Related papers: Software package for simulations using the coarse-…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…
This chapter provides a brief introduction to the theory and practice of spatial stochastic simulations. It begins with an overview of different methods available for biochemical simulations highlighting their strengths and limitations.…
Quantum simulation is a leading candidate for demonstrating practical quantum advantage over classical computation, as it is believed to provide exponentially more compute power than any classical system. It offers new means of studying the…
We present the first open access version of the QMeCha (Quantum MeCha) code, a quantum Monte Carlo (QMC) package developed to study many-body interactions between different types of quantum particles, with a modular and easy-to-expand…
Due to the very long timescales involved (us-s), theoretical modeling of fundamental biological processes including folding, misfolding, and mechanical unraveling of biomolecules, under physiologically relevant conditions, is challenging…
We present a technique designed for parallelizing large rigid body simulations, capable of exploiting multiple CPU cores within a computer and across a network. Our approach can be applied to simulate both unilateral and bilateral…
QwaveMPS is an open-source Python library for simulating one-dimensional quantum many-body waveguide systems using matrix product states (MPS). It provides a user-friendly interface for constructing, evolving, and analyzing quantum states…
We developed a portable code for dissipative particle dynamics (DPD) simulations. This Fortran program named CAMUS has a couple of notable features. One is the omission of constructing the so-called neighboring particles list, providing a…
Warm dense matter systems created in the laboratory are highly dynamical. In such cases electron dynamics is often needed to accurately simulate the evolution and properties of the system. Large systems force one to make simple…
Here we give a detailed description of MOLS 2.0.The source code and binary of MOLS 2.0 are distributed free (under GNU Lesser General Public License) for the scientific community. They are freely available for download at…
Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources…
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…
For the self-consistent description of various plasma sources operated in the low-pressure (nonlocal, kinetic) regime, the Particle-In-Cell simulation approach, combined with the Monte Carlo treatment of collision processes (PIC/MCC), has…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…
We present release 2.0 of the ALPS (Algorithms and Libraries for Physics Simulations) project, an open source software project to develop libraries and application programs for the simulation of strongly correlated quantum lattice models…
In this work, we review previously developed coarse-grained (CG) particle models for biological membrane and red blood cells (RBCs) and discuss the advantages of the CG particle method over the continuum and atomic simulations on modeling…
Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory,…
In this paper we announce the public release of a massively-parallel, GPU-accelerated software, which is the first to combine both coarse-grained molecular dynamics and field-theoretical simulations in one simulation package. MATILDA.FT…
Protein folding processes are a vital aspect of molecular biology that is hard to simulate with conventional computers. Quantum algorithms have been proven superior for certain problems and may help tackle this complex life science…