Simulated applications

Gerber, P. R., Mark, A. E., van Gunsteren, W. F. An approximate but efficient method to calculate free energy trends by computer simulation Application to dihydrofolate reductase-inhibitor complexes. J. Comp. Aid. Mol. Desgn 7 (1993) 305-323... 

Our work is targeted to biomolecular simulation applications, where the objective is to illuminate the structure and function of biological molecules (proteins, enzymes, etc) ranging in size from dozens of atoms to tens of thousands of atoms today, with the desire to increase this limit to millions of atoms in the near future. Such molecular dynamics (MD) simulations simply apply Newton s law to each atom in the system, with the force on each atom being determined by evaluating the gradient of the potential field at each atom s position. The potential includes contributions from bonding forces. 

Jorgensen W L, J K Buckner, S Boudon and J Tirado-Reeves 1988. Efficient Computation of Absoluti Free Energies of Binding by Computer Simulations - Applications to the Methane Dimer ir Water. Journal of Chemical Physics 89 3742-3746. 

WL Jorgensen, JK Buckner, S Boudon, J Tirado-Rives. Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer m water. J Chem Phys 89 3742-3746, 1988. 

Integral error criteria are ideally suited to simulation applications since only one additional program statement is required for the simulation. The optimal control parameters Kp, Tj and Xq can be then found at minimal ITAE. For this, it is useful to be able to apply the available optimisation tools implemented in such programs as MATLAB, SIMUSOLV and ESL. 

Quirke, N. Jacucci, G., Energy difference functions in Monte Carlo simulations application to the calculation of free energy of liquid nitrogen. II. The calculation of fluctuation in Monte Carlo averages, Mol. Phys. 1982, 45, 823-838... 

Beveridge, D. L. DiCapua, F. M., Free energy via molecular simulation applications to chemical and biomolecular systems, Anna. Rev. Biophys. Biophys. 1989, 18, 431-492... 

Tsai, C.J. Jordan, K.D., Use of the histogram and jump-walking methods for overcoming slow barrier crossing behavior in Monte Carlo simulations applications to the phase transitions in the (Ar)i3 and (FbOjs clusters, J. Chem. Phys. 1993, 99, 6957... 

Meijer, E. J. Azhar, F. El, Novel procedure to determine coexistence lines by computer simulation, application to hard-core Yukawa model for charge-stabilized colloids, J. Chem. Phys. 1997,106, 4678-4683... 

Hermans, J. Pathiaseril, A. Anderson, A., Excess free-energy of liquids from molecular-dynamics simulations — application to water models, J. Am. Chem. Soc. 1988,110, 5982-5986. 

D. L. Beveridge and F. M. DiCapua, Free energy via molecular simulation Application to... 

The complete procedure, together with a simulation application for a continuous stirred tank reactor, can be found in McBrayer and Edgar (1995). 

Bernacki, K., Hetenyi, B., Berne, B.J. Multiple "time step" Monte Carlo simulations application to charged systems with Ewald summation. J. Chem. Phys. 2004, 121, 44-50. 

MusollT, Andre. Shape Memory Alloys. Available online. URL http // www.smaterial.com/SMA/sma.html. Accessed May 28, 2009. This richly illustrated and highly informative Web site describes shape-memory alloy from the perspective of models, crystallography, simulation, applications, and research. 

Baveridge DL, DiCapua FM, Free Energy Via Molecular Simulation Applications to Chemical and Biomolecular Systems, Ann Rev Biophys Chem 18, 431-492 (1989)... 

Beveridge DL, Dicapua FM (1989) Free energy via molecular simulations application to chemical and biochemical sytems, Annu Rev Biopys Chem, 18 431—492... 

Balci, O. (2001). A methodology for accreditation of modeling and simulation applications. Transactions on Modeling and Computer Simulation, 11, 352-ill. 

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