Related papers: Particle-Particle, Particle-Scaling function (P3S)…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
To simulate the dynamics of fluid with polydisperse particles on macroscale level, one has to solve hydrodynamic equations with several relaxation terms, representing momentum transfer from fluid to particles and vice versa. For small…
We present a 3D finite element solver for the nonlinear Poisson-Nernst-Planck (PNP) equations for electrodiffusion, coupled to the Stokes system of fluid dynamics. The model serves as a building block for the simulation of macromolecule…
We construct an accurate estimate for the root mean square force error of the particle-particle-particle-mesh (P3M) algorithm by extending a single particle pair error measure which has been given by Hockney and Eastwood. We also derive an…
We report a development of a new fast surface-based method for numerical calculations of solvation energy of biomolecules with a large number of charged groups. The procedure scales linearly with the system size both in time and memory…
We present a computational algorithm for computing short range forces between particles. The algorithm has two distinguishing features. First, it is optimized for multi-processor computers, and will use as many processors as are available.…
Coulomb interactions of point charges can be calculated in $\mathcal{O}$(N) computation using the fast multipole method and direct calculations between charges nearby. It reduces computational cost dramatically, however, because of its…
Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure.…
The hybrid method combining particle-in-cell and magnetohydrodynamics can be used to study the interaction between energetic particles and global plasma modes. In this paper we introduce the M3D-C1-K code, which is developed based on the…
In this paper, we present a new hybrid algorithm for the time integration of collisional N-body systems. In this algorithm, gravitational force between two particles is divided into short-range and long-range terms, using a…
A common feature of wall-bounded turbulent particle-laden flows is enhanced particle concentrations in a thin layer near the wall due to a phenomenon known as turbophoresis. Even at relatively low bulk volume fractions, particle-particle…
We describe the implementation and performance of the ${\rm P^3T}$ (Particle-Particle Particle-Tree) scheme for simulating dense stellar systems. In ${\rm P^3T}$, the force experienced by a particle is split into short-range and long-range…
The Tree-Particle-Mesh (TPM) N-body algorithm couples the tree algorithm for directly computing forces on particles in an hierarchical grouping scheme with the extremely efficient mesh based PM structured approach. The combined TPM…
This paper will suggest a new finite element method to find a $P^4$-velocity and a $P^3$-pressure solving incompressible Stokes equations at low cost. The method solves first the decoupled equation for a $P^4$-velocity. Then, using the…
We propose and justify a new approach for fast calculation of the electrostatic interaction energy of clusters of charged particles in constrained energy minimization in the framework of rigid protein-ligand docking. Our ``blind search''…
Particle methods are less computationally efficient than grid based numerical solution of the Navier Stokes equation. However, they have important advantages including rigorous mass conservation, momentum conservation and isotropy. In…
We present a new, simple, fast algorithm to numerically evolve disks of inelastically colliding particles surrounding a central star. Our algorithm adds negligible computational cost to the fastest existing collisionless N-body codes, and…
Coulomb interaction, following an inverse-square force-law, quantifies the amount of force between two stationary and electrically charged particles. The long-range nature of Coulomb interactions poses a major challenge to molecular…
We devise automated workflows for the calculation of Helmholtz and Gibbs free energies and their temperature and pressure dependence and provide the corresponding computational tools. We employ non-equilibrium thermodynamics for evaluating…
In preparation to the exascale era, an alternative approach to calculate the electrostatic forces in Particle Mesh (PM) methods is proposed. While the traditional techniques are based on the calculation of the electrostatic potential by…