Related papers: Performance Evaluation of the Zero-Multipole Summa…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
A four-way coupling scheme for the direct numerical simulation of particle-laden flows is developed and analyzed. It employs a novel adaptive multi-relaxation time lattice Boltzmann method to simulate the fluid phase efficiently. The…
The swept-field experiments on magnetic molecular solids such as \Fe8 are studied using Monte Carlo simulations. A kinetic equation is developed to understand the phenomenon. It is found that the simulations provide a quantitatively…
We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…
Entropy and free-energy estimation are key in thermodynamic characterization of simulated systems ranging from spin models through polymers, colloids, protein structure, and drug-design. Current techniques suffer from being model specific,…
The integration time step is a critical determinant of performance in molecular dynamics simulations, governing the trade-off between speed and fidelity. Although 2 fs remains the standard in atomistic biomolecular simulations, the push for…
Recently, a new framework to compute the photoionization rate in streamer discharges accurately and efficiently using the integral form and the fast multipole method (FMM) was presented. This paper further improves the efficiency of this…
We propose extensions and improvements of the statistical analysis of distributed multipoles (SADM) algorithm put forth by Chipot et al. in [6] for the derivation of distributed atomic multipoles from the quantum-mechanical electrostatic…
The Dynamic Monte Carlo (DMC) method is an established molecular simulation technique for the analysis of the dynamics in colloidal suspensions. An excellent alternative to Brownian Dynamics or Molecular Dynamics simulation, DMC is…
Fast multipole methods (FMM) were originally developed for accelerating $N$-body problems for particle-based methods. FMM is more than an $N$-body solver, however. Recent efforts to view the FMM as an elliptic Partial Differential Equation…
In this paper, a fast multipole method (FMM) is proposed to compute long-range interactions of wave sources embedded in 3-D layered media. The layered media Green's function for the Helmholtz equation, which satisfies the transmission…
This paper proposes a Sieve Simulated Method of Moments (Sieve-SMM) estimator for the parameters and the distribution of the shocks in nonlinear dynamic models where the likelihood and the moments are not tractable. An important concern…
Power flow feasibility assessment is computationally challenging for unbalanced three-phase distribution networks. This paper develops a vectorized semidefinite program (SDP) based on the bus injection model (BIM) and reformulates its dual…
The recently introduced quantum particle swarm optimization (QPSO) algorithm is employed to find infinitesimal dipole models (IDM) for antennas with known near-fields (measured or computed). The IDM can predict accurately both the…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
A molecular dynamics (MD) simulation is used to quantitatively analyze the induced membrane potential for an applied external field varied between 0.4 V/nm to 2.0 V/nm. The change in the electrostatic potential in the DPPC is directly…
We consider fast kernel summations in high dimensions: given a large set of points in $d$ dimensions (with $d \gg 3$) and a pair-potential function (the {\em kernel} function), we compute a weighted sum of all pairwise kernel interactions…
A number of problems arise when long-range forces, such as those governed by Bessel functions, are used in particle-particle simulations. If a simple cut-off for the interaction is used, the system may find an equilibrium configuration at…
Density-functional theory (DFT) has become the workhorse of modern computational chemistry, with dispersion corrections such as the exchange-hole dipole moment (XDM) model playing a key role in high-accuracy modelling of large-scale…
Density functionals at the level of the Generalized Gradient Approximation (GGA) and a plane-wave basis set are widely used today to perform ab initio molecular dynamics (AIMD) simulations. Going up in the ladder of accuracy of density…