Doros N. Theodorou

Bio: Doros N. Theodorou is an academic researcher from National Technical University of Athens. The author has contributed to research in topics: Monte Carlo method & Molecular dynamics. The author has an hindex of 62, co-authored 250 publications receiving 13753 citations. Previous affiliations of Doros N. Theodorou include Massachusetts Institute of Technology & University of Patras.

Atomistic modeling of mechanical properties of polymeric glasses

Abstract: Methodes pour la prevision des constantes elastiques d'un polymere amorphe par deformation de faible amplitude de structures modeles detaillees microscopiquement

Prediction of adsorption of aromatic hydrocarbons in silicalite from grand canonical Monte Carlo simulations with biased insertions

Abstract: Adsorption isotherms and isosteric heats of adsorption for benzene and p-xylene in silicalite have been calculated from molecular simulations. The simulations were performed using newly developed grand canonical ensemble Monte Carlo (GCMC) techniques in which insertion attempts are biased toward the most favorable regions of the zeolite pore space. The new techniques result in a substantial improvement in the efficiency of the simulations compared to traditional GCMC. The adsorption thermodynamics and molecular-level structure were studied for benzene and p-xylene in silicalite with Pnma symmetry (ORTHO) and P2[sub 1]2[sub 1]2[sub 1] symmetry (PARA). The subtle differences between ORTHO and PARA silicalite result in qualitatively different sorption behavior. An explanation of the experimentally observed step in the adsorption isotherm is presented, based on the results of the simulations and the ORTHO to PARA framework transformation that is observed experimentally. Predictions of the adsorption isotherms, isosteric heats, and siting locations of the adsorbates are in good agreement with experiment. 59 refs., 14 refs., 4 tabs.

Transport diffusivity of methane in silicalite from equilibrium and nonequilibrium simulations

Abstract: The results of equilibrium and nonequilibrium simulations designed to predict the transport diffusivity of methane in silicalite are presented. The results are compared with equilibrium molecular dynamics calculations of the self-diffusivity for the same system, as well as with the Darken model, which is often invoked to relate self-diffusivities and transport diffusivities in zeolites. Good agreement is found between simulation results and the Darken model. Systems that are expected to deviate from the Darken model are discussed. 47 refs., 9 figs.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

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.

Stochastic Processes in Physics and Chemistry

Abstract: N G van Kampen 1981 Amsterdam: North-Holland xiv + 419 pp price Dfl 180 This is a book which, at a lower price, could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes, as well as those who just enjoy a beautifully written book. It provides an extensive graduate-level introduction which is clear, cautious, interesting and readable.

Direct determination of phase coexistence properties of fluids by Monte Carlo simulation in a new ensemble

Abstract: A methodology is presented for Monte Carlo simulation of fluids in a new ensemble that can be used to obtain phase coexistence properties of multicomponent systems from a single computer experiment. The method is based on performing a simulation simultaneously in two distinct physical regions of generally different densities and compositions. Three types of perturbations are performed, a random displacement of molecules that ensures equilibrium within each region, an equal and opposite change in the volume of the two regions that results in equality of pressures, and random transfers of molecules that equalize the chemical potentials of each component in the two regions. The method is applied to the calculation of the liquid-gas coexistence envelope for the pure Lennard-Jones (6, 12) fluid for several reduced temperatures from the vicinity of the triple point to close to the critical point (T* = 0·75 to T* = 1·30). Good overall agreement with previously available literature results is obtained, with some ...

TRANSITION PATH SAMPLING: Throwing Ropes Over Rough Mountain Passes, in the Dark

Abstract: This article reviews the concepts and methods of transition path sampling. These methods allow computational studies of rare events without requiring prior knowledge of mechanisms, reaction coordinates, and transition states. Based upon a statistical mechanics of trajectory space, they provide a perspective with which time dependent phenomena, even for systems driven far from equilibrium, can be examined with the same types of importance sampling tools that in the past have been applied so successfully to static equilibrium properties.