All Publications

  • A MC-based anthropomorphic test case for commissioning model-based dose calculation in interstitial breast 192-Ir HDR brachytherapy. Medical physics Peppa, V., Thomson, R. M., Enger, S. A., Fonseca, G. P., Lee, C., Lucero, J. N., Mourtada, F., Siebert, F. A., Vijande, J., Papagiannis, P. 2023; 50 (7): 4675-4687


    To provide the first clinical test case for commissioning of 192 Ir brachytherapy model-based dose calculation algorithms (MBDCAs) according to the AAPM TG-186 report workflow.A computational patient phantom model was generated from a clinical multi-catheter 192 Ir HDR breast brachytherapy case. Regions of interest (ROIs) were contoured and digitized on the patient CT images and the model was written to a series of DICOM CT images using MATLAB. The model was imported into two commercial treatment planning systems (TPSs) currently incorporating an MBDCA. Identical treatment plans were prepared using a generic 192 Ir HDR source and the TG-43-based algorithm of each TPS. This was followed by dose to medium in medium calculations using the MBDCA option of each TPS. Monte Carlo (MC) simulation was performed in the model using three different codes and information parsed from the treatment plan exported in DICOM radiation therapy (RT) format. Results were found to agree within statistical uncertainty and the dataset with the lowest uncertainty was assigned as the reference MC dose distribution.The dataset is available online at, Files include the treatment plan for each TPS in DICOM RT format, reference MC dose data in RT Dose format, as well as a guide for database users and all files necessary to repeat the MC simulations.The dataset facilitates the commissioning of brachytherapy MBDCAs using TPS embedded tools and establishes a methodology for the development of future clinical test cases. It is also useful to non-MBDCA adopters for intercomparing MBDCAs and exploring their benefits and limitations, as well as to brachytherapy researchers in need of a dosimetric and/or a DICOM RT information parsing benchmark. Limitations include specificity in terms of radionuclide, source model, clinical scenario, and MBDCA version used for its preparation.

    View details for DOI 10.1002/mp.16455

    View details for PubMedID 37194638

  • Bayesian Information Engine that Optimally Exploits Noisy Measurements. Physical review letters Saha, T. K., Lucero, J. N., Ehrich, J., Sivak, D. A., Bechhoefer, J. 2022; 129 (13): 130601


    We have experimentally realized an information engine consisting of an optically trapped, heavy bead in water. The device raises the trap center after a favorable "up" thermal fluctuation, thereby increasing the bead's average gravitational potential energy. In the presence of measurement noise, poor feedback decisions degrade its performance; below a critical signal-to-noise ratio, the engine shows a phase transition and cannot store any gravitational energy. However, using Bayesian estimates of the bead's position to make feedback decisions can extract gravitational energy at all measurement noise strengths and has maximum performance benefit at the critical signal-to-noise ratio.

    View details for DOI 10.1103/PhysRevLett.129.130601

    View details for PubMedID 36206430

  • Maximizing power and velocity of an information engine PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Saha, T. K., Lucero, J. E., Ehrich, J., Sivak, D. A., Bechhoefer, J. 2021; 118 (20)


    Information-driven engines that rectify thermal fluctuations are a modern realization of the Maxwell-demon thought experiment. We introduce a simple design based on a heavy colloidal particle, held by an optical trap and immersed in water. Using a carefully designed feedback loop, our experimental realization of an "information ratchet" takes advantage of favorable "up" fluctuations to lift a weight against gravity, storing potential energy without doing external work. By optimizing the ratchet design for performance via a simple theory, we find that the rate of work storage and velocity of directed motion are limited only by the physical parameters of the engine: the size of the particle, stiffness of the ratchet spring, friction produced by the motion, and temperature of the surrounding medium. Notably, because performance saturates with increasing frequency of observations, the measurement process is not a limiting factor. The extracted power and velocity are at least an order of magnitude higher than in previously reported engines.

    View details for DOI 10.1073/pnas.2023356118

    View details for Web of Science ID 000656222000009

    View details for PubMedID 33972432

    View details for PubMedCentralID PMC8157929

  • Maximal fluctuation exploitation in Gaussian information engines PHYSICAL REVIEW E Lucero, J., Ehrich, J., Bechhoefer, J., Sivak, D. 2021; 104 (4): 16
  • Nonequilibrium Energy Transduction in Stochastic Strongly Coupled Rotary Motors JOURNAL OF PHYSICAL CHEMISTRY LETTERS Lathouwers, E., Lucero, J. E., Sivak, D. A. 2020; 11 (13): 5273-5278


    Living systems at the molecular scale are composed of many constituents with strong and heterogeneous interactions, operating far from equilibrium, and subject to strong fluctuations. These conditions pose significant challenges to efficient, precise, and rapid free energy transduction, yet nature has evolved numerous molecular machines that do just this. Using a simple model of the ingenious rotary machine FoF1-ATP synthase, we investigate the interplay between nonequilibrium driving forces, thermal fluctuations, and interactions between strongly coupled subsystems. This model reveals design principles for effective free energy transduction. Most notably, while tight coupling is intuitively appealing, we find that output power is maximized at intermediate-strength coupling, which permits lubrication by stochastic fluctuations with only minimal slippage.

    View details for DOI 10.1021/acs.jpclett.0c01055

    View details for Web of Science ID 000547468400051

    View details for PubMedID 32501698

  • Optimal control of rotary motors PHYSICAL REVIEW E Lucero, J. E., Mehdizadeh, A., Sivak, D. A. 2019; 99 (1): 012119


    Single-molecule experiments have found near-perfect thermodynamic efficiency in the rotary motor F_{1}-ATP synthase. To help elucidate the principles underlying nonequilibrium energetic efficiency in such stochastic machines, we investigate driving protocols that minimize dissipation near equilibrium in a simple model rotary mechanochemical motor, as determined by a generalized friction coefficient. Our simple model has a periodic friction coefficient that peaks near system energy barriers. This implies a minimum-dissipation protocol that proceeds rapidly when the system is overwhelmingly in a single macrostate but slows significantly near energy barriers, thereby harnessing thermal fluctuations to kick the system over energy barriers with minimal work input. This model also manifests a phenomenon not seen in otherwise similar nonperiodic systems: Sufficiently fast protocols can effectively lap the system. While this leads to a trade-off between accuracy of driving and energetic cost, we find that our designed protocols outperform naive protocols.

    View details for DOI 10.1103/PhysRevE.99.012119

    View details for Web of Science ID 000455686300002

    View details for PubMedID 30780326