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We introduce an analysis method to measure elliptic flow (v_2) fluctuations using the PHOBOS detector for Au+Au collisions at sqrt(s) = 200 GeV. In this method, v_2 is determined event-by-event by a maximum likelihood fit. The…
During a crossover via a switching mechanism from one 2-body potential to another as might be applied in modeling (chemical) reactions in the vicinity of bond formation, energy violations would occur due to finite step size which determines…
Determining the 3D structures of proteins is essential in understanding their behavior in the cellular environment. Computational methods of predicting protein structures have advanced, but assessing prediction accuracy remains a challenge.…
Boundary condition (BC) calibration to assimilate clinical measurements is an essential step in any subject-specific simulation of cardiovascular fluid dynamics. Bayesian calibration approaches have successfully quantified the uncertainties…
We investigate the long-range statistical correlations, whereby discuss the nature of the undermining interacting/ noninteracting domains and associated phase transitions under variations of the quark mass and the mass scale that…
Multiscale dynamics are frequently present in real-world processes, such as the atmosphere-ocean and climate science. Because of time scale separation between a small set of slowly evolving variables and much larger set of rapidly changing…
Although machine-learning potentials have recently had substantial impact on molecular simulations, the construction of a robust training set can still become a limiting factor, especially due to the requirement of a reference ab initio…
In the past the study of reaction-diffusion systems has greatly contributed to our understanding of the behavior of many-body systems far from equilibrium. In this paper we aim at characterizing the properties of diffusion limited reactions…
Energy evaluation using fast Fourier transforms enables sampling billions of putative complex structures and hence revolutionized rigid protein-protein docking. However, in current methods efficient acceleration is achieved only in either…
Various biological system models have been proposed in systems biology, which are based on the complex biological reactions kinetic of various components. These models are not practical because we lack of kinetic information. In this paper,…
The dominant reaction pathway (DRP) is a rigorous framework to microscopically compute the most probable trajectories, in non-equilibrium transitions. In the low-temperature regime, such dominant pathways encode the information about the…
Despite its widespread use in materials science, conventional molecular dynamics (MD) simulations are severely constrained by timescale limitations. To address this shortcoming, we propose an empirical formulation of accelerated MD method,…
A Redox Flow Battery (RFB) is one of the promising energy storage systems in power grid. An RFB has many advantages such as a quick response, a large capacity, and a scalability. Due to these advantages, an RFB can operate in mixed time…
Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous…
Molecular dynamics (MD) simulations give access to equilibrium structures and dynamic properties given an ergodic sampling and an accurate force-field. The force-field parameters are calibrated to reproduce properties measured by…
Recently, an analytical expression for the system size dependence and direction-dependence of self-diffusion coefficients for neat liquids due to hydrodynamic interactions has been derived for molecular dynamics (MD) simulations using…
Batteries are pivotal components in overcoming some of today's greatest technological challenges. Yet to date there is no self-consistent atomistic description of a complete battery. We take first steps toward modeling of a battery as a…
Advanced experimental measurements are crucial for driving theoretical developments and unveiling novel phenomena in condensed matter and material physics, which often suffer from the scarcity of facility resources and increasing…
Detailed studies of the intriguing field-dependent dynamics and transport properties of confined flowing ferrofluids require efficient mesoscopic simulation methods that account for fluctuating ferrohydrodynamics. Here, we propose such a…
We present the explicit bonding Reaction ensemble Monte Carlo (eb-RxMC) method, designed to sample reversible bonding reactions in macromolecular systems in thermodynamic equilibrium. Our eb-RxMC method is based on the Reaction ensemble…