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We present two approaches capable of describing the dynamics of an interacting many body system on a lattice coupled globally to a dissipative bosonic mode. Physical realizations are for example ultracold atom gases in optical lattice…
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…
We present the ALPS (Algorithms and Libraries for Physics Simulations) project, an international open source software project to develop libraries and application programs for the simulation of strongly correlated quantum lattice models…
We describe a new hybrid N-body/hydrodynamical code based on the particle-mesh (PM) method and the piecewise-parabolic method (PPM) for use in solving problems related to the evolution of large-scale structure, galaxy clusters, and…
An approximate approach to quantum vibrational dynamics, "Brownian Chain Molecular Dynamics (BCMD)", is proposed to alleviate the chain resonance and curvature problems in the imaginary time-based path integral (PI) simulation. Here the…
We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a…
Partially-observed Boolean dynamical systems (POBDS) are a general class of nonlinear models with application in estimation and control of Boolean processes based on noisy and incomplete measurements. The optimal minimum mean square error…
We develop a Monte Carlo wave function algorithm for the quantum linear Boltzmann equation, a Markovian master equation describing the quantum motion of a test particle interacting with the particles of an environmental background gas. The…
We present a soft-potential-enhanced Poisson-Boltzmann (SPB) theory to efficiently capture ion distributions and electrostatic potential around rodlike charged macromolecules. The SPB model is calibrated with a coarse-grained particle-based…
This article presents a hardware architecture independent implementation of an adaptive mesh refinement Poisson solver that is integrated into the electrostatic Particle-In-Cell beam dynamics code OPAL. The Poisson solver is solely based on…
The Many-Body Expansion (MBE) is a useful tool to simulate condensed phase chemical systems, often avoiding the steep computational cost of usual electronic structure methods. However, it often requires higher than 2-body terms to achieve…
In this chapter we review the electrostatic properties of charged membranes in aqueous solutions, with or without added salt, employing simple physical models. The equilibrium ionic profiles close to the membrane are governed by the…
The Box-Ball System (BBS) is a cellular automaton introduced by Takahashi and Satsuma in the 1990s. The system is a discrete counterpart of the KdV equation and exhibits solitonic behavior. Recently, the BBS started from a random two-sided…
The mathematical theory of integrable Painleve/Toda type systems sheds new light on the behavior of solutions to the Poisson-Boltzmann equation for the potential due to a long rod-like macroion. We investigate here the case of symmetric…
openCOSMO-RS is an open-source predictive thermodynamic model that can be applied to a broad range of systems in various chemical and biochemical engineering domains. This study focuses on improving openCOSMO-RS by introducing a new…
Active subspace (AS) methods are a valuable tool for understanding the relationship between the inputs and outputs of a Physics simulation. In this paper, an elegant generalization of the traditional ASM is developed to assess the…
A new approach to the kinetic simulation of plasmas in complex geometries, based on the Particle-in- Cell (PIC) simulation method, is explored. In the two dimensional (2d) electrostatic version of our method, called the Arbitrary…
We develop Random Batch Methods for interacting particle systems with large number of particles. These methods use small but random batches for particle interactions, thus the computational cost is reduced from $O(N^2)$ per time step to…
The proximal bundle method (PBM) is a fundamental and computationally effective algorithm for solving optimization problems with nonsmooth components. In this paper, we conduct a theoretical investigation of a modified proximal bundle…
Continuum kinetic theories provide an important tool for the analysis and simulation of particle suspensions. When those particles are anisotropic, the addition of a particle orientation vector to the kinetic description yields a $2d-1$…