Dynamic simulation computations

Hilbers P A J and Esselink K 1993 Parallel computing and molecular dynamics simulations Computer Simulation In Chemloal Physios /o 397 NATO ASI Series Ced M P Allen and D J Tlldesley (Dordrecht Kluwer) pp 473-95... 

P. A. J Hilbers and K. Esselink, Parallel computing and molecular dynamics simulations , Computer Simulations in Chemical Physics, Proc. of the NATO advanced study institute on new perspectives in computer simulations in chemical physics, 473-95, 1993. 

Park A. J. and Ortoleva P. J. (2003) WRIS.TEQ multi-mineraUc water-rock interaction, mass-transfer and textural dynamics simulator. Comput. Geosci. 29, 277—290. 

S. Gupta, Computing aspects of molecular dynamics simulation, Comput. Phys. Commun., 70 (1992), 243-270. 

S. S. Pitty, W. Li, A. Adhitya, R. Srinivasan, and I. A. Karimi, 2007, Decision Support for Integrated Refinery Supply Chains. 1. Dynamic Simulation, Computers and Chemical Engineering (In Press). 

V. Aquilanti, E. Carmona-Novillo, E. Garcia, A. Lombardi, M.B. Sevryuk, and E. Yurtsever, Invariant energy partitions in chemical reactions and cluster dynamics simulations. Computational Materials Science, 35 187-191, 2005. 

The R D activities for the process and equipment developments will be performed at prototypical conditions based on a high pressure and temperature and metallic-based equipment. On the other hand, a dynamic simulation computer code to analyse the transient state of an advanced SI process will be developed by 2009. This computer code will be applied for the dynamic analysis of the pilot and demo scale SI facilities. 

Electronic Structure/Basic Theory Molecular Dynamics Simulations Computer-Aided Chemical Discovery... 

Pitty, S., Li, W., Adhitya, A., Srinivasan, R., and Karimi, I. Decision support for integrated refinery supply chains Part 1. dynamic simulation. Computers Chemical Engineering, 32(ll) 2767-2786, 2008. 

Key words Lipid bilayer - molecular dynamics simulations - computer simulation - permeability - transport... 

Hase WL, Song K, Gordon MS (2003) Direct dynamics simulations. Comput Sci Eng 5 36-44... 

Progress in the theoretical description of reaction rates in solution of course correlates strongly with that in other theoretical disciplines, in particular those which have profited most from the enonnous advances in computing power such as quantum chemistry and equilibrium as well as non-equilibrium statistical mechanics of liquid solutions where Monte Carlo and molecular dynamics simulations in many cases have taken on the traditional role of experunents, as they allow the detailed investigation of the influence of intra- and intemiolecular potential parameters on the microscopic dynamics not accessible to measurements in the laboratory. No attempt, however, will be made here to address these areas in more than a cursory way, and the interested reader is referred to the corresponding chapters of the encyclopedia. 

SchlickT, Mandziuk M, Skeel R D and Srinivas K 1998 Nonlinear resonance artifacts in molecular dynamics simulations J. Comput. Phys. 140 1-29... 

Ciccotti G and Ryckaert J P 1986 Molecular dynamics simulation of rigid molecules Comput. Phys. Rep. 4 345-92... 

Tuckerman M E and Hughes A 1998 Path integral molecular dynamics a computational approach to quantum statistical mechanics Classical and Quantum Dynamics In Condensed Phase Simulations ed B J Berne, G Ciccotti and D F Coker (Singapore World Scientific) pp 311-57... 

Madura J D, Davis M E, Gilson, M K, Wade R C, Luty B A and McCammon J A 1994 Biological applications of electrostatic calculations and Brownian dynamics simulations Rev. Comput. Chem. 5 229-67... 

Another topic that received increasing attention is the incorporation of quantum methods into dynamic simulations. True quantum dynamics for hundreds of particles is beyond any foreseeable computational capability, and only approximations are viable. We should distinguish ... 

Prenkel, D. Pree energy computation and first order phase transitions. In Molecular Dynamic Simulation of Statistical Mechanical Systems, Enrico Fermi Summer School, Varenna 1985, G. Ciccotti and W. Hoover, eds. North Holland, Amsterdam (1986) 43-65. 

Field, M.J., Bash, P.A., Karplus, M. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J. Comput. Chem. 11 (1990) 700-733. 

Guenot, J., Kollman, P.A. Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation. J. Comput. Chem. 14 (1993) 295-311. 

Molecular dynamics simulations ([McCammon and Harvey 1987]) propagate an atomistic system by iteratively solving Newton s equation of motion for each atomic particle. Due to computational constraints, simulations can only be extended to a typical time scale of 1 ns currently, and conformational transitions such as protein domains movements are unlikely to be observed. 

Ligand-Protein Interactions The energy of formation of ligand-protein contacts can be computed as a sum of non-bonded (Lennard-Jones and electrostatic) terms similar to those used in a molecular dynamics simulation. 

Such a free energy is called a potential of mean force. Average values of Fs can be computed in dynamics simulations (which sample a Boltzmann distribution), and the integral can be estimated from a series of calculations at several values of s. A third method computes the free energy for perturbing the system by a finite step in s, for example, from si to S2, with... 

J. D. Turner, P. K. Weiner, H. M. Chun, V. Lupi, S. Gallion, and U. C. Singh. Variable reduction techniques applied to molecular dynamics simulations. In W. F. van Gunsteren, P. K. Weiner, and A. J. Wilkinson, editors. Computer Simulation of Biomolecular Systems Theoretical and Experimental Applications, volume 2, chapter 24. ESCOM, Leiden, The Netherlands, 1993. 

Extending time scales of Molecular Dynamics simulations is therefore one of the prime challenges of computational biophysics and attracted considerable attention [2-5]. Most efforts focus on improving algorithms for solving the initial value differential equations, which are in many cases, the Newton s equations of motion. 

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