Robert Zwanzig

Bio: Robert Zwanzig is an academic researcher from National Institutes of Health. The author has contributed to research in topics: Master equation & Dielectric. The author has an hindex of 44, co-authored 86 publications receiving 16098 citations. Previous affiliations of Robert Zwanzig include National Institute of Standards and Technology.

High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases

Abstract: A theoretical study is made of the equations of state of argon and nitrogen, at high temperatures and densities. The intermolecular potential used is of the Lennard‐Jones form, with an adjustable rigid sphere cutoff. A perturbation theory is developed, by which the thermodynamic properties of one system may be related to those of a slightly different system and to the difference in the intermolecular potentials of the two systems. In this article, the unperturbed system is a rigid sphere fluid, and the Lennard‐Jones potential is the perturbation. The results are in fair agreement with experiment, and also lead to an experimental test of the theoretical rigid sphere equation of state.

Nonequilibrium statistical mechanics

Abstract: 1. Brownian Motion and Langevin equations 2. Fokker-Planck equations 3. Master equations 4. Reaction rates 5. Kinetic models 6. Quantum dynamics 7. Linear response theory 8. Projection operators 9. Nonlinear problems 10. The paradoxes of irreversibility Appendices

Ensemble Method in the Theory of Irreversibility

Abstract: We describe a new formulation of methods introduced in the theory of irreversibility by Van Hove and Prigogine, with the purpose of making their ideas easier to understand and to apply. The main tool in this reformulation is the use of projection operators in the Hilbert space of Gibbsian ensemble densities. Projection operators are used to separate an ensemble density into a ``relevant'' part, needed for the calculation of mean values of specified observables, and the remaining ``irrelevant'' part. The relevant part is shown to satisfy a kinetic equation which is a generalization of Van Hove's ``master equation to general order.'' Diagram summation methods are not used. The formalism is illustrated by a new derivation of the Prigogine‐Brout master equation for a classical weakly interacting system.

Memory Effects in Irreversible Thermodynamics

Abstract: A new generalization of Onsager's theory of irreversible processes is presented. The main purpose is to allow for memory effects or causal time behavior, so that the response to a thermodynamic force comes later than the application of the force. This is accomplished by a statistical mechanical derivation of an exact non-Markoffian kinetic equation for the probability distribution in the space of macroscopic state variables. The memory effect in the resulting transport equations is represented by a time convolution of the thermodynamic forces with memory functions. The latter are time-correlation functions in the rates of change of the phase functions corresponding to macroscopic quantities. The resulting transport equations are not restricted to small deviations from thermal equilibrium. Onsager's theory is shown to be the low-frequency limit of our causal theory.

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

Abstract: CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.

Scalable molecular dynamics with NAMD

Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.

CHARMM: the biomolecular simulation program.

Abstract: CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecu- lar simulation program. It has been developed over the last three decades with a primary focus on molecules of bio- logical interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estima- tors, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numer- ous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.