Hans Andersen
David Mulvane Ehrsam and Edward Curtis Franklin Professor in Chemistry, Emeritus
Web page: http://web.stanford.edu/~hca/
Bio
Professor Emeritus Hans C. Andersen applies statistical mechanics to develop theoretical understanding of the structure and dynamics of liquids and new computer simulation methods to aid in these studies.
He was born in 1941 in Brooklyn, New York. He studied chemistry as an undergraduate, then physical chemistry as a doctoral candidate at the Massachusetts Institute of Technology (B.S. 1962, Ph.D. 1966). At MIT he first learned about using a combination of mathematical techniques and the ideas of statistical mechanics to investigate problems of chemical and physical interest. This has been the focus of his research ever since. He joined the Stanford Department of Chemistry as Assistant Professor in 1968, and became Professor of Chemistry in 1980. He was named David Mulvane Ehrsam and Edward Curtis Franklin Professor in Chemistry in 1994. Professor Andersen served as department chairman from 2002 through 2005. Among many honors, his work has been recognized in the Theoretical Chemistry Award and Hildebrand Award in Theoretical and Experimental Chemistry of Liquids from the American Chemical Society, as well as the Dean's Award for Distinguished Teaching and Walter J. Gores Award for Excellence in Teaching at Stanford. He has been elected a member of the National Academy of Sciences, and a fellow of both the American Academy of Arts and Sciences and American Association for the Advancement of Science.
Professor Andersen’s research program has used both traditional statistical mechanical theory and molecular dynamics computer simulation. Early in his career, he was one of the developers of what has come to be known as the WeeksChandlerAndersen theory of liquids, which is a way of understanding the structure, thermodynamics, and dynamics of simple dense liquids. Later, he developed several new simulation techniques – now in common use – for exploring the behavior of liquids, such as simulation of a system under constant pressure and/or temperature. He used computer simulations of normal and supercooled liquids to study the temperature dependence of molecular motion in liquids, crystallization in supercooled liquids, and the structure of amorphous solids.
Professor Andersen also developed and analyzed a class of simple lattice models, called facilitated kinetic Ising models, which were then widely used by others to provide insight into the dynamics of real liquids. He simulated simple models of rigid rod polymers to understand the dynamics of this type of material. More recently, in collaboration with Professor Greg Voth of the University of Chicago, he has applied statistical mechanical ideas to the development of coarse grained models of liquids and biomolecules. Such models can be used to simulate molecular systems on long time scales. He has also used mode coupling theory to describe and interpret experiments on rotational relaxation in supercooled liquids and nematogens, in collaboration with Professor Michael Fayer of the Stanford Chemistry Department.
Administrative Appointments

Chair, Stanford University Department of Chemistry (2002  2005)

Associate Dean for Natural Sciences, Stanford University School of Humanities and Sciences (1996  1999)

David Mulvane Ehrsam and Edward Curtis Franklin Professor in Chemistry, Stanford University (1994  Present)

Acting Director, Stanford University Center for Materials Research (1994  1995)

Deputy Director, Stanford University Center for Materials Research (1989  1995)

Codirector, Stanford University Center for Materials Research (1988  1989)

Visiting Professor of Chemistry, Columbia University (1981  1982)

Professor of Chemistry, Stanford University (1980  Present)

Associate Professor of Chemistry, Stanford University (1974  1980)

Assistant Professor of Chemistry, Stanford University (1968  1974)

Junior Fellow, Harvard University Society of Fellows (1965  1968)
Honors & Awards

Theoretical Chemistry Award, American Chemical Society (2006)

Dean's Award for Distinguished Teaching, Stanford University (1992)

Fellow, American Academy of Arts and Sciences (1992)

Member, National Academy of Sciences (1992)

Fellow, American Association for the Advancement of Science (1991)

Joel Henry Hildebrand Award in the Theoretical and Experimental Chemistry of Liquids, American Chemical Society (1988)

Fellow, American Physical Society (1984)

John Simon Guggenheim Fellowship, John Simon Guggenheim Foundation (197677)

University Fellow, Stanford University (197578)

Walter J. Gores Award for Excellence in Teaching, Stanford University (1973)

Sloan Foundation Fellow, Alfred P. Sloan Foundation (197274)
Boards, Advisory Committees, Professional Organizations

Member, Editorial Board, Proceedings of the National Academy of Sciences (2001  2005)

Member, Board on Chemical Sciences and Technology, National Research Council (1995  1998)

Member, Panel on Mathematical Challenges from Computational Chemistry, National Research Council (1994  1994)

Chairman, Gordon Research Conference on the Physics and Chemistry of Liquids (1991  1991)

Vicechairman, Gordon Research Conference on the Physics and Chemistry of Liquids (1989  1989)

Chairman, Allocation Committee, San Diego Supercomputer Center (1988  1989)

Member, Advisory Board, Journal of Physical Chemistry (1987  1992)

Member, Editorial Board, Chemical Physics (1986  1997)

Member, Allocation Committee, San Diego Supercomputer Center (1986  1989)

Chairman, ACS Physical Chemistry Division (1986  1986)

Chairman Elect and Program Chairman, ACS Physical Chemistry Division (1985  1986)

Member, Editorial Board, Journal of Chemical Physics (1984  1986)

Vicechair, ACS Physical Chemistry Division (1984  1985)

Member, Editorial Committee, Annual Review of Physical Chemistry (1983  1987)
Professional Education

Junior Fellow, Society of Fellows, Harvard University, Statistical mechanics (1968)

PhD, Massachusetts Institute of Technology, Physical Chemistry (1966)

BS, Massachusetts Institute of Technology, Chemistry (1962)
202122 Courses
 Science in the News
CHEM 25N (Aut) 
Prior Year Courses
202021 Courses
 Science in the News
CHEM 25N (Aut)
 Science in the News
All Publications

Dynamic force matching: Construction of dynamic coarsegrained models with realistic short time dynamics and accurate long time dynamics
JOURNAL OF CHEMICAL PHYSICS
2016; 145 (22)
Abstract
We recently developed a dynamic force matching technique for converting a coarsegrained (CG) model of a molecular system, with a CG potential energy function, into a dynamic CG model with realistic dynamics [A. Davtyan et al., J. Chem. Phys. 142, 154104 (2015)]. This is done by supplementing the model with additional degrees of freedom, called "fictitious particles." In that paper, we tested the method on CG models in which each molecule is coarsegrained into one CG point particle, with very satisfactory results. When the method was applied to a CG model of methanol that has two CG point particles per molecule, the results were encouraging but clearly required improvement. In this paper, we introduce a new type (called type3) of fictitious particle that exerts forces on the center of mass of two CG sites. A CG model constructed using type3 fictitious particles (as well as type2 particles previously used) gives a much more satisfactory dynamic model for liquid methanol. In particular, we were able to construct a CG model that has the same selfdiffusion coefficient and the same rotational relaxation time as an allatom model of liquid methanol. Type3 particles and generalizations of it are likely to be useful in converting more complicated CG models into dynamic CG models.
View details for DOI 10.1063/1.4971430
View details for Web of Science ID 000391582700010
View details for PubMedID 27984910

Critical Slowing of Density Fluctuations Approaching the IsotropicNematic Transition in Liquid Crystals: 2D IR Measurements and Mode Coupling Theory.
journal of physical chemistry. B
2016; 120 (28): 70037015
Abstract
Twodimensional infrared (2D IR) data are presented for a vibrational probe in three nematogens: 4cyano4'pentylbiphenyl, 4cyano4'octylbiphenyl, and 4(trans4amylcyclohexyl)benzonitrile. The spectral diffusion time constants in all three liquids in the isotropic phase are proportional to [T*/(T  T*)](1/2), where T* is 0.51 K below the isotropicnematic phase transition temperature (TNI). Rescaling to a reduced temperature shows that the decays of the frequencyfrequency correlation function (FFCF) for all three nematogens fall on the same curve, suggesting a universal dynamic behavior of nematogens above TNI. Spectral diffusion is complete before significant orientational relaxation in the liquid, as measured by optically heterodyne detectedoptical Kerr effect (OHDOKE) spectroscopy, and before any significant orientational randomization of the probe measured by polarization selective IR pumpprobe experiments. To interpret the OHDOKE and FFCF data, we constructed a mode coupling theory (MCT) schematic model for the relationships among three correlation functions: ϕ1, a correlator for large wave vector density fluctuations; ϕ2, the orientational correlation function whose time derivative is the observable in the OHDOKE experiment; and ϕ3, the FFCF for the 2D IR experiment. The equations for ϕ1 and ϕ2 match those in the previous MCT schematic model for nematogens, and ϕ3 is coupled to the first two correlators in a straightforward manner. Resulting models fit the data very well. Across liquid crystals, the temperature dependences of the coupling constants show consistent, nonmonotonic behavior. A remarkable change in coupling occurs at ∼5 K above TNI, precisely where the rate of spectral diffusion in 5CB was observed to deviate from that of a similar nonmesogenic liquid.
View details for DOI 10.1021/acs.jpcb.6b04997
View details for PubMedID 27363680

Dynamic force matching: A method for constructing dynamical coarsegrained models with realistic time dependence
JOURNAL OF CHEMICAL PHYSICS
2015; 142 (15)
Abstract
Coarsegrained (CG) models of molecular systems, with fewer mechanical degrees of freedom than an allatom model, are used extensively in chemical physics. It is generally accepted that a coarsegrained model that accurately describes equilibrium structural properties (as a result of having a well constructed CG potential energy function) does not necessarily exhibit appropriate dynamical behavior when simulated using conservative Hamiltonian dynamics for the CG degrees of freedom on the CG potential energy surface. Attempts to develop accurate CG dynamic models usually focus on replacing Hamiltonian motion by stochastic but Markovian dynamics on that surface, such as Langevin or Brownian dynamics. However, depending on the nature of the system and the extent of the coarsegraining, a Markovian dynamics for the CG degrees of freedom may not be appropriate. In this paper, we consider the problem of constructing dynamic CG models within the context of the MultiScale Coarsegraining (MSCG) method of Voth and coworkers. We propose a method of converting a MSCG model into a dynamic CG model by adding degrees of freedom to it in the form of a small number of fictitious particles that interact with the CG degrees of freedom in simple ways and that are subject to Langevin forces. The dynamic models are members of a class of nonlinear systems interacting with special heat baths that were studied by Zwanzig [J. Stat. Phys. 9, 215 (1973)]. The properties of the fictitious particles can be inferred from analysis of the dynamics of allatom simulations of the system of interest. This is analogous to the fact that the MSCG method generates the CG potential from analysis of equilibrium structures observed in allatom simulation data. The dynamic models generate a nonMarkovian dynamics for the CG degrees of freedom, but they can be easily simulated using standard molecular dynamics programs. We present tests of this method on a series of simple examples that demonstrate that the method provides realistic dynamical CG models that have nonMarkovian or close to Markovian behavior that is consistent with the actual dynamical behavior of the allatom system used to construct the CG model. Both the construction and the simulation of such a dynamic CG model have computational requirements that are similar to those of the corresponding MSCG model and are good candidates for CG modeling of very large systems.
View details for DOI 10.1063/1.4917454
View details for Web of Science ID 000353307700005
View details for PubMedID 25903863

A diagrammatic kinetic theory of density fluctuations in simple liquids in the overdamped limit. I. A long time scale theory for high density
JOURNAL OF CHEMICAL PHYSICS
2014; 140 (15)
View details for DOI 10.1063/1.4871111
View details for Web of Science ID 000336045800027

A diagrammatic kinetic theory of density fluctuations in simple liquids in the overdamped limit. II. The oneloop approximation
JOURNAL OF CHEMICAL PHYSICS
2014; 140 (15)
View details for DOI 10.1063/1.4871112
View details for Web of Science ID 000336045800028

Modified scaling principle for rotational relaxation in a model for suspensions of rigid rods
JOURNAL OF CHEMICAL PHYSICS
2013; 139 (4)
Abstract
We have performed simulations of the model of infinitely thin rigid rods undergoing rotational and translational diffusion, subject to the restriction that no two rods can cross one another, for various concentrations well into the semidilute regime. We used a modification of the algorithm of Doi et al. [J. Phys. Soc. Jpn. 53, 3000 (1984)] that simulates diffusive dynamics using a Monte Carlo method and a nonzero time step. In the limit of zero time step, this algorithm is an exact description of diffusive dynamics subject to the noncrossing restriction. For a wide range of concentrations in the semidilute regime, we report values of the long time rotational diffusion constant of the rods, extrapolated to the limit of zero time step, for various sets of values of the infinite dilution (bare) diffusion constants. These results are compared with the results of a previous simulation of the model by Doi et al. and of previous simulations of rods with finite aspect ratio by Fixman and by Cobb and Butler that had been extrapolated to the limit of infinitely thin rods. The predictions of the DoiEdwards (DE) scaling law do not hold for this model for the concentrations studied. The simulation data for the model display two deviations from the predictions of the DE theory that have been observed in experimental systems in the semidilute regime, namely, the very slow approach toward DE scaling behavior as the concentration is increased and the large value of the prefactor in the DE scaling law. We present a modified scaling principle for this model that is consistent with the simulation results for a broad range of concentrations in the semidilute regime. The modified scaling principle takes into account two physical effects, which we call "leakage" and "drift," that were found to be important for the transport properties of a simpler model of nonrotating rods on a lattice [Y.L. S. Tse and H. C. Andersen, J. Chem. Phys. 136, 024904 (2012)].
View details for DOI 10.1063/1.4816001
View details for Web of Science ID 000322949300067
View details for PubMedID 23902017

The multiscale coarsegraining method. IX. A general method for construction of three body coarsegrained force fields
JOURNAL OF CHEMICAL PHYSICS
2012; 136 (19)
Abstract
The multiscale coarsegraining (MSCG) method is a method for constructing a coarsegrained (CG) model of a system using data obtained from molecular dynamics simulations of the corresponding atomically detailed model. The formal statistical mechanical derivation of the method shows that the potential energy function extracted from an MSCG calculation is a variational approximation for the true potential of mean force of the CG sites, one that becomes exact in the limit that a complete basis set is used in the variational calculation if enough data are obtained from the atomistic simulations. Most applications of the MSCG method have employed a representation for the nonbonded part of the CG potential that is a sum of all possible pair interactions. This approach, despite being quite successful for some CG models, is inadequate for some others. Here we propose a systematic method for including three body terms as well as two body terms in the nonbonded part of the CG potential energy. The current method is more general than a previous version presented in a recent paper of this series [L. Larini, L. Lu, and G. A. Voth, J. Chem. Phys. 132, 164107 (2010)], in the sense that it does not make any restrictive choices for the functional form of the three body potential. We use hierarchical multiresolution functions that are similar to wavelets to develop very flexible basis function expansions with both two and three body basis functions. The variational problem is solved by a numerical technique that is capable of automatically selecting an appropriate subset of basis functions from a large initial set. We apply the method to two very different coarsegrained models: a solvent free model of a two component solution made of identical LennardJones particles and a one site model of SPC/E water where a site is placed at the center of mass of each water molecule. These calculations show that the inclusion of three body terms in the nonbonded CG potential can lead to significant improvement in the accuracy of CG potentials and hence of CG simulations.
View details for DOI 10.1063/1.4705417
View details for Web of Science ID 000304303500015
View details for PubMedID 22612087

The multiscale coarsegraining method. X. Improved algorithms for constructing coarsegrained potentials for molecular systems
JOURNAL OF CHEMICAL PHYSICS
2012; 136 (19)
Abstract
The multiscale coarsegraining (MSCG) method uses simulation data for an atomistic model of a system to construct a coarsegrained (CG) potential for a coarsegrained model of the system. The CG potential is a variational approximation for the true potential of mean force of the degrees of freedom retained in the CG model. The variational calculation uses information about the atomistic positions and forces in the simulation data. In principle, the resulting MSCG potential will be an accurate representation of the true CG potential if the basis set for the variational calculation is complete enough and the canonical distribution of atomistic states is well sampled by the data set. In practice, atomistic configurations that have very high potential energy are not sampled. As a result there usually is a region of CG configuration space that is not sampled and about which the data set contains no information regarding the gradient of the true potential. The MSCG potential obtained from a variational calculation will not necessarily be accurate in this unsampled region. A priori considerations make it clear that the true CG potential of mean force must be very large and positive in that region. To obtain an MSCG potential whose behavior in the sampled region is determined by the atomistic data set, and whose behavior in the unsampled region is large and positive, it is necessary to intervene in the variational calculation in some way. In this paper, we discuss and compare two such methods of intervention, which have been used in previous MSCG calculations for dealing with nonbonded interactions. For the test systems studied, the two methods give similar results and yield MSCG potentials that are limited in accuracy only by the incompleteness of the basis set and the statistical error of associated with the set of atomistic configurations used. The use of such methods is important for obtaining accurate CG potentials.
View details for DOI 10.1063/1.4705420
View details for Web of Science ID 000304303500016
View details for PubMedID 22612088

The multiscale coarsegraining method. VIII. Multiresolution hierarchical basis functions and basis function selection in the construction of coarsegrained force fields
JOURNAL OF CHEMICAL PHYSICS
2012; 136 (19)
Abstract
The multiscale coarsegraining (MSCG) method is a method for determining the effective potential energy function for a coarsegrained (CG) model of a molecular system using data obtained from molecular dynamics simulation of the corresponding atomically detailed model. The coarsegrained potential obtained using the MSCG method is a variational approximation for the exact manybody potential of mean force for the coarsegrained sites. Here we propose a new numerical algorithm with noise suppression capabilities and enhanced numerical stability for the solution of the MSCG variational problem. The new method, which is a variant of the elastic net method [Friedman et al., Ann. Appl. Stat. 1, 302 (2007)], allows us to construct a large basis set, and for each value of a socalled "penalty parameter" the method automatically chooses a subset of the basis that is most important for representing the MSCG potential. The size of the subset increases as the penalty parameter is decreased. The appropriate value to choose for the penalty parameter is the one that gives a basis set that is large enough to fit the data in the simulation data set without fitting the noise. This procedure provides regularization to mitigate potential numerical problems in the associated linear least squares calculation, and it provides a way to avoid fitting statistical error. We also develop new basis functions that are similar to multiresolution Haar functions and that have the differentiability properties that are appropriate for representing CG potentials. We demonstrate the feasibility of the combined use of the elastic net method and the multiresolution basis functions by performing a variational calculation of the CG potential for a relatively simple system. We develop a method to choose the appropriate value of the penalty parameter to give the optimal basis set. The combined effect of the new basis functions and the regularization provided by the elastic net method opens the possibility of using very large basis sets for complicated CG systems with many interaction potentials without encountering numerical problems in the variational calculation.
View details for DOI 10.1063/1.4705384
View details for Web of Science ID 000304303500014
View details for PubMedID 22612086

A lattice model of the translational dynamics of nonrotating rigid rods
JOURNAL OF CHEMICAL PHYSICS
2012; 136 (2)
Abstract
We present a lattice model of oriented, nonrotating, rigid rods in three dimensions with random walk dynamics, computer simulation results for the model, and a theory for the translational diffusion constant of the rods in the perpendicular direction, D(⊥), in the semidilute regime. The theory is based on the "tube model" of DoiEdwards (DE) theory for the rotational diffusion constant of rods that can both translate and rotate in continuous space. The theory predicts that D(⊥) is proportional to (νL(3))(2), where ν is the concentration of rods and L is the length of the rods, which is analogous to the DoiEdwards scaling law for rotational diffusion. The simulations find that, as νL(3) is increased, the approach to the limit of DE scaling is slow, and the 2 power in the DE scaling law is never quite achieved even at the highest concentration (νL(3) = 200) simulated. We formulate a quantitative theory for the prefactor in the scaling relationship using only DE ideas, but it predicts a proportionality constant that is much too small. To explain this discrepancy, we modify the DE approach to obtain a more accurate estimate of the average tube radius and take into account effects of perpendicular motion of rods that are not included in the original DE theory. With these changes, the theory predicts values of D(⊥) that are in much better agreement with the simulations. We propose a new scaling relationship that fits the data very well. This relationship suggests that the DE scaling law is the correct description of the scaling for infinitely thin rods only in the limit of infinite concentration, and that corrections to the DE scaling law because of finite concentration are significant even at concentrations that are well inside the semidilute regime. The implications of these results for the DE theory of rotating rods are discussed.
View details for DOI 10.1063/1.3673791
View details for Web of Science ID 000299126400058
View details for PubMedID 22260613

A Bayesian method for construction of Markov models to describe dynamics on various timescales
JOURNAL OF CHEMICAL PHYSICS
2010; 133 (14)
Abstract
The dynamics of many biological processes of interest, such as the folding of a protein, are slow and complicated enough that a single molecular dynamics simulation trajectory of the entire process is difficult to obtain in any reasonable amount of time. Moreover, one such simulation may not be sufficient to develop an understanding of the mechanism of the process, and multiple simulations may be necessary. One approach to circumvent this computational barrier is the use of Markov state models. These models are useful because they can be constructed using data from a large number of shorter simulations instead of a single long simulation. This paper presents a new Bayesian method for the construction of Markov models from simulation data. A Markov model is specified by (τ,P,T), where τ is the mesoscopic time step, P is a partition of configuration space into mesostates, and T is an N(P)×N(P) transition rate matrix for transitions between the mesostates in one mesoscopic time step, where N(P) is the number of mesostates in P. The method presented here is different from previous Bayesian methods in several ways. (1) The method uses Bayesian analysis to determine the partition as well as the transition probabilities. (2) The method allows the construction of a Markov model for any chosen mesoscopic timescale τ. (3) It constructs Markov models for which the diagonal elements of T are all equal to or greater than 0.5. Such a model will be called a "consistent mesoscopic Markov model" (CMMM). Such models have important advantages for providing an understanding of the dynamics on a mesoscopic timescale. The Bayesian method uses simulation data to find a posterior probability distribution for (P,T) for any chosen τ. This distribution can be regarded as the Bayesian probability that the kinetics observed in the atomistic simulation data on the mesoscopic timescale τ was generated by the CMMM specified by (P,T). An optimization algorithm is used to find the most probable CMMM for the chosen mesoscopic time step. We applied this method of Markov model construction to several toy systems (random walks in one and two dimensions) as well as the dynamics of alanine dipeptide in water. The resulting Markov state models were indeed successful in capturing the dynamics of our test systems on a variety of mesoscopic timescales.
View details for DOI 10.1063/1.3496438
View details for Web of Science ID 000283200400016
View details for PubMedID 20949993

Statistical mechanical basis of coarse graining
AMER CHEMICAL SOC. 2010
View details for Web of Science ID 000208164702360

The multiscale coarsegraining method. V. Isothermalisobaric ensemble
JOURNAL OF CHEMICAL PHYSICS
2010; 132 (16)
Abstract
The multiscale coarsegraining (MSCG) method is a method for determining the effective potential energy function for a coarsegrained (CG) model of a system using the data obtained from molecular dynamics simulation of the corresponding atomically detailed model. The MSCG method, as originally formulated for systems at constant volume, has previously been given a rigorous statistical mechanical basis for the canonical ensemble. Here, we propose and test a version of the MSCG method suitable for the isothermalisobaric ensemble. The method shows how to construct an effective potential energy function for a CG system that generates the correct volume fluctuations as well as correct distribution functions in the configuration space of the CG sites. The formulation of the method requires introduction of an explicitly volume dependent term in the potential energy function of the CG system. The theory is applicable to simulations with isotropic volume fluctuations and cases where both the atomistic and CG models do not have any intramolecular constraints, but it is straightforward to extend the theory to more general cases. The present theory deals with systems that have short ranged interactions. (The extension to Coulombic forces using Ewald methods requires additional considerations.) We test the theory for constant pressure MSCG simulations of a simple model of a solution. We show that both the volume dependent and the coordinate dependent parts of the potential are transferable to larger systems than the one used to obtain these potentials.
View details for DOI 10.1063/1.3394862
View details for Web of Science ID 000277241500010
View details for PubMedID 20441257

Efficient, Regularized, and Scalable Algorithms for Multiscale CoarseGraining
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
2010; 6 (3): 954965
View details for DOI 10.1021/ct900643r
View details for Web of Science ID 000275189400032

Kinetic theories of dynamics and persistent caging in a onedimensional lattice gas
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2009; 106 (36): 1514215147
Abstract
The onedimensional, singleoccupancy lattice gas exhibits highly cooperative particle motion and provides an interesting challenge for theoretical methods designed to describe caging in liquids. We employ this model in an effort to gain insight into caging phenomena in more realistic models of liquids, using a diagrammatic kinetic theory of density fluctuations to develop a series of approximations to the kinetic equations for the van Hove selfcorrelation function. The approximations are formulated in terms of the irreducible memory function, and we assess their efficacy by comparing their solutions with computer simulation results and the wellknown subdiffusive behavior of a tagged particle at long times. The first approximation, a mode coupling theory, factorizes the 4point propagators that contribute to the irreducible memory function into products of independent singleparticle propagators. This approximation fails to capture the subdiffusive behavior of a tagged particle at long times. Analysis of the mode coupling approximation in terms of the diagrammatic kinetic theory leads to the development of two additional approximations that can be viewed as diagrammatic extensions or modifications of mode coupling theory. The first, denoted MC1, captures the longtime subdiffusive behavior of a tagged particle. The second, denoted MC2, captures the subdiffusive behavior of a tagged particle and also yields the correct amplitude of its mean square displacement at long times. Numerical and asymptotic solutions of the approximate kinetic equations share many qualitative and quantitative features with simulation results at all timescales.
View details for DOI 10.1073/pnas.0901693106
View details for Web of Science ID 000269632400012
View details for PubMedID 19564606

The multiscale coarsegraining method. III. A test of pairwise additivity of the coarsegrained potential and of new basis functions for the variational calculation
JOURNAL OF CHEMICAL PHYSICS
2009; 131 (3)
Abstract
The multiscale coarsegraining (MSCG) method, proposed by Izvekov and Voth [J. Phys. Chem. B 109, 2469 (2005); Izvekov and VothJ. Chem. Phys. 123, 134105 (2005)], is a method for determining the effective potential energy function for a coarsegrained model of a fluid using data obtained from molecular dynamics (MD) simulation of the corresponding atomically detailed model. The method has been given a rigorous statistical mechanical basis [Noid et al. J. Chem. Phys. 128, 244114 (2008); Noid et al., J. Chem. Phys. 128, 244115 (2008)]. The coarsegrained (CG) potentials obtained using the MSCG method are an approximate variational solution for the exact manybody potential of mean force for the coarsegrained sites. In this paper we apply this method to study the manybody potential of mean force among solutes in a simple model of a solution of LennardJones particles. We use a new set of basis functions for the variational calculation that is useful when the coarsegrained potential is approximately equal to an arbitrarily complicated pairwise additive, central interaction among the sites of the coarsegrained model. For this model, pairwise additivity of the manybody potential of mean force is a very good approximation when the solute concentration is low, and it becomes less accurate for high concentrations, indicating the importance of manybody contributions to the coarsegrained potential. The best possible pairwise additive CG potential of the solute particles is found to be quite long ranged for all concentrations except those for which the mole fraction of solute is very close to unity. We discuss strategies for construction of shortranged potentials for efficient but accurate CG MD simulation. We also discuss how the choice of basis functions for the variational calculation can be used to provide smoothing of the calculated CG potential function to overcome statistical sampling error in the atomistic simulation data used for the generation of the potential.
View details for DOI 10.1063/1.3173812
View details for Web of Science ID 000268206800008
View details for PubMedID 19624176

Scaling Analysis of Dynamic Heterogeneity in a Supercooled LennardJones Liquid
PHYSICAL REVIEW LETTERS
2008; 101 (26)
Abstract
We have performed molecular dynamics computer simulations of a dense LennardJones liquid mixture to study dynamic heterogeneity from normal liquid temperatures down to a supercooled temperature 15% above the previously identified modecoupling temperature Tc of the model. A temperaturedependent correlation length associated with the correlation function of mobility fluctuations is calculated. The results are used to test two sets of scaling hypotheses for the dynamic heterogeneity. The results are in close agreement with the inhomogeneous modecoupling theory of Biroli et al. [Phys. Rev. Lett. 97, 195701 (2006)] for both the alpha and beta relaxation regimes. Comparison with results for kinetically constrained models suggest that the LennardJones mixture studied is more similar to models of fragile liquids than models of very strong liquids.
View details for DOI 10.1103/PhysRevLett.101.267802
View details for Web of Science ID 000262247100081
View details for PubMedID 19437674

The multiscale coarsegraining method. II. Numerical implementation for coarsegrained molecular models
JOURNAL OF CHEMICAL PHYSICS
2008; 128 (24)
Abstract
The multiscale coarsegraining (MSCG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to determine an interaction potential for a CG model from simulations of an atomically detailed model of the same system. The companion paper proved that, if no restrictions regarding the form of the CG interaction potential are introduced and if the equilibrium distribution of the atomistic model has been adequately sampled, then the MSCG variational principle determines the exact manybody potential of mean force (PMF) governing the equilibrium distribution of CG sites generated by the atomistic model. In practice, though, CG force fields are not completely flexible, but only include particular types of interactions between CG sites, e.g., nonbonded forces between pairs of sites. If the CG force field depends linearly on the force field parameters, then the vector valued functions that relate the CG forces to these parameters determine a set of basis vectors that span a vector subspace of CG force fields. The companion paper introduced a distance metric for the vector space of CG force fields and proved that the MSCG variational principle determines the CG force force field that is within that vector subspace and that is closest to the force field determined by the manybody PMF. The present paper applies the MSCG variational principle for parametrizing molecular CG force fields and derives a linear least squares problem for the parameter set determining the optimal approximation to this manybody PMF. Linear systems of equations for these CG force field parameters are derived and analyzed in terms of equilibrium structural correlation functions. Numerical calculations for a onesite CG model of methanol and a molecular CG model of the EMIM(+)NO(3) () ionic liquid are provided to illustrate the method.
View details for DOI 10.1063/1.2938857
View details for Web of Science ID 000257284000018
View details for PubMedID 18601325

The multiscale coarsegraining method. I. A rigorous bridge between atomistic and coarsegrained models
JOURNAL OF CHEMICAL PHYSICS
2008; 128 (24)
Abstract
Coarsegrained (CG) models provide a computationally efficient method for rapidly investigating the long time and lengthscale processes that play a critical role in many important biological and soft matter processes. Recently, Izvekov and Voth introduced a new multiscale coarsegraining (MSCG) method [J. Phys. Chem. B 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] for determining the effective interactions between CG sites using information from simulations of atomically detailed models. The present work develops a formal statistical mechanical framework for the MSCG method and demonstrates that the variational principle underlying the method may, in principle, be employed to determine the manybody potential of mean force (PMF) that governs the equilibrium distribution of positions of the CG sites for the MSCG models. A CG model that employs such a PMF as a "potential energy function" will generate an equilibrium probability distribution of CG sites that is consistent with the atomically detailed model from which the PMF is derived. Consequently, the MSCG method provides a formal multiscale bridge rigorously connecting the equilibrium ensembles generated with atomistic and CG models. The variational principle also suggests a class of practical algorithms for calculating approximations to this manybody PMF that are optimal. These algorithms use computer simulation data from the atomically detailed model. Finally, important generalizations of the MSCG method are introduced for treating systems with rigid intramolecular constraints and for developing CG models whose equilibrium momentum distribution is consistent with that of an atomically detailed model.
View details for DOI 10.1063/1.2938860
View details for Web of Science ID 000257284000017
View details for PubMedID 18601324

A diagrammatic formulation of the kinetic theory of fluctuations in equilibrium classical fluids. VI. Binary collision approximations for the memory function for selfcorrelation functions
JOURNAL OF CHEMICAL PHYSICS
2007; 127 (6)
Abstract
We use computer simulation results for a dense LennardJones fluid for a range of temperatures to test the accuracy of various binary collision approximations for the memory function for density fluctuations in liquids. The approximations tested include the moderate density approximation of the generalized BoltzmannEnskog memory function (MGBE) of Mazenko and Yip [Statistical Mechanics. Part B. TimeDependent Processes, edited by B. J. Berne (Plenum, New York, 1977)], the binary collision approximation (BCA) and the short time approximation (STA) of Ranganathan and Andersen [J. Chem. Phys. 121, 1243 (2004); J. Phys. Chem. 109, 21437 (2005)] and various other approximations we derived by using diagrammatic methods. The tests are of two types. The first is a comparison of the correlation functions predicted by each approximate memory function with the simulation results, especially for the selflongitudinal current correlation (SLCC) function. The second is a direct comparison of each approximate memory function with a memory function numerically extracted from the correlation function data. The MGBE memory function is accurate at short times but decays to zero too slowly and gives a poor description of the correlation function at intermediate times. The BCA is exact at zero time, but it predicts a correlation function that diverges at long times. The STA gives a reasonable description of the SLCC but does not predict the correct temperature dependence of the negative dip in the function that is associated with caging at low temperatures. None of the other binary collision approximations is a systematic improvement on the STA. The extracted memory functions have a rapidly decaying short time part, much like the STA, and a much smaller, more slowly decaying part of the type predicted by a mode coupling theory. Theories that use mode coupling commonly include a binary collision term in the memory function but do not discuss in detail the nature of that term. It is clear from the present work that the short time part of the memory function has a behavior associated with brief binary repulsive collisions, such as those described by the STA. Collisions that include attractive as well as repulsive interactions, such as those of the MGBE, have a much longer duration, and theories that include them have memory functions that decay to zero much too slowly to provide a good first approximation of the correlation function. This leads us to speculate that the memory function for density fluctuations can be usefully regarded as a sum of at least three parts: a contribution from repulsive binary collisions (the STA or something similar to it), another short time part that is related to all the other interactions (but whose nature is not understood), and a longer time slowly decaying part that describes caging (of the type predicted by the mode coupling theory).
View details for DOI 10.1063/1.2752153
View details for Web of Science ID 000248760300026
View details for PubMedID 17705607

A mode coupling theory description of the short and longtime dynamics of nematogens in the isotropic phase
JOURNAL OF CHEMICAL PHYSICS
2006; 124 (1)
Abstract
Optical heterodynedetected optical Kerr effect (OHDOKE) experimental data are presented on nematogens 4(trans4noctylcyclohexyl)isothiocyanatobenzene (8CHBT), and 4(4pentylcyclohexyl)benzonitrile (5PCH) in the isotropic phase. The 8CHBT and 5PCH data and previously published data on 4pentyl4biphenylcarbonitrile (5CB) are analyzed using a modification of a schematic mode coupling theory (MCT) that has been successful in describing the dynamics of supercooled liquids. At long time, the OHDOKE data (orientational relaxation) are well described with the standard Landaude Gennes (LdG) theory. The data decay as a single exponential. The decay time diverges as the isotropic to nematic phase transition is approached from above. Previously there has been no theory that can describe the complex dynamics that occur at times short compared to the LdG exponential decay. Earlier, it has been noted that the shorttime nematogen dynamics, which consist of several power laws, have a functional form identical to that observed for the short time behavior of the orientational relaxation of supercooled liquids. The temperaturedependent orientational dynamics of supercooled liquids have recently been successfully described using a schematic mode coupling theory. The schematic MCT theory that fits the supercooled liquid data does not reproduce the nematogen data within experimental error. The similarities of the nematogen data to the supercooled liquid data are the motivation for applying a modification of the successful MCT theory to nematogen dynamics in the isotropic phase. The results presented below show that the new schematic MCT theory does an excellent job of reproducing the nematogen isotropic phase OHDOKE data on all time scales and at all temperatures.
View details for DOI 10.1063/1.2145679
View details for Web of Science ID 000234428900043
View details for PubMedID 16409058

Diagrammatic formulation of the kinetic theory of fluctuations in equilibrium classical fluids. V. The short time approximation for the memory function
JOURNAL OF PHYSICAL CHEMISTRY B
2005; 109 (45): 2143721444
Abstract
The correlation function for density fluctuations in a monatomic fluid obeys a formally exact kinetic equation containing a memory function. A previously derived short time approximation (STA) for this memory function is tested by comparing its predictions with the results of molecular dynamic simulations of a dense LennardJones fluid at a variety of temperatures. This approximation takes into account the contribution to the correlation function of uncorrelated repulsive binary collisions. The qualitative changes of predicted correlation functions with temperature and wave vector are generally correct. The major exception to this is the transverse current correlation function for small wave vector. The quantitative accuracy is better at short times than long times and better at high temperatures than low temperatures. The major failing of the STA is its underestimation of the amplitudes of the negative dips in the current autocorrelation functions and of the temperature dependence of the amplitudes of the dips. Despite its deficiencies in predicting the time dependence of current correlation functions, the STA gives accurate results for the selfdiffusion coefficient and the shear viscosity coefficient at the highest temperatures studied.
View details for DOI 10.1021/jp0523017
View details for Web of Science ID 000233280600029
View details for PubMedID 16853781

Boson peak in supercooled liquids: Time domain observations and mode coupling theory
JOURNAL OF CHEMICAL PHYSICS
2005; 123 (6)
Abstract
Optical heterodynedetected optical Kerr effect (OHDOKE) experiments are presented for the supercooled liquid acetylsalicylic acid (aspirin  ASP). The ASP data and previously published OHDOKE data on supercooled dibutylphthalate (DBP) display highly damped oscillations with a periods of approximately 2 ps as the temperature is reduced to and below the mode coupling theory (MCT) temperature T(C). The oscillations become more pronounced below T(C). The oscillations can be interpreted as the time domain signature of the boson peak. Recently a schematic MCT model, the Sjogren model, was used to describe the OHDOKE data for a number of supercooled liquids by Gotze and Sperl [W. Gotze and M. Sperl, Phys. Rev. E 92, 105701 (2004)] , but the shorttime and lowtemperature behaviors were not addressed. Franosch et al. [T. Franosch, W. Gotze, M. R. Mayr, and A. P. Singh, Phys. Rev. E 55, 3183 (1997)] found that the Sjogren model could describe the boson peak observed by depolarized lightscattering (DLS) experiments on glycerol. The OHDOKE experiment measures a susceptibility that is a time domain equivalent of the spectrum measured in DLS. Here we present a detailed analysis of the ASP and DBP data over a broad range of times and temperatures using the Sjogren model. The MCT schematic model is able to describe the data very well at all temperatures and relevant time scales. The trajectory of MCT parameters that fit the hightemperature data (no shorttime oscillations) when continued below T(C) results in calculations that reproduce the oscillations seen in the data. The results indicate that increasing translationalrotational coupling is responsible for the appearance of the boson peak as the temperature approaches and drops below T(C).
View details for DOI 10.1063/1.2000235
View details for Web of Science ID 000231310500043
View details for PubMedID 16122327

Molecular dynamics studies of heterogeneous dynamics and dynamic crossover in supercooled atomic liquids
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2005; 102 (19): 66866691
Abstract
Supercooled liquids near the glass transition exhibit the phenomenon of heterogeneous relaxation; at any specific time, a nominally homogeneous equilibrium fluid undergoes dynamic fluctuations in its structure on a molecular distance scale with rates that are very different in different regions of the sample. Several theoretical and simulation studies have suggested a change in the nature of the dynamics of fluids as they are supercooled, leading to the concept of a dynamic crossover that is often associated with mode coupling theory. Here, we will review the use of molecular dynamics computer simulation methods to investigate heterogeneous dynamics and dynamic crossovers in models of atomic liquids.
View details for DOI 10.1073/pnas.05009464102
View details for Web of Science ID 000229048500010
View details for PubMedID 15870201
View details for PubMedCentralID PMC1100779

Tests of an approximate scaling principle for dynamics of classical fluids
JOURNAL OF PHYSICAL CHEMISTRY B
2005; 109 (7): 29852994
Abstract
We used molecular dynamics computer simulations to test an approximate scaling principle that conjectures that two equilibrium atomic liquids have very similar dynamical properties if they have the same density and similar static pair correlation functions when the length scales of the two liquids are adjusted appropriately, even if they have different interatomic potentials and different temperatures. The simulations were performed on two types of model atomic liquids at various temperatures at the same density. In the first type, the interatomic potential is the LennardJones potential (LJ). In the second type, the interatomic potential is the repulsive part of the LennardJones potential (RLJ). We identified pairs of systems that have very similar pair correlation functions despite the fact that they had different potentials. Each pair consisted of an LJ liquid at a specific temperature and a corresponding RLJ liquid at a lower temperature. We compared various time correlation functions and transport coefficients of the two systems in each pair. Many dynamical properties are very similar in each pair, in accordance with the approximate scaling principle, whereas others are significantly different. The results indicate that certain dynamical properties are very insensitive to large changes in the interatomic potential that leave the pair correlation function largely unchanged, whereas other dynamical properties are much more sensitive to such changes in the potential. The transport coefficients for diffusion and viscosity are among the dynamical properties that are insensitive to such changes in the potential, and this may be part of the reason transport properties of many fluids have been calculated or rationalized in terms of a simple hard sphere model of liquids.
View details for DOI 10.1021/jp0454927
View details for Web of Science ID 000227108800071
View details for PubMedID 16851313

A diagrammatic formulation of the kinetic theory of fluctuations in equilibrium classical fluids. IV. The short time behavior of the memory function
JOURNAL OF CHEMICAL PHYSICS
2004; 121 (3): 12431257
Abstract
Using a recently developed diagrammatic formulation of the kinetic theory of fluctuations in liquids, we investigate the short time behavior of the memory function for density fluctuations in a classical atomic fluid. At short times, the memory function has a large contribution that is generated by the repulsive part of the interatomic potential. We introduce a small parameter that is a measure of the softness of the repulsive part of the potential. The diagrams in the memory function that contribute to lowest order in that small parameter are identified and summed to give an explicit expression for the dominant contribution to the memory function at short times. The result leads to a theory for fluids with continuous potentials that is similar to the Enskog theory for hard sphere fluids.
View details for DOI 10.1063/1.1764492
View details for Web of Science ID 000222663300009
View details for PubMedID 15260665

A diagrammatic formulation of the kinetic theory of fluctuations in equilibrium classical fluids. II. Equations of motion of the fluctuation fields and their diagrammatic solution
JOURNAL OF PHYSICAL CHEMISTRY B
2003; 107 (37): 1022610233
View details for DOI 10.1021/jp034753u
View details for Web of Science ID 000185345400043

Diagrammatic formulation of the kinetic theory of fluctuations in equilibrium classical fluids. III. Cluster analysis of the renormalized interactions and a second diagrammatic representation of the correlation functions
JOURNAL OF PHYSICAL CHEMISTRY B
2003; 107 (37): 1023410242
View details for DOI 10.1021/jp034754m
View details for Web of Science ID 000185345400044

Dynamical corrections to quantum transition state theory
JOURNAL OF CHEMICAL PHYSICS
2003; 118 (21): 95429551
View details for DOI 10.1063/1.1570404
View details for Web of Science ID 000182890000011

A scaling principle for the dynamics of density fluctuations in atomic liquids
JOURNAL OF CHEMICAL PHYSICS
2003; 118 (8): 34473450
View details for DOI 10.1063/1.1553757
View details for Web of Science ID 000180803800001

A diagrammatic theory of time correlation functions of facilitated kinetic Ising models
JOURNAL OF CHEMICAL PHYSICS
2001; 114 (3): 11011114
View details for Web of Science ID 000166213100006

Facilitated spin models, mode coupling theory, and ergodicnonergodic transitions
JOURNAL OF CHEMICAL PHYSICS
2000; 113 (19): 86718679
View details for Web of Science ID 000165083500031

The meaning of the irreducible memory function in stochastic theories of dynamics with detailed balance
JOURNAL OF CHEMICAL PHYSICS
2000; 113 (10): 39453950
View details for Web of Science ID 000089034900003

Functional and graphical methods for classical statistical dynamics. I. A formulation of the MartinSiggiaRose method
JOURNAL OF MATHEMATICAL PHYSICS
2000; 41 (4): 19792020
View details for Web of Science ID 000086056600025

Local parabolic reference approximation of thermal Feynman path integrals in quantum Monte Carlo simulations
JOURNAL OF CHEMICAL PHYSICS
1997; 107 (23): 1012110130
View details for Web of Science ID A1997YK98200047

Dynamics of a supercooled LennardJones system: Qualitative and quantitative tests of modecoupling theory
PROGRESS OF THEORETICAL PHYSICS SUPPLEMENT
1997: 3542
View details for Web of Science ID A1997XK52400008

Observation of a twostage melting transition in two dimensions
PHYSICAL REVIEW E
1996; 53 (4): 37943803
View details for Web of Science ID A1996UH48200022

Properties of quantum transition state theory and its corrections
JOURNAL OF PHYSICAL CHEMISTRY
1996; 100 (4): 11371143
View details for Web of Science ID A1996TR60600007

Computer simulation study of the melting transition in two dimensions
PHYSICAL REVIEW LETTERS
1996; 76 (2): 255258
View details for Web of Science ID A1996TN76100025

TESTING MODECOUPLING THEORY FOR A SUPERCOOLED BINARY LENNARDJONES MIXTURE .2. INTERMEDIATE SCATTERING FUNCTION AND DYNAMIC SUSCEPTIBILITY
PHYSICAL REVIEW E
1995; 52 (4): 41344153
View details for Web of Science ID A1995TA52500023

TESTING MODECOUPLING THEORY FOR A SUPERCOOLED BINARY LENNARDJONES MIXTURE  THE VAN HOVE CORRELATIONFUNCTION
PHYSICAL REVIEW E
1995; 51 (5): 46264641
View details for Web of Science ID A1995QZ15500014

A COMPUTERSIMULATION METHOD FOR THE CALCULATION OF CHEMICALPOTENTIALS OF LIQUIDS AND SOLIDS USING THE BICANONICAL ENSEMBLE
JOURNAL OF CHEMICAL PHYSICS
1995; 102 (7): 28512863
View details for Web of Science ID A1995QF82100021

A NEW FORMULATION OF QUANTUM TRANSITIONSTATE THEORY FOR ADIABATIC RATE CONSTANTS
JOURNAL OF CHEMICAL PHYSICS
1994; 101 (7): 60326037
View details for Web of Science ID A1994PH98700061

SCALING BEHAVIOR IN THE BETARELAXATION REGIME OF A SUPERCOOLED LENNARDJONES MIXTURE
PHYSICAL REVIEW LETTERS
1994; 73 (10): 13761379
View details for Web of Science ID A1994PE72700017

SCALING BEHAVIOR IN THE DYNAMICS OF A SUPERCOOLED LENNARDJONES MIXTURE
NUOVO CIMENTO DELLA SOCIETA ITALIANA DI FISICA DCONDENSED MATTER ATOMIC MOLECULAR AND CHEMICAL PHYSICS FLUIDS PLASMAS BIOPHYSICS
1994; 16 (8): 12911295
View details for Web of Science ID A1994RE31700036

A NEW FORMULATION OF THE HARTREEFOCKROOTHAAN METHOD FOR ELECTRONICSTRUCTURE CALCULATIONS ON CRYSTALS
JOURNAL OF CHEMICAL PHYSICS
1994; 101 (1): 375393
View details for Web of Science ID A1994NT52100041

KINETIC LATTICEGAS MODEL OF CAGE EFFECTS IN HIGHDENSITY LIQUIDS AND A TEST OF MODECOUPLING THEORY OF THE IDEALGLASS TRANSITION
PHYSICAL REVIEW E
1993; 48 (6): 43644377
View details for Web of Science ID A1993MQ16400034

THE ADVANTAGES OF THE GENERAL HARTREEFOCK METHOD FOR FUTURE COMPUTERSIMULATION OF MATERIALS
JOURNAL OF CHEMICAL PHYSICS
1993; 99 (3): 19011913
View details for Web of Science ID A1993LN78200048

ABINITIO AND SEMIEMPIRICAL METHODS FOR MOLECULARDYNAMICS SIMULATIONS BASED ON GENERAL HARTREEFOCK THEORY
JOURNAL OF CHEMICAL PHYSICS
1993; 99 (1): 523532
View details for Web of Science ID A1993LJ30800055

INTERATOMIC POTENTIALS AND THE PHASEDIAGRAM OF XE/PT(111)
JOURNAL OF CHEMICAL PHYSICS
1993; 98 (9): 76367647
View details for Web of Science ID A1993LA76300113

RELAXATION DYNAMICS IN A LATTICEGAS  A TEST OF THE MODECOUPLING THEORY OF THE IDEAL GLASSTRANSITION
PHYSICAL REVIEW E
1993; 47 (5): 32813302
View details for Web of Science ID A1993LF06700037

THERMODYNAMICS, STATISTICAL THERMODYNAMICS, AND COMPUTERSIMULATION OF CRYSTALS WITH VACANCIES AND INTERSTITIALS
PHYSICAL REVIEW A
1992; 46 (8): 45394548
View details for Web of Science ID A1992JW97400020

MOLECULARDYNAMICS SIMULATION OF SILICA LIQUID AND GLASS
JOURNAL OF CHEMICAL PHYSICS
1992; 97 (4): 26822689
View details for Web of Science ID A1992JJ41100055

TEST OF A PAIRWISE ADDITIVE IONIC POTENTIAL MODEL FOR SILICA
JOURNAL OF CHEMICAL PHYSICS
1991; 94 (7): 50565060
View details for Web of Science ID A1991FF82000038

INTERATOMIC POTENTIAL FOR SILICON CLUSTERS, CRYSTALS, AND SURFACES
PHYSICAL REVIEW B
1990; 41 (15): 1056810585
View details for Web of Science ID A1990DF14100028

A REACTIVEFLUX THEORY OF CHEMICAL SURFACEDIFFUSION
JOURNAL OF CHEMICAL PHYSICS
1990; 92 (10): 62176224
View details for Web of Science ID A1990DD72500055

10(6)PARTICLE MOLECULARDYNAMICS STUDY OF HOMOGENEOUS NUCLEATION OF CRYSTALS IN A SUPERCOOLED ATOMIC LIQUID
PHYSICAL REVIEW B
1990; 41 (10): 70427054
View details for Web of Science ID A1990CY12400038

LOWTEMPERATURE APPROXIMATIONS FOR FEYNMAN PATHINTEGRALS AND THEIR APPLICATIONS IN QUANTUM EQUILIBRIUM AND DYNAMIC PROBLEMS
JOURNAL OF CHEMICAL PHYSICS
1990; 92 (5): 29532965
View details for Web of Science ID A1990CQ90700031

ICOSAHEDRAL ORDERING IN THE LENNARDJONES LIQUID AND GLASS
PHYSICAL REVIEW LETTERS
1988; 60 (22): 22952298
View details for Web of Science ID A1988N594300019

MONTECARLO STUDIES OF DIFFUSION ON INHOMOGENEOUS SURFACES
JOURNAL OF CHEMICAL PHYSICS
1988; 88 (6): 40524061
View details for Web of Science ID A1988M666800080

MOLECULARDYNAMICS STUDY OF MELTING AND FREEZING OF SMALL LENNARDJONES CLUSTERS
JOURNAL OF PHYSICAL CHEMISTRY
1987; 91 (19): 49504963
View details for Web of Science ID A1987K065400015

MOLECULARDYNAMICS COMPUTERSIMULATION OF AMORPHOUS MOLYBDENUMGERMANIUM ALLOYS
PHYSICAL REVIEW B
1987; 36 (5): 26752686
View details for Web of Science ID A1987J819600018

THEORETICALSTUDY OF THE LOCALIZATIONDELOCALIZATION TRANSITION IN AMORPHOUS MOLYBDENUMGERMANIUM ALLOYS
PHYSICAL REVIEW B
1987; 36 (5): 26872694
View details for Web of Science ID A1987J819600019

MOLECULARDYNAMICS SIMULATION OF AMORPHOUSGERMANIUM
PHYSICAL REVIEW B
1986; 34 (10): 69876991
View details for Web of Science ID A1986E842800053

TRUNCATION OF COULOMBIC INTERACTIONS IN COMPUTERSIMULATIONS OF LIQUIDS
JOURNAL OF CHEMICAL PHYSICS
1986; 85 (5): 30273041
View details for Web of Science ID A1986D739900084

SMALL SYSTEM SIZE ARTIFACTS IN THE MOLECULARDYNAMICS SIMULATION OF HOMOGENEOUS CRYSTAL NUCLEATION IN SUPERCOOLED ATOMIC LIQUIDS
JOURNAL OF PHYSICAL CHEMISTRY
1986; 90 (8): 15851589
View details for Web of Science ID A1986A860900026

MOLECULARDYNAMICS STUDY OF THE HYDROPHOBIC INTERACTION IN AN AQUEOUSSOLUTION OF KRYPTON
JOURNAL OF PHYSICAL CHEMISTRY
1986; 90 (5): 795802
View details for Web of Science ID A1986A255400020

FACILITATED KINETIC ISINGMODELS AND THE GLASSTRANSITION
JOURNAL OF CHEMICAL PHYSICS
1985; 83 (11): 58225831
View details for Web of Science ID A1985AUR0400063

MACROMOLECULAR PAIR CORRELATIONFUNCTIONS FROM FLUORESCENCE DEPOLARIZATION EXPERIMENTS
JOURNAL OF POLYMER SCIENCE PART BPOLYMER PHYSICS
1985; 23 (3): 591599
View details for Web of Science ID A1985ADN6900014

A COMPARISON OF THE MOLECULARDYNAMICS METHOD AND ENERGY MINIMIZATION METHODS FOR MODELING THE STRUCTURE OF AMORPHOUS METALS
JOURNAL OF NONCRYSTALLINE SOLIDS
1985; 75 (13): 225236
View details for Web of Science ID A1985ATE3500031

EFFECTS OF 3BODY INTERACTIONS ON THE STRUCTURE OF CLUSTERS
SURFACE SCIENCE
1985; 156 (JUN): 548555
View details for Web of Science ID A1985AMF8200066

HOPPING TRANSPORT ON A RANDOMLY SUBSTITUTED LATTICE FOR LONGRANGE AND NEAREST NEIGHBOR INTERACTIONS
JOURNAL OF CHEMICAL PHYSICS
1984; 80 (11): 57315744
View details for Web of Science ID A1984SV51900052

KINETIC ISINGMODEL OF THE GLASSTRANSITION
PHYSICAL REVIEW LETTERS
1984; 53 (13): 12441247
View details for Web of Science ID A1984TJ67300011

A MOLECULARDYNAMICS METHOD FOR CALCULATING THE SOLUBILITY OF GASES IN LIQUIDS AND THE HYDROPHOBIC HYDRATION OF INERTGAS ATOMS IN AQUEOUSSOLUTION
JOURNAL OF PHYSICAL CHEMISTRY
1984; 88 (26): 65486556
View details for Web of Science ID A1984TZ31000015

ELECTRONIC EXCITEDSTATE TRANSPORT AND TRAPPING ON POLYMERCHAINS
MACROMOLECULES
1984; 17 (1): 5459
View details for Web of Science ID A1984SB10300010

ELECTRONIC EXCITATION TRANSPORT AS A PROBE OF CHAIN FLEXIBILITY
MACROMOLECULES
1984; 17 (8): 14961499
View details for Web of Science ID A1984TF17900013

HOPPING TRANSPORT ON A RANDOMLY SUBSTITUTED LATTICE IN THE PRESENCE OF DILUTE DEEP TRAPS
CHEMICAL PHYSICS
1984; 85 (1): 149164
View details for Web of Science ID A1984SH34000014

MOLECULARDYNAMICS SIMULATIONS OF A SUPERCOOLED MONATOMIC LIQUID AND GLASS
JOURNAL OF PHYSICAL CHEMISTRY
1984; 88 (18): 40194027
View details for Web of Science ID A1984TH00500032

THE EFFECT OF PERIODIC BOUNDARYCONDITIONS ON HOMOGENEOUS NUCLEATION OBSERVED IN COMPUTERSIMULATIONS
CHEMICAL PHYSICS LETTERS
1984; 108 (6): 535538
View details for Web of Science ID A1984TE30400003

THE ROLE OF LONG RANGED FORCES IN DETERMINING THE STRUCTURE AND PROPERTIES OF LIQUID WATER
JOURNAL OF CHEMICAL PHYSICS
1983; 79 (9): 45764584
View details for Web of Science ID A1983RN51200063

VANDERWAALS PICTURE OF LIQUIDS, SOLIDS, AND PHASETRANSFORMATIONS
SCIENCE
1983; 220 (4599): 787794
Abstract
The van der Waals picture focuses on the differing roles of the strong shortranged repulsive intermolecular forces and the longer ranged attractions in determining the structure and dynamics of dense fluids and solids. According to this physical picture, the attractive interactions help fix the volume of the system, but the arrangements and motions of molecules within that volume are determined primarily by the local packing and steric effects produced by the repulsive forces. This very useful approach, its limitations, and its successful application to a wide variety of static and dynamic phenomena in condensed matter systems are reviewed.
View details for Web of Science ID A1983QP69600006
View details for PubMedID 17834156

CLUSTER EXPANSIONS FOR HYDROGENBONDED FLUIDS .3. WATER
JOURNAL OF CHEMICAL PHYSICS
1983; 78 (4): 19621979
View details for Web of Science ID A1983QD40400043

ELECTRONIC EXCITEDSTATE TRANSPORT AND TRAPPING AS A PROBE OF INTRAMOLECULAR POLYMER STRUCTURE
JOURNAL OF CHEMICAL PHYSICS
1983; 79 (7): 35723580
View details for Web of Science ID A1983RJ50400051

A THEORY OF THE ANOMALOUS THERMODYNAMIC PROPERTIES OF LIQUID WATER
JOURNAL OF CHEMICAL PHYSICS
1983; 78 (4): 19801993
View details for Web of Science ID A1983QD40400044

ELECTRONIC EXCITEDSTATE TRANSPORT ON ISOLATED POLYMERCHAINS
MACROMOLECULES
1983; 16 (9): 14561464
View details for Web of Science ID A1983RG93400009

EXCITATION TRANSPORT ON SUBSTITUTIONALLY DISORDERED LATTICES
AMER INST PHYSICS. 1983: 1389–89
View details for Web of Science ID A1983RL10600060

EXCITATION TRANSPORT ON SUBSTITUTIONALLY DISORDERED LATTICES
PHYSICAL REVIEW LETTERS
1983; 50 (17): 13241327
View details for Web of Science ID A1983QL86700027

RATTLE  A VELOCITY VERSION OF THE SHAKE ALGORITHM FOR MOLECULARDYNAMICS CALCULATIONS
JOURNAL OF COMPUTATIONAL PHYSICS
1983; 52 (1): 2434
View details for Web of Science ID A1983RQ23800002

ELECTRONIC EXCITEDSTATE TRANSPORT AND TRAPPING IN SOLUTION
JOURNAL OF CHEMICAL PHYSICS
1982; 76 (4): 20152027
View details for Web of Science ID A1982NB26300051

A THEORY OF EFFECTS OF PROTONS AND DIVALENTCATIONS ON PHASEEQUILIBRIA IN CHARGED BILAYERMEMBRANES  COMPARISON WITH EXPERIMENT
BIOCHEMISTRY
1982; 21 (12): 28112820
Abstract
We summarize the concepts in the recently developed statistical mechanical theory of the effects of proton binding and divalent cation binding on phase equilibria in bilayer membrane composed of acidic phospholipids. The theory is used to calculate membrane phase transition temperatures for different aqueous concentrations of protons, divalent cations and monovalent salt. We discuss methods for calculating transition temperatures even for systems in which there is not an excess of protons or divalent cations relative to lipids. The results are compared with existing experimental data for a number of lipids. There is good agreement between calculated transition temperature vs. pH curves and experimental data for dimyristoylmethylphosphatidic acid, dimyristoylphosphatidylglycerol, dipalmitoylphosphatidylglycerol, dipalmitoylphosphatidylserine, and dimyristoylphosphatidic acid. General thermodynamic considerations are used to derive in Clapeyronlike equation for the rate of variation in membrane transition temperature with divalent cation concentration. This equation and some available experimental data are used to argue that the large increase in solid to fluid phase transition temperature that is observed experimentally as the divalent cation concentration is increased is the result of the metastable solid phase that exists at low but not high divalent cation concentration. A calculated coexistence diagram is compared with existing experimental data for transition temperatures of dimyristoylphosphatidylglycerol membranes at different total calcium concentrations. Good agreement is obtained when the existence of a metastable solid phase is assumed.
View details for Web of Science ID A1982NS33900001
View details for PubMedID 6285955

A COMPUTERSIMULATION METHOD FOR THE CALCULATION OF EQUILIBRIUMCONSTANTS FOR THE FORMATION OF PHYSICAL CLUSTERS OF MOLECULES  APPLICATION TO SMALL WATER CLUSTERS
JOURNAL OF CHEMICAL PHYSICS
1982; 76 (1): 637649
View details for Web of Science ID A1982MW46500084

MOLECULARDYNAMICS SIMULATION OF THE GLASSTRANSITION
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
1981; 371 (OCT): 123135
View details for Web of Science ID A1981MS72500009

A THEORY FOR ION BINDING AND PHASEEQUILIBRIA IN CHARGED LIPIDMEMBRANES .2. COMPETITIVE AND COOPERATIVE BINDING
JOURNAL OF CHEMICAL PHYSICS
1981; 74 (4): 25482558
View details for Web of Science ID A1981LE27100065

A THEORY OF ION BINDING AND PHASEEQUILIBRIA IN CHARGED LIPIDMEMBRANES .1. PROTON BINDING
JOURNAL OF CHEMICAL PHYSICS
1981; 74 (4): 25362547
View details for Web of Science ID A1981LE27100064

THEORY OF PHOTONECHOES FROM A PAIR OF COUPLED 2 LEVEL SYSTEMS  IMPURITY DIMERS AND ENERGYTRANSFER IN MOLECULARCRYSTALS
JOURNAL OF CHEMICAL PHYSICS
1981; 75 (7): 31953202
View details for Web of Science ID A1981MF63600004

CORRELATIONFUNCTION ANALYSIS OF COHERENT OPTICAL TRANSIENTS AND FLUORESCENCE FROM A QUASI2LEVEL SYSTEM
PHYSICAL REVIEW A
1981; 24 (4): 19942008
View details for Web of Science ID A1981ML75100038

QUANTUMTHEORY OF COHERENT RAMANSCATTERING BY OPTICALLYACTIVE ISOTROPIC MATERIALS
JOURNAL OF CHEMICAL PHYSICS
1980; 72 (7): 41324140
View details for Web of Science ID A1980JP80900038

A THEORY OF THE EFFECTS OF HEADGROUP STRUCTURE AND CHAIN UNSATURATION ON THE CHAIN MELTING TRANSITION OF PHOSPHOLIPID DISPERSIONS
BIOCHEMISTRY
1980; 19 (18): 42794293
Abstract
We have developed statistical mechanical descriptions of the effects of headgroup structure and acyl chain unsaturation on the chain melting phase transition of aqueous dispersions of bilayers containing glycerophosphocholines and glycerophosphoethanolamines. The theoretical framework is an extension of the model of Jacobs et al. [Jacobs, R. E., Hudson, B. S., & Andersen, H. C. (1975) Proc. Natl. Acad. Sci. U.S.A. 72, 3993]. There are several systematic trends in the experimental transition data for various types of phospholipids. Assumptions about the physical origins of these trends were incorporated into statistical mechanical models, which were used to calculate transition temperatures and enthalpies. The extent to which the calculated results of a model reproduce the experimental trends is taken as a measure of the validity of the assumptions on which the model is based. We found that the gross differences among the transition temperatures of phospholipids with two saturated chains, two transunsaturated chains, two cisunsaturated chains, and one cisunsaturated and one saturated chain can all be explained in terms of the effect of the double bonds on molecular shape and the subsequent effect of shape on the ability of molecules to pack together into a lowenergy state at high density. The dependence of transition temperature on the location of the double bond in cisunsaturated molecules can be understood on the same basis. The differences between the transition temperatures of glycerophosphocholines and glycerophosphoethanolamines with the same hydrocarbon chains can be explained in terms of a larger intermolecular attraction (or smaller repulsion) for the latter than for the former. These differences depend on the presence or absence of unsaturation in the hydrocarbon chains in a way that is consistent with the postulate that hydrogen bonding between glycerophosphoethanolamines is responsible for the differences.
View details for Web of Science ID A1980KG31600021
View details for PubMedID 7417405

MOLECULARDYNAMICS SIMULATIONS AT CONSTANT PRESSURE ANDOR TEMPERATURE
JOURNAL OF CHEMICAL PHYSICS
1980; 72 (4): 23842393
View details for Web of Science ID A1980JK06800026

QUANTUMTHEORY OF COHERENT HYPERRAMAN SCATTERING FROM ISOTROPIC MATERIALS
JOURNAL OF CHEMICAL PHYSICS
1980; 73 (4): 18271835
View details for Web of Science ID A1980KG73000042

ELECTRONIC EXCITEDSTATE TRANSPORT IN SOLUTION
JOURNAL OF CHEMICAL PHYSICS
1979; 70 (9): 42544271
View details for Web of Science ID A1979GU87400035

QUANTUMTHEORY OF LINESHAPES IN COHERENT RAMANSPECTROSCOPY OF GASES AND LIQUIDS
JOURNAL OF CHEMICAL PHYSICS
1979; 70 (9): 41304148
View details for Web of Science ID A1979GU87400019

PROBES OF MEMBRANE STRUCTURE
ANNUAL REVIEW OF BIOCHEMISTRY
1978; 47: 359383
View details for Web of Science ID A1978FH01600011
View details for PubMedID 209727

GLASSTRANSITION OF ATOMIC GLASSES
JOURNAL OF CHEMICAL PHYSICS
1978; 69 (6): 23232331
View details for Web of Science ID A1978FS43400007

THEORY OF PHASETRANSITIONS AND PHASEDIAGRAMS FOR ONECOMPONENT AND 2COMPONENT PHOSPHOLIPID BILAYERS
BIOCHEMISTRY
1977; 16 (20): 43494359
Abstract
A statistical mechanical partition function for phospholipid bilayers is constructed to obtain a theoretical description of the chain melting phase transition in lipid bilayer membranes and of the phase diagrams for twocomponent bilayers. In addition to providing an accurate representation of the transition temperatures and enthalpies of onecomponent bilayers composed of 1,2diacylphosphatidylcholines, the theory can also account for the shapes of the phase diagrams observed for bilayers which are binary mixtures of these compounds with two different hydrocarbon chain lenghts.
View details for Web of Science ID A1977DW50400004
View details for PubMedID 911760

CROSSSECTIONS FOR PHOTODETACHMENT OF ELECTRONS FROM NEGATIVEIONS NEAR THRESHOLD
JOURNAL OF CHEMICAL PHYSICS
1976; 64 (4): 13681375
View details for Web of Science ID A1976BH06300016

INFRARED AND RAMAN STUDIES OF ROTATIONAL CORRELATIONFUNCTIONS IN LIQUIDS
CHEMICAL PHYSICS
1975; 9 (3): 339358
View details for Web of Science ID A1975AL80100008

REPULSIVE PART OF EFFECTIVE INTERATOMIC POTENTIAL FOR LIQUIDMETALS
CHEMICAL PHYSICS
1975; 10 (1): 7385
View details for Web of Science ID A1975AP89800009

THEORY OF CHAIN MELTING PHASETRANSITION OF AQUEOUS PHOSPHOLIPID DISPERSIONS
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
1975; 72 (10): 39933997
Abstract
A model for the chain melting phase transition in dilute aqueous phospholipid bilayer dispersions is presented. This model includes interactions between head groups, between hydrocarbon chains, and within the chains. The head groups are modeled as hard disks which are constrained to lie on a twodimensional surface separating the aqueous and hydrocarbon regions. The chain statistics problem is treated in an approximate manner using an approach motivated by scaled particle theory to describe the interchain steric repulsions in a mathematically tractable way. In this approach the whole system interacts with any given chain through an average lateral pressure which is proportional to the hard disk pressure. Following Nagle, we assume that the steric repulsions between chains and between head groups and the transgauche rotation energies are the dominant interactions in determining the transition and we describe the effect of the other interactions with a mean field approximation. Using the known transition temperature of a series of 1,2diacyl phosphatidyl cholines to adjust two parameters in the theory, the model gives enthalpy and area changes that are in quite reasonable agreement with experiment. Moreover, the curvature observed in the plot of the transition temperature against acyl chain length is reproduced.
View details for Web of Science ID A1975AW35900045
View details for PubMedID 1060080

STRUCTURE OF LIQUIDS
ANNUAL REVIEW OF PHYSICAL CHEMISTRY
1975; 26: 145166
View details for Web of Science ID A1975AW32800008

LIGHTSCATTERING MEASUREMENT AND THEORETICAL INTERPRETATION OF MUTUAL DIFFUSIONCOEFFICIENTS IN BINARYLIQUID MIXTURES
CHEMICAL PHYSICS
1975; 11 (3): 451473
View details for Web of Science ID A1975BA93300010

THEORY OF TRANSPORT IN LIQUIDMETALS .2. CALCULATION OF SHEAR VISCOSITY COEFFICIENTS
CHEMICAL PHYSICS
1975; 8 (12): 1726
View details for Web of Science ID A1975AC13700002

CLUSTER EXPANSIONS FOR HYDROGENBONDED FLUIDS .2. DENSE LIQUIDS
JOURNAL OF CHEMICAL PHYSICS
1974; 61 (12): 49854992
View details for Web of Science ID A1974V247000006

THEORY OF TRANSPORT IN LIQUIDMETALS .1. CALCULATION OF SELFDIFFUSION COEFFICIENTS
JOURNAL OF CHEMICAL PHYSICS
1973; 59 (1): 1525
View details for Web of Science ID A1973Q264400002

CLUSTER EXPANSIONS FOR HYDROGENBONDED FLUIDS .1. MOLECULAR ASSOCIATION IN DILUTE GASES
JOURNAL OF CHEMICAL PHYSICS
1973; 59 (9): 47144725
View details for Web of Science ID A1973R679800020

OPTIMIZED CLUSTER EXPANSIONS FOR CLASSICAL FLUIDS .1. GENERAL THEORY AND VARIATIONAL FORMULATION OF MEAN SPHERICAL MODEL AND HARDSPHERE PERCUSYEVICK EQUATIONS
JOURNAL OF CHEMICAL PHYSICS
1972; 57 (5): 1918?
View details for Web of Science ID A1972N317900019

OPTIMIZED CLUSTER EXPANSIONS FOR CLASSICAL FLUIDS .3. APPLICATIONS TO IONIC SOLUTIONS AND SIMPLE LIQUIDS
JOURNAL OF CHEMICAL PHYSICS
1972; 57 (7): 2626?
View details for Web of Science ID A1972N596100003

OPTIMIZED CLUSTER EXPANSIONS FOR CLASSICAL FLUIDS .2. THEORY OF MOLECULAR LIQUIDS
JOURNAL OF CHEMICAL PHYSICS
1972; 57 (5): 1930?
View details for Web of Science ID A1972N317900020

ROLES OF REPULSIVE AND ATTRACTIVE FORCES IN LIQUIDS  OPTIMIZED RANDOM PHASE APPROXIMATION
JOURNAL OF CHEMICAL PHYSICS
1972; 56 (8): 3812?
View details for Web of Science ID A1972M268000015

MODE EXPANSION IN EQUILIBRIUM STATISTICAL MECHANICS .3. OPTIMIZED CONVERGENCE AND APPLICATION TO IONIC SOLUTION THEORY
JOURNAL OF CHEMICAL PHYSICS
1971; 55 (4): 1497?
View details for Web of Science ID A1971K101100001

MODE EXPANSION IN EQUILIBRIUM STATISTICAL MECHANICS .2. A RAPIDLY CONVERGENT THEORY OF IONIC SOLUTIONS
JOURNAL OF CHEMICAL PHYSICS
1971; 54 (1): 26?
View details for Web of Science ID A1971I124500004

ROLE OF REPULSIVE FORCES IN DETERMINING EQUILIBRIUM STRUCTURE OF SIMPLE LIQUIDS
JOURNAL OF CHEMICAL PHYSICS
1971; 54 (12): 5237?
View details for Web of Science ID A1971J630300035

RELATIONSHIP BETWEEN HARDSPHERE FLUID AND FLUIDS WITH REALISTIC REPULSIVE FORCES
PHYSICAL REVIEW AGENERAL PHYSICS
1971; 4 (4): 1597?
View details for Web of Science ID A1971K409600034

KINETIC EQUATIONS FOR ORIENTATIONAL AND SHEAR RELAXATION AND DEPOLARIZED LIGHT SCATTERING IN LIQUIDS
JOURNAL OF CHEMICAL PHYSICS
1971; 54 (6): 2584?
View details for Web of Science ID A1971J001500038

MODE EXPANSION IN EQUILIBRIUM STATISTICAL MECHANICS .1. GENERAL THEORY AND APPLICATION TO CLASSICAL ELECTRON GAS
JOURNAL OF CHEMICAL PHYSICS
1970; 53 (2): 547?
View details for Web of Science ID A1970G908800012