Related papers: Optimizing Replica Exchange Moves For Molecular Dy…

The histogram reweighting technique, widely used to analyze Monte Carlo data, is shown to be applicable to dynamic properties obtained from Molecular Dynamics simulations. The theory presented here is based on the fact that the correlation…

Ongoing investigations to introduce software techniques suitable to support new experimental requirements for multi-scale simulation are discussed.

In biomolecular systems (especially all-atom models) with many degrees of freedom such as proteins and nucleic acids, there exist an astronomically large number of local-minimum-energy states. Conventional simulations in the canonical…

Recently, there has been a surge in the interest of non-equilibrium collective quantum models, where particle dispersion and spin are examples of effects taken into account. Here, we derive a kinetic plasma model con- taining fermion…

Molecular line data for the rotational transitions of a number of astrophysically interesting species have been collected and are made publically available through the www. These data, including energy levels, statistical weights, Einstein…

Optimal prediction approximates the average solution of a large system of ordinary differential equations by a smaller system. We present how optimal prediction can be applied to a typical problem in the field of molecular dynamics, in…

A recombination reaction model for high-temperature chemical kinetics is derived from ab initio simulations data. A kinetic recombination rate model is derived using a recently developed ab initio state-specific dissociation model and the…

Deposition of smaller granular particles on a larger nucleus particle has been simulated in two-dimension using molecular dynamics method. Variation of sequences of velocity of deposited particles is conducted and reported in this work. The…

Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…

Despite the increasing prevalence of vector observations, computation of optimal experimental design for multi-response models has received limited attention. To address this problem within the framework of approximate designs, we introduce…

Metastable condensed matter typically fluctuates about local energy minima at the femtosecond time scale before transitioning between local minima after nanoseconds or microseconds. This vast scale separation limits the applicability of…

Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…

We combined the genetic crossover, which is one of the operations of genetic algorithm, and replica-exchange method in parallel molecular dynamics simulations. The genetic crossover and replica-exchange method can search the global…

We propose a class of subspace ascent methods for computing optimal approximate designs that covers both existing as well as new and more efficient algorithms. Within this class of methods, we construct a simple, randomized exchange…

Numerical and analytical methods are developed for the investigation of contact sets in electrostatic-elastic deflections modeling micro-electro mechanical systems. The model for the membrane deflection is a fourth-order semi-linear partial…

We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…

We outline a modeling and optimization strategy for investigating dynamic metabolic engineering interventions. Our framework is particularly useful at the early stages of research and development, often constrained by limited knowledge and…

We propose a simple model of network co-evolution in a game-dynamical system of interacting agents that play repeated games with their neighbors, and adapt their behaviors and network links based on the outcome of those games. The…

A new, very fast, implementation of the exact (Fock) exchange operator for electronic structure calculations within the plane-wave pseudopotential method is described in detail for both molecular and periodic systems, and carefully…

Systems switching between different dynamical phases is an ubiquitous phenomenon. The general understanding of such a process is limited. To this end, we present a general expression that captures fluctuations of a system exhibiting a…