & REDOX SIGNALING Sriram, K., Vazquez, B. Y., Yalcin, O., Johnson, P. C., Intaglietta, M., Tartakovsky, D. M. 2011; 14 (2): 175-185

  Abstract

  We report the development of a mathematical model that quantifies the effects of small changes in systemic hematocrit (Hct) on the transport of nitric oxide (NO) in the microcirculation. The model consists of coupled transport equations for NO and oxygen (O2) and accounts for both shear-induced NO production by the endothelium and the effect of changing systemic Hct on the rate of NO production and the rate of NO scavenging by red blood cells. To incorporate the dependence of the plasma layer width on changes in Hct, the model couples the hemodynamics of blood in arterioles with NO and O2 transport in the plasma layer. A sensitivity analysis was conducted to determine the effects of uncertain model parameters (the thicknesses of endothelial surface layers and diffusion coefficients of NO and O2 in muscle tissues and vascular walls) on the model's predictions. Our analysis reveals that small increases in Hct may raise NO availability in the vascular wall. This finding sheds new light on the experimental data that show that the blood circulation responds to systematic increases of Hct in a manner that is consistent with increasing NO production followed by a plateau.

  View details for DOI 10.1089/ars.2010.3266

  View details for Web of Science ID 000285390800001

  View details for PubMedID 20560785

  View details for PubMedCentralID PMC3014765

• PROBABILISTIC PREDICTIONS OF INFILTRATION INTO HETEROGENEOUS MEDIA WITH UNCERTAIN HYDRAULIC PARAMETERS INTERNATIONAL JOURNAL FOR UNCERTAINTY QUANTIFICATION Wang, P., Tartakovsky, D. M. 2011; 1 (1): 35-47

  View details for DOI 10.1615/Int.J.UncertaintyQuantification.v1.i1.30

  View details for Web of Science ID 000209099900003

• Probability density functions for passive scalars dispersed in random velocity fields GEOPHYSICAL RESEARCH LETTERS Dentz, M., Tartakovsky, D. M. 2010; 37

  View details for DOI 10.1029/2010GL045748

  View details for Web of Science ID 000285840700003

• Stochastic hybrid modeling of intracellular calcium dynamics JOURNAL OF CHEMICAL PHYSICS Choi, T., Maurya, M. R., Tartakovsky, D. M., Subramaniam, S. 2010; 133 (16)

  Abstract

  Deterministic models of biochemical processes at the subcellular level might become inadequate when a cascade of chemical reactions is induced by a few molecules. Inherent randomness of such phenomena calls for the use of stochastic simulations. However, being computationally intensive, such simulations become infeasible for large and complex reaction networks. To improve their computational efficiency in handling these networks, we present a hybrid approach, in which slow reactions and fluxes are handled through exact stochastic simulation and their fast counterparts are treated partially deterministically through chemical Langevin equation. The classification of reactions as fast or slow is accompanied by the assumption that in the time-scale of fast reactions, slow reactions do not occur and hence do not affect the probability of the state. Our new approach also handles reactions with complex rate expressions such as Michaelis-Menten kinetics. Fluxes which cannot be modeled explicitly through reactions, such as flux of Ca(2+) from endoplasmic reticulum to the cytosol through inositol 1,4,5-trisphosphate receptor channels, are handled deterministically. The proposed hybrid algorithm is used to model the regulation of the dynamics of cytosolic calcium ions in mouse macrophage RAW 264.7 cells. At relatively large number of molecules, the response characteristics obtained with the stochastic and deterministic simulations coincide, which validates our approach in the limit of large numbers. At low doses, the response characteristics of some key chemical species, such as levels of cytosolic calcium, predicted with stochastic simulations, differ quantitatively from their deterministic counterparts. These observations are ubiquitous throughout dose response, sensitivity, and gene-knockdown response analyses. While the relative differences between the peak-heights of the cytosolic [Ca(2+)] time-courses obtained from stochastic (mean of 16 realizations) and deterministic simulations are merely 1%-4% for most perturbations, it is specially sensitive to levels of G(βγ) (relative difference as large as 90% at very low G(βγ)).

  View details for DOI 10.1063/1.3496996

  View details for Web of Science ID 000283753600055

  View details for PubMedID 21033822

  View details for PubMedCentralID PMC2998048

• Uncertainty quantification in modeling flow and transport in porous media STOCHASTIC ENVIRONMENTAL RESEARCH AND RISK ASSESSMENT Guadagnini, A., Tartakovsky, D. M. 2010; 24 (7): 953-954

  View details for DOI 10.1007/s00477-010-0396-x

  View details for Web of Science ID 000284070200001

• Probability density functions for advective-reactive transport in radial flow STOCHASTIC ENVIRONMENTAL RESEARCH AND RISK ASSESSMENT Broyda, S., Dentz, M., Tartakovsky, D. M. 2010; 24 (7): 985-992

  View details for DOI 10.1007/s00477-010-0401-4

  View details for Web of Science ID 000284070200004

• Elastic Response of Carbon Nanotube Forests to Aerodynamic Stresses PHYSICAL REVIEW LETTERS Battiato, I., Bandaru, P. R., Tartakovsky, D. M. 2010; 105 (14)

  Abstract

  The ability to determine static and (hydro)dynamic properties of carbon nanotubes (CNTs) is crucial for many applications. While their static properties (e.g., solubility and wettability) are fairly well understood, their mechanical responses (e.g., deflection under shear) to ambient fluid flow are to a large extent unknown. We analyze the elastic response of single-walled CNT forests, attached to the bottom wall of a channel, to the aerodynamic loading exerted by both laminar and turbulent flows. Our analysis yields analytical expressions for velocity distributions, the drag coefficient, and bending profiles of individual CNTs. This enables us to determine flexural rigidity of CNTs in wind-tunnel experiments. The model predictions agree with laboratory experiments for a large range of channel velocities.

  View details for DOI 10.1103/PhysRevLett.105.144504

  View details for Web of Science ID 000282362600004

  View details for PubMedID 21230836

• Uncertainty quantification via random domain decomposition and probabilistic collocation on sparse grids JOURNAL OF COMPUTATIONAL PHYSICS Lin, G., Tartakovsky, A. M., Tartakovsky, D. M. 2010; 229 (19): 6995-7012

  View details for DOI 10.1016/j.jcp.2010.05.036

  View details for Web of Science ID 000281570700020

• Random walk particle tracking simulations of non-Fickian transport in heterogeneous media JOURNAL OF COMPUTATIONAL PHYSICS Srinivasan, G., Tartakovsky, D. M., Dentz, M., Viswanathan, H., Berkowitz, B., Robinson, B. A. 2010; 229 (11): 4304-4314

  View details for DOI 10.1016/j.jcp.2010.02.014

  View details for Web of Science ID 000276922100017

• On the use of analytical solutions to design pumping tests in leaky aquifers connected to a stream JOURNAL OF HYDROLOGY Christensen, S., Zlotnik, V. A., Tartakovsky, D. M. 2010; 381 (3-4): 341-351

  View details for DOI 10.1016/j.jhydrol.2009.12.007

  View details for Web of Science ID 000274927700015

• Predicting Vertical Connectivity Within an Aquifer System BAYESIAN ANALYSIS Short, M., Higdon, D., Guadagnini, L., Guadagnini, A., Tartakovsky, D. M. 2010; 5 (3): 557-581

  View details for DOI 10.1214/10-BA522

  View details for Web of Science ID 000282051600009

• Functional optical imaging at the microscopic level JOURNAL OF BIOMEDICAL OPTICS Salazar Vazquez, B. Y., Hightower, C. M., Sapuppo, F., Tartakovsky, D. M., Intaglietta, M. 2010; 15 (1)

  Abstract

  Functional microscopic imaging of in vivo tissues aims at characterizing parameters at the level of the unitary cellular components under normal conditions, in the presence of blood flow, to understand and monitor phenomena that lead to maintaining homeostatic balance. Of principal interest are the setting of shear stress on the endothelium; formation of the plasma layer, where the balance between nitric oxide production and scavenging is established; and formation of the oxygen gradients that determine the distribution of oxygen from blood into the tissue. Optical techniques that enable the analysis of functional microvascular processes are the measurement of blood vessel dimensions by image shearing, the photometric analysis of the extent of the plasma layer, the dual-slit methodology for measuring blood flow velocity, and the direct measurement of oxygen concentration in blood and tissue. Each of these technologies includes the development of paired, related mathematical approaches that enable characterizing the transport properties of the blood tissue system. While the technology has been successful in analyzing the living tissue in experimental conditions, deployment to clinical settings remains an elusive goal, due to the difficulty of obtaining optical access to the depth of the tissue.

  View details for DOI 10.1117/1.3280270

  View details for Web of Science ID 000276944200012

  View details for PubMedID 20210428

  View details for PubMedCentralID PMC2816989

• On breakdown of macroscopic models of mixing-controlled heterogeneous reactions in porous media ADVANCES IN WATER RESOURCES BATTIATO, I., Tartakovsky, D. M., Tartakovsky, A. M., Scheibe, T. 2009; 32 (11): 1664-1673

  View details for DOI 10.1016/j.advwatres.2009.08.008

  View details for Web of Science ID 000271677100010

• Optimal design of pumping tests in leaky aquifers for stream depletion analysis JOURNAL OF HYDROLOGY Christensen, S., Zlotnik, V. A., Tartakovsky, D. M. 2009; 375 (3-4): 554-565

  View details for DOI 10.1016/j.jhydrol.2009.07.006

  View details for Web of Science ID 000270472100024

• Abrupt-Interface Solution for Carbon Dioxide Injection into Porous Media TRANSPORT IN POROUS MEDIA Dentz, M., Tartakovsky, D. M. 2009; 79 (1): 15-27

  View details for DOI 10.1007/s11242-008-9268-y

  View details for Web of Science ID 000268446400002

• Closure to "Stream Depletion by Groundwater Pumping in Leaky Aquifers" by Vitaly A. Zlotnik and Daniel M. Tartakovsky JOURNAL OF HYDROLOGIC ENGINEERING Zlotnik, V. A., Tartakovsky, D. M. 2009; 14 (8): 889-891

  View details for Web of Science ID 000268065900017

• Response to "Comments on Abrupt-Interface Solution for Carbon Dioxide Injection into Porous Media by Dentz and Tartakovsky (2008)" by Lu et al. TRANSPORT IN POROUS MEDIA Dentz, M., Tartakovsky, D. M. 2009; 79 (1): 39-41

  View details for DOI 10.1007/s11242-009-9363-8

  View details for Web of Science ID 000268446400004

• Probability density functions for advective-reactive transport with uncertain reaction rates WATER RESOURCES RESEARCH Tartakovsky, D. M., Dentz, M., Lichtner, P. C. 2009; 45

  View details for DOI 10.1029/2008WR007383

  View details for Web of Science ID 000268096300001

• Effects of spatio-temporal variability of precipitation on contaminant migration in the vadose zone GEOPHYSICAL RESEARCH LETTERS Wang, P., Quinlan, P., Tartakovsky, D. M. 2009; 36

  View details for DOI 10.1029/2009GL038347

  View details for Web of Science ID 000267186400005

• Probabilistic risk analysis of groundwater remediation strategies WATER RESOURCES RESEARCH Bolster, D., Barahona, M., Dentz, M., Fernandez-Garcia, D., Sanchez-Vila, X., TRINCHERO, P., Valhondo, C., Tartakovsky, D. M. 2009; 45

  View details for DOI 10.1029/2008WR007551

  View details for Web of Science ID 000267005400004

• Perspective on theories of non-Fickian transport in heterogeneous media ADVANCES IN WATER RESOURCES Neuman, S. P., Tartakovsky, D. M. 2009; 32 (5): 670-680

  View details for DOI 10.1016/j.advwatres.2008.08.005

  View details for Web of Science ID 000266253900005

• Delineation of geological facies from poorly differentiated data ADVANCES IN WATER RESOURCES Wohlberg, B., Tartakovsky, D. M. 2009; 32 (2): 225-230

  View details for DOI 10.1016/j.advwatres.2008.10.014

  View details for Web of Science ID 000264512000009

• Hydrogeophysical Approach for Identification of Layered Structures of the Vadose Zone from Electrical Resistivity Data VADOSE ZONE JOURNAL Tartakovsky, A. M., Bolster, D., Tartakovsky, D. M. 2008; 7 (4): 1207-1214

  View details for DOI 10.2136/vzj2008.0009

  View details for Web of Science ID 000261384600014

• Probabilistic risk analysis of building contamination INDOOR AIR Bolster, D. T., Tartakovsky, D. M. 2008; 18 (5): 351-364

  Abstract

  We present a general framework for probabilistic risk assessment (PRA) of building contamination. PRA provides a powerful tool for the rigorous quantification of risk in contamination of building spaces. A typical PRA starts by identifying relevant components of a system (e.g. ventilation system components, potential sources of contaminants, remediation methods) and proceeds by using available information and statistical inference to estimate the probabilities of their failure. These probabilities are then combined by means of fault-tree analyses to yield probabilistic estimates of the risk of system failure (e.g. building contamination). A sensitivity study of PRAs can identify features and potential problems that need to be addressed with the most urgency. Often PRAs are amenable to approximations, which can significantly simplify the approach. All these features of PRA are presented in this paper via a simple illustrative example, which can be built upon in further studies.The tool presented here can be used to design and maintain adequate ventilation systems to minimize exposure of occupants to contaminants.

  View details for DOI 10.1111/j.1600-0668.2008.00536.x

  View details for Web of Science ID 000259236800002

  View details for PubMedID 18681912

• Stochastic Langevin model for flow and transport in porous media PHYSICAL REVIEW LETTERS Tartakovsky, A. M., Tartakovsky, D. M., Meakin, P. 2008; 101 (4)

  Abstract

  We present a new model for fluid flow and solute transport in porous media, which employs smoothed particle hydrodynamics to solve a Langevin equation for flow and dispersion in porous media. This allows for effective separation of the advective and diffusive mixing mechanisms, which is absent in the classical dispersion theory that lumps both types of mixing into dispersion coefficient. The classical dispersion theory overestimates both mixing-induced effective reaction rates and the effective fractal dimension of the mixing fronts associated with miscible fluid Rayleigh-Taylor instabilities. We demonstrate that the stochastic (Langevin equation) model overcomes these deficiencies.

  View details for DOI 10.1103/PhysRevLett.101.044502

  View details for Web of Science ID 000258427100025

  View details for PubMedID 18764333

• A reduced complexity model for probabilistic risk assessment of groundwater contamination WATER RESOURCES RESEARCH Winter, C. L., Tartakovsky, D. M. 2008; 44 (6)

  View details for DOI 10.1029/2007WR006599

  View details for Web of Science ID 000256571800001

• Self-consistent four-point closure for transport in steady random flows PHYSICAL REVIEW E Dentz, M., Tartakovsky, D. M. 2008; 77 (6)

  Abstract

  Ensemble averaging of advection-dispersion equations describing transport of a passive scalar in incompressible random velocity fields requires a closure approximation. Commonly used approaches, such as the direct interaction approximation and large-eddy simulations as well as equivalent renormalization schemes, employ so-called two-point (or one-loop) closures. These approaches have proven to be adequate for transport in zero-mean (unbiased) time-dependent random velocity fields with increasing accuracy for decreasing temporal coherence. In the opposite limit of steady velocity fields with finite bias, however, these schemes fail to predict effective transport properties both quantitatively and qualitatively, leading to an obvious inconsistency for transverse dispersion in two spatial dimensions. For this case, two-point closures predict that macroscopic transverse dispersion increases as the square root of the disorder variance while it has been proven rigorously that there is no disorder-induced contribution to macroscopic transverse dispersion for purely advective transport. Furthermore, two-point closures significantly underestimate the disorder-induced contribution to longitudinal dispersion. We derive a four-point closure for stochastically averaged transport equations that goes beyond classical one-loop schemes and demonstrate that it is exact for transverse dispersion and correctly predicts an increase of the longitudinal disorder-induced dispersion coefficient with the square of the variance of the strong disorder. The predicted values of asymptotic longitudinal dispersion coefficients are consistent with those obtained via Monte Carlo random walk simulations.

  View details for DOI 10.1103/PhysRevE.77.066307

  View details for Web of Science ID 000257287600049

  View details for PubMedID 18643371

• Nonlinear localization of light in disordered optical fiber arrays PHYSICAL REVIEW A Srinivasan, G., Aceves, A., Tartakovsky, D. M. 2008; 77 (6)

  View details for DOI 10.1103/PhysRevA.77.063806

  View details for Web of Science ID 000257288800166

• Stream depletion by groundwater pumping in leaky aquifers JOURNAL OF HYDROLOGIC ENGINEERING Zlotnik, V. A., Tartakovsky, D. M. 2008; 13 (2): 43-50

  View details for DOI 10.1061/(ASCE)1084-0699(2008)13:2(43)

  View details for Web of Science ID 000252566200001

• Uncertain future of hydrogeology Fall Annual Meeting of the American-Geophysical-Union Tartakovsky, D. M., Winter, C. L. ASCE-AMER SOC CIVIL ENGINEERS. 2008: 37–39

  View details for DOI 10.1061/(ASCE)1084-0699(2008)13:1(37)

  View details for Web of Science ID 000251852900007

• Machine learning methods for inverse modeling GEOENV VI - GEOSTATISTICS FOR ENVIRONMENTAL APPLICATIONS, PROCEEDINGS Tartakovsky, D. M., Guadagnini, A., Wohlberg, B. E. 2008; 15: 117-125

  View details for Web of Science ID 000255270800010

• HYBRID SIMULATIONS OF REACTION-DIFFUSION SYSTEMS IN POROUS MEDIA SIAM JOURNAL ON SCIENTIFIC COMPUTING Tartakovsky, A. M., Tartakovsky, D. M., Scheibe, T. D., Meakin, P. 2008; 30 (6): 2799-2816

  View details for DOI 10.1137/070691097

  View details for Web of Science ID 000260850200006

• Hybrid numerical methods for multiscale simulations of subsurface biogeochemical processes SCIDAC 2008: SCIENTIFIC DISCOVERY THROUGH ADVANCED COMPUTING Scheibe, T. D., Tartakovsky, A. M., Tartakovsky, D. M., Redden, G. D., Meakin, P., Palmer, B. J., Schuchardt, K. L. 2008; 125

  View details for DOI 10.1088/1742-6596/125/1/012054

  View details for Web of Science ID 000260370700055

• Quantification of uncertainty in geochemical reactions WATER RESOURCES RESEARCH Srinivasan, G., Tartakovsky, D. M., Robinson, B. A., Aceves, A. B. 2007; 43 (12)

  View details for DOI 10.1029/2007WR006003

  View details for Web of Science ID 000252017200002

• Type curve interpretation of late-time pumping test data in randomly heterogeneous aquifers WATER RESOURCES RESEARCH Neuman, S. P., Blattstein, A., Riva, M., Tartakovsky, D. M., Guadagnini, A., Ptak, T. 2007; 43 (10)

  View details for DOI 10.1029/2007WR005871

  View details for Web of Science ID 000250452600005

• Analytical models of contaminant transport in coastal aquifers ADVANCES IN WATER RESOURCES Bolster, D. T., Tartakovsky, D. M., Dentz, M. 2007; 30 (9): 1962-1972

  View details for DOI 10.1016/j.advwatres.2007.03.007

  View details for Web of Science ID 000248435700007

• Nearest-neighbor classification for facies delineation WATER RESOURCES RESEARCH Tartakovsky, D. M., Wohlberg, B., Guadagnini, A. 2007; 43 (7)

  View details for DOI 10.1029/2007WR005968

  View details for Web of Science ID 000248291300002

• Probabilistic risk analysis in subsurface hydrology GEOPHYSICAL RESEARCH LETTERS Tartakovsky, D. M. 2007; 34 (5)

  View details for DOI 10.1029/2007GL029245

  View details for Web of Science ID 000245016100008

• Ergodicity of pumping tests WATER RESOURCES RESEARCH Sanchez-Vila, X., Tartakovsky, D. M. 2007; 43 (3)

  View details for DOI 10.1029/2006WR005241

  View details for Web of Science ID 000244902000002

• Stochastic modeling of complex systems COMPUTING IN SCIENCE & ENGINEERING Tartakovsky, D. M., Xiu, D. 2007; 9 (2): 8-9

  View details for Web of Science ID 000244159600004

• Particle methods for simulation of subsurface multiphase fluid flow and biogeochemical processes SCIDAC 2007: SCIENTIFIC DISCOVERY THROUGH ADVANCED COMPUTING Meakin, P., Tartakovsky, A., Scheibe, T., Tartakovsky, D., Redden, G., Long, P. E., Brooks, S. C., Xu, Z. 2007; 78

  View details for DOI 10.1088/1742-6596/78/1/012047

  View details for Web of Science ID 000250667200047

• Hybrid numerical methods for multiscale simulations of subsurface biogeochemical processes SCIDAC 2007: SCIENTIFIC DISCOVERY THROUGH ADVANCED COMPUTING Scheibe, T. D., Tartakovsky, A. M., Tartakovsky, D. M., Redden, G. D., Meakin, P. 2007; 78

  View details for DOI 10.1088/1742-6596/78/1/012063

  View details for Web of Science ID 000250667200063

• Stochastic analysis of transport in tubes with rough walls JOURNAL OF COMPUTATIONAL PHYSICS Tartakovsky, D. M., Xiu, D. 2006; 217 (1): 248-259

  View details for DOI 10.1016/j.jcp.2006.02.029

  View details for Web of Science ID 000239904500014

• Multivariate sensitivity analysis of saturated flow through simulated highly heterogeneous groundwater aquifers JOURNAL OF COMPUTATIONAL PHYSICS Winter, C. L., Guadagnini, A., Nychka, D., Tartakovsky, D. M. 2006; 217 (1): 166-175

  View details for DOI 10.1016/j.jcp.2006.01.047

  View details for Web of Science ID 000239904500010

• Delay mechanisms of non-Fickian transport in heterogeneous media GEOPHYSICAL RESEARCH LETTERS Dentz, M., Tartakovsky, D. M. 2006; 33 (16)

  View details for DOI 10.1029/2006GL027054

  View details for Web of Science ID 000240330800005

• Variable-density flow in porous media JOURNAL OF FLUID MECHANICS Dentz, M., Tartakovsky, D. M., Abarca, E., Guadagnini, A., Sanchez-Vila, X., Carrera, J. 2006; 561: 209-235

  View details for DOI 10.1017/S0022112006000668

  View details for Web of Science ID 000240323700008

• Asymptotic analysis of cross-hole hydraulic tests in fractured granite GROUND WATER Illman, W. A., Tartakovsky, D. M. 2006; 44 (4): 555-563

  Abstract

  Illman and Tartakovsky (2005a, 2005b) developed a new approach for the interpretation of three-dimensional pneumatic well tests conducted in porous or fractured geologic media, which is based on a straight-line analysis of late-time data. We modify this approach to interpret three-dimensional well tests in the saturated zone and use it to analyze the cross-hole hydraulic test data collected in the Full-Scale Engineered Barrier Experiment gallery at the Grimsel Test Site in Switzerland. The equivalent hydraulic conductivity and specific storage obtained from our analysis increase with the radial distance between the centroids of the pumping and monitoring intervals. Since this scale effect is observed from a single test type (cross-hole tests), it is less ambiguous than scale effects typically inferred from laboratory and multiple types of hydraulic tests (e.g., slug, single- and cross-hole tests). The statistical analysis of the estimated hydraulic parameters shows a strong correlation between equivalent hydraulic conductivity and specific storage.

  View details for DOI 10.1111/j.1745-6584.2006.00201.x

  View details for Web of Science ID 000238655300013

  View details for PubMedID 16857033

• Numerical methods for differential equations in random domains SIAM JOURNAL ON SCIENTIFIC COMPUTING Xiu, D., Tartakovsky, D. M. 2006; 28 (3): 1167-1185

  View details for DOI 10.1137/040613160

  View details for Web of Science ID 000239701100018

• Subsurface characterization with support vector machines IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING Wohlberg, B., Tartakovsky, D. M., Guadagnini, A. 2006; 44 (1): 47-57

  View details for DOI 10.1109/TGRS.2005.859953

  View details for Web of Science ID 000234367900005

• Asymptotic analysis of cross-hole pneumatic injection tests in unsaturated fractured tuff ADVANCES IN WATER RESOURCES Illman, W. A., Tartakovsky, D. M. 2005; 28 (11): 1217-1229

  View details for DOI 10.1016/j.advwatres.2005.03.011

  View details for Web of Science ID 000232768000005

• Algorithm refinement for stochastic partial differential equations: II. Correlated systems JOURNAL OF COMPUTATIONAL PHYSICS Alexander, F. J., Garcia, A. L., Tartakovsky, D. M. 2005; 207 (2): 769-787

  View details for DOI 10.1016/j.jcp.2005.02.004

  View details for Web of Science ID 000229711100016

• Noise in algorithm refinement methods COMPUTING IN SCIENCE & ENGINEERING Alexander, F. J., Tartakovsky, D. M., Garcia, A. L. 2005; 7 (3): 32-38

  View details for Web of Science ID 000228487100007

• Asymptotic analysis of three-dimensional pressure interference tests: A point source solution WATER RESOURCES RESEARCH Illman, W. A., Tartakovsky, D. M. 2005; 41 (1)

  View details for DOI 10.1029/2004WR003431

  View details for Web of Science ID 000226549300002

• Delineation of geologic facies with statistical learning theory GEOPHYSICAL RESEARCH LETTERS Tartakovsky, D. M., Wohlberg, B. E. 2004; 31 (18)

  View details for DOI 10.1029/2004GL020864

  View details for Web of Science ID 000224126200004

• Probabilistic reconstruction of geologic facies JOURNAL OF HYDROLOGY Guadagnini, L., Guadagnini, A., Tartakovsky, D. M. 2004; 294 (1-3): 57-67

  View details for DOI 10.1016/j.jhydrol.2004.02.007

  View details for Web of Science ID 000222282900005

• Nonlocal and localized analyses of conditional mean transient flow in bounded, randomly heterogeneous porous media WATER RESOURCES RESEARCH Ye, M., Neuman, S. P., Guadagnini, A., Tartakovsky, D. M. 2004; 40 (5)

  View details for DOI 10.1029/2003WR002099

  View details for Web of Science ID 000221476100001

• Transient flow in a heterogeneous vadose zone with uncertain parameters VADOSE ZONE JOURNAL Tartakovsky, A. M., Garcia-Naranjo, L., Tartakovsky, D. M. 2004; 3 (1): 154-163

  View details for Web of Science ID 000227397800013

• A geostatistical model for distribution of facies in highly heterogeneous aquifers GEOENV IV - GEOSTATISTICS FOR ENVIRONMENTAL APPLICATIONS: PROCEEDINGS Guadagnini, L., Guadagnini, A., Tartakovsky, D. M. 2004; 13: 211-222

  View details for Web of Science ID 000222630400018

• Effective properties of random composites SIAM JOURNAL ON SCIENTIFIC COMPUTING Tartakovsky, D. M., Guadagnini, A. 2004; 26 (2): 625-635

  View details for DOI 10.1137/S106482750342711X

  View details for Web of Science ID 000226823100016

• A two-scale nonperturbative approach to uncertainty analysis of diffusion in random composites MULTISCALE MODELING & SIMULATION Xiu, D. B., Tartakovsky, D. M. 2004; 2 (4): 662-674

  View details for DOI 10.1137/03060268X

  View details for Web of Science ID 000224122300006

• A perturbation solution to the transient Henry problem for seawater intrusion COMPUTATIONAL METHODS IN WATER RESOURCES, VOLS 1 AND 2 Tartakovsky, D. A., Guadagnini, A., Sanchez-Vila, X., Dentz, M., Carrera, J. 2004; 55: 1573-1581

  View details for Web of Science ID 000228987900134

• Uncertainty quantification for flow in highly heterogeneous porous media COMPUTATIONAL METHODS IN WATER RESOURCES, VOLS 1 AND 2 Xiu, D., Tartakovsky, D. M. 2004; 55: 695-703

  View details for Web of Science ID 000228987900061

• Stochastic analysis of effective rate constant for heterogeneous reactions ModelCARE 2002 Conference Lichtner, P. C., Tartakovsky, D. M. SPRINGER. 2003: 419–29

  View details for DOI 10.1007/s00477-003-0163-3

  View details for Web of Science ID 000186979400007

• Random domain decomposition for flow in heterogeneous stratified aquifers ModelCARE 2002 Conference Guadagnini, A., Guadagnini, L., Tartakovsky, D. M., Winter, C. L. SPRINGER. 2003: 394–407

  View details for DOI 10.1007/s00477-003-0157-1

  View details for Web of Science ID 000186979400005

• Stochastic averaging of nonlinear flows in heterogeneous porous media JOURNAL OF FLUID MECHANICS Tartakovsky, D. M., Guadagnini, A., Riva, M. 2003; 492: 47-62

  View details for DOI 10.1017/S002211200300538X

  View details for Web of Science ID 000186099500003

• Unsaturated flow in heterogeneous soils with spatially distributed uncertain hydraulic parameters JOURNAL OF HYDROLOGY Tartakovsky, D. M., Lu, Z. M., Guadagnini, A., Tartakovsky, A. M. 2003; 275 (3-4): 182-193

  View details for DOI 10.1016/S0022-1694(03)00042-8

  View details for Web of Science ID 000182625800004

• Algorithm refinement for Stochastic partial differential equations RAREFIED GAS DYNAMICS Alexander, F. J., Garcia, A. L., Tartakovsky, D. M. 2003; 663: 915-922

  View details for Web of Science ID 000183372100113

• PDF methods for reactive transport in porous media Conference on Calibration and Reliability in Groundwater Modelling (ModelCARE 2002) Tartakovsky, D. M., Lichtner, P. C., Pawar, R. J. INT ASSOC HYDROLOGICAL SCIENCES. 2003: 162–67

  View details for Web of Science ID 000189478600023

• Solution of moment equations of groundwater flow in random composite layered aquifers Conference on Calibration and Reliability in Groundwater Modelling (ModelCARE 2002) Guadagnini, A., Guadagnini, L., Tartakovsky, D. M., Winter, C. L. INT ASSOC HYDROLOGICAL SCIENCES. 2003: 108–14

  View details for Web of Science ID 000189478600015

• Moment differential equations for flow in highly heterogeneous porous media SURVEYS IN GEOPHYSICS Winter, C. L., Tartakovsky, D. M., Guadagnini, A. 2003; 24 (1): 81-106

  View details for Web of Science ID 000180750900003

• Algorithm refinement for stochastic partial differential equations. I. Linear diffusion JOURNAL OF COMPUTATIONAL PHYSICS Alexander, F. J., Garcia, A. L., Tartakovsky, D. M. 2002; 182 (1): 47-66

  View details for DOI 10.1006/jcph.2002.7149

  View details for Web of Science ID 000179183200003

• Localization of mean flow and apparent transmissivity tensor for bounded randomly heterogeneous aquifers TRANSPORT IN POROUS MEDIA Tartakovsky, D. M., Guadagnini, A., Ballio, F., Tartakovsky, A. M. 2002; 49 (1): 41-58

  View details for Web of Science ID 000176415600004

• Groundwater flow in heterogeneous composite aquifers WATER RESOURCES RESEARCH Winter, C. L., Tartakovsky, D. M. 2002; 38 (8)

  View details for DOI 10.1029/2001WR000450

  View details for Web of Science ID 000179643600003

• Theoretical interpretation of a pronounced permeability scale effect in unsaturated fractured tuff WATER RESOURCES RESEARCH Hyun, Y., Neuman, S. P., Vesselinov, V. V., Illman, W. A., Tartakovsky, D. M., Di Federico, V. 2002; 38 (6)

  View details for DOI 10.1029/2001WR000658

  View details for Web of Science ID 000178936000004

• Numerical solutions of moment equations for flow in heterogeneous composite aquifers WATER RESOURCES RESEARCH Winter, C. L., Tartakovsky, D. M., Guadagnini, A. 2002; 38 (5)

  View details for DOI 10.1029/2001WR000222

  View details for Web of Science ID 000178935000010

• Conditional moment analysis of steady state unsaturated flow in bounded, randomly heterogeneous soils WATER RESOURCES RESEARCH Lu, Z. M., Neuman, S. P., Guadagnini, A., Tartakovsky, D. M. 2002; 38 (4)

  View details for DOI 10.1029/2001WR000278

  View details for Web of Science ID 000178932200005

• Mean and variance of DNAPL finger development in a saturated, randomly heterogeneous porous medium COMPUTATIONAL METHODS IN WATER RESOURCES, VOLS 1 AND 2, PROCEEDINGS Tartakovsky, A. M., Neuman, S. P., Tartakovsky, D. M. 2002; 47: 1307-1314

  View details for Web of Science ID 000178839400170

• Nonlocal and localized analyses of conditional mean transient flow in bounded, randomly nonuniform domains COMPUTATIONAL METHODS IN WATER RESOURCES, VOLS 1 AND 2, PROCEEDINGS Ye, M., Neuman, S. P., Guadagnini, A., Tartakovsky, D. M. 2002; 47: 1155-1162

  View details for Web of Science ID 000178839400151

• Theoretical foundation for conductivity scaling GEOPHYSICAL RESEARCH LETTERS Winter, C. L., Tartakovsky, D. M. 2001; 28 (23): 4367-4369

  View details for Web of Science ID 000172425700007

• Prior mapping for nonlinear flows in random environments PHYSICAL REVIEW E Tartakovsky, D. M., Guadagnini, A. 2001; 64 (3)

  Abstract

  We analyze nonlinear flows in randomly heterogeneous environments, which are characterized by state-dependent diffusion coefficients with spatially correlated structures. The prior Kirchhoff mapping is used to describe such systems by linear stochastic partial differential equations with multiplicative noise. These are solved through moment equations which are closed, alternatively, either by perturbation expansions, or by a posterior linear mapping closure. The latter relies on the assumption that the state variable is a spatially distributed Gaussian field. We demonstrate that the former approach is more robust.

  View details for Web of Science ID 000171136400010

  View details for PubMedID 11580383

• Dynamics of free surfaces in random porous media SIAM JOURNAL ON APPLIED MATHEMATICS Tartakovsky, D. M., Winter, C. L. 2001; 61 (6): 1857-1876

  View details for Web of Science ID 000169070100002

• Kinematic structure of minipermeameter flow WATER RESOURCES RESEARCH Tartakovsky, D. M., Moulton, J. D., Zlotnik, V. A. 2000; 36 (9): 2433-2442

  View details for Web of Science ID 000089184100003

• Effective hydraulic conductivity and transmissivity for heterogeneous aquifers MATHEMATICAL GEOLOGY Tartakovsky, D. M., Guadagnini, A., Guadagnini, L. 2000; 32 (6): 751-759

  View details for Web of Science ID 000088291000005

• Mean flow in composite porous media GEOPHYSICAL RESEARCH LETTERS Winter, C. L., Tartakovsky, D. M. 2000; 27 (12): 1759-1762

  View details for Web of Science ID 000087658000020

• An analytical solution for two-dimensional contaminant transport during groundwater extraction JOURNAL OF CONTAMINANT HYDROLOGY Tartakovsky, D. M. 2000; 42 (2-4): 273–83

  View details for DOI 10.1016/S0169-7722(99)00086-8

  View details for Web of Science ID 000085841000008

• Effective hydraulic conductivity in multiscale random fields with truncated power variograms Symposium on Theory, Modeling, and Field Investigation in Hydrogeology in Honor of Shlomo P Neumans 60th Birthday Di Federico, V., Tartakovsky, D. M. GEOLOGICAL SOC AMER INC. 2000: 81–89

  View details for Web of Science ID 000169503900008

• Stochastic analysis of groundwater pumping from bounded, randomly heterogeneous aquifers Symposium on Theory, Modeling, and Field Investigation in Hydrogeology in Honor of Shlomo P Neumans 60th Birthday Guadagnini, A., Tartakovsky, D. M. GEOLOGICAL SOC AMER INC. 2000: 73–79

  View details for Web of Science ID 000169503900007

• Propagation of measurement errors in reservoir modeling XIIIth International Conference on Computational Methods in Water Resources Pawar, R. J., Tartakovsky, D. M. A A BALKEMA PUBLISHERS. 2000: 15–20

  View details for Web of Science ID 000088804700003

• Direct solution of unsaturated flow in randomly heterogeneous soils XIIIth International Conference on Computational Methods in Water Resources Lu, Z. M., Neuman, S. P., Guadagnini, A., Tartakovsky, D. M. A A BALKEMA PUBLISHERS. 2000: 785–792

  View details for Web of Science ID 000088804700108

• Three-dimensional steady state flow to a well in a randomly heterogeneous aquifer ModelCARE 1999 Conference Riva, M., Guadagnini, A., Neuman, S. P., Tartakovsky, D. M. INT ASSOC HYDROLOGICAL SCIENCES. 2000: 131–36

  View details for Web of Science ID 000173564800020

• Anisotropy, lacunarity, and upscaled conductivity and its autocovariance in multiscale random fields with truncated power variograms WATER RESOURCES RESEARCH Di Federico, V., Neuman, S. P., Tartakovsky, D. M. 1999; 35 (10): 2891-2908

  View details for Web of Science ID 000082832400001

• Extension of "Transient flow in bounded randomly heterogeneous domains, 1, Exact conditional moment equations and recursive approximations" WATER RESOURCES RESEARCH Tartakovsky, D. M., Neuman, S. P. 1999; 35 (6): 1921-1925

  View details for Web of Science ID 000080453800021

• Conditional stochastic averaging of steady state unsaturated flow by means of Kirchhoff transformation WATER RESOURCES RESEARCH Tartakovsky, D. M., Neuman, S. P., Lu, Z. M. 1999; 35 (3): 731-745

  View details for Web of Science ID 000078771700011

• Some aspects of head-variance evaluation COMPUTATIONAL GEOSCIENCES Tartakovsky, D. M., Mitkov, I. 1999; 3 (1): 89-92

  View details for Web of Science ID 000084624700005

• Dynamics of wetting fronts in porous media PHYSICAL REVIEW E Mitkov, I., Tartakovsky, D. M., Winter, C. L. 1998; 58 (5): R5245-R5248

  View details for Web of Science ID 000077052100012

• Transient flow in bounded randomly heterogeneous domains 2. Localization of conditional mean equations and temporal nonlocality effects WATER RESOURCES RESEARCH Tartakovsky, D. M., Neuman, S. P. 1998; 34 (1): 13-20

  View details for Web of Science ID 000071367100002

• Transient flow in bounded randomly heterogeneous domains 1. Exact conditional moment equations and recursive approximations WATER RESOURCES RESEARCH Tartakovsky, D. M., Neuman, S. P. 1998; 34 (1): 1-12

  View details for Web of Science ID 000071367100001

• Transient effective hydraulic conductivities under slowly and rapidly varying mean gradients in bounded three-dimensional random media WATER RESOURCES RESEARCH Tartakovsky, D. M., Neuman, S. P. 1998; 34 (1): 21-32

  View details for Web of Science ID 000071367100003

• An analytical solution for contaminant transport in nonuniform flow TRANSPORT IN POROUS MEDIA Tartakovsky, D. M., Di Federico, V. 1997; 27 (1): 85-97

  View details for Web of Science ID A1997XE05500005

• Effective hydraulic conductivity of bounded, strongly heterogeneous porous media WATER RESOURCES RESEARCH Paleologos, E. K., Neuman, S. P., Tartakovsky, D. 1996; 32 (5): 1333-1341

  View details for Web of Science ID A1996UH88200018