Action-derived molecular dynamics for the simulation of rare event and slow mode systems is reviewed. Theoretical background, implementation details, and comparison with other methods are presented. Numerical examples demonstrated include the structural formation and transformation of carbon fullerenes, and molecular reconfiguration of alanine dipeptide and valine dipeptide. It is shown that th...

Discrete-event simulation based optimization is the process of finding the optimum design of a stochastic system when the performance measure(s) could only be estimated via simulation. Randomness in simulation outputs often challenges the correct selection of the optimum. We propose an algorithm that merges Ranking and Selection procedures with a large class of random search methods for continu...

Despite a steady improvement of computational hardware, results of numerical simulation are still tightly bound to the simulation tool and strategy used, and may substantially vary across available simulation tools or for different settings within the same simulator. Clockdriven simulation strategies proved efficient for large and highly active networks but are outperformed with respect to prec...

Recent advances in nanotechnology are paving the way to attain control over individual microscopic objects. The ability to prepare, manipulate, couple and measure single microscopic systems facilitate the study of single quantum systems at the level of individual events. Such experiments address the most fundamental aspects of quantum theory. Indeed, quantum theory gives us only a recipe to com...

Molecular dynamic simulation is a powerful method that monitors all variations in the atomic level in explicit solvent. By this method we can calculate many chemical and biochemical properties of large scale biological systems. In this work all-atom molecular dynamics simulation of polyalanine (PA) was investigated in the presence of 0.224, 0.448, 0.673, 0.897 and 1.122 M of guanidinium chlorid...

A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. SEDMD combines event-driven molecular dynamics (EDMD) with the Direct Simulation Monte Carlo (DSMC) method. The polymers are represented as chains of hard-spheres tethered by square wells and interact with the solvent particles with hard-core potentials....