Jdpd: an open java simulation kernel for molecular fragment dissipative particle dynamics

  title={Jdpd: an open java simulation kernel for molecular fragment dissipative particle dynamics},
  author={Karina van den Broek and Hubert Kuhn and Achim Zielesny},
  journal={Journal of Cheminformatics},
Jdpd is an open Java simulation kernel for Molecular Fragment Dissipative Particle Dynamics with parallelizable force calculation, efficient caching options and fast property calculations. It is characterized by an interface and factory-pattern driven design for simple code changes and may help to avoid problems of polyglot programming. Detailed input/output communication, parallelization and process control as well as internal logging capabilities for debugging purposes are supported. The new… 

MFsim—an open Java all-in-one rich-client simulation environment for mesoscopic simulation

The new environment comprises the complete preparation-simulation–evaluation triad of a mesoscopic simulation task and especially enables biomolecular simulation tasks with peptides and proteins.

Notes on the Treatment of Charged Particles for Studying Cyclotide/Membrane Interactions with Dissipative Particle Dynamics

Different charge treatment approaches are examined for cyclotide-induced plasma membrane disruption by lipid extraction studied with dissipative particle dynamics. A pure Coulomb approach with

Quantitative Estimation of Cyclotide-Induced Bilayer Membrane Disruption by Lipid Extraction with Mesoscopic Simulation

The obtained bioactivity trends for cyclotides Kalata B1, Cycloviolacin O2, and selected mutants with different membrane types are in agreement with experimental findings and can be applied as a fast and easy-to-use tool for exploring structure-activity relationships of cyclotide/membrane systems.

Ocular lamellar crystalline gels for sustained release and enhanced permeation of resveratrol against corneal neovascularization

A resveratrol-loaded ocular lamellar crystalline gel (ROLG) was developed for high inhibition of CNV, resulting from the attenuation of corneal VEGF expression and then cornea healing was improved and the ROLG was a promising ocular medicine for the prevention of C NV.



Understanding molecular simulation: from algorithms to applications

The physics behind the "recipes" of molecular simulation for materials science is explained and the implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text.

Towards better integrators for dissipative particle dynamics simulations

It is demonstrated that commonly used integration schemes in dissipative particle dynamics give rise to pronounced artifacts in physical quantities such as the compressibility and the diffusion coefficient.

Splitting for Dissipative Particle Dynamics

We study numerical methods for dissipative particle dynamics, a system of stochastic differential equations for simulating particles interacting pairwise according to a soft potential at constant

Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics

We present a novel method for simulating hydrodynamic phenomena. This particle-based method combines features from molecular dynamics and lattice-gas automata. It is shown theoretically as well as in

Integration schemes for dissipative particle dynamics simulations: From softly interacting systems towards hybrid models

We examine the performance of various commonly used integration schemes in dissipative particle dynamics simulations. We consider this issue using three different model systems, which characterize a

A molecular fragment cheminformatics roadmap for mesoscopic simulation

A complete cheminformatics roadmap that frames a mesoscopic Molecular Fragment Dynamics (MFD) simulation kernel to allow its efficient use and practical application and it is shown that the requirements of the roadmap may be partly covered by already existing open-source chemin formatics software.

Self-consistent dissipative particle dynamics algorithm

An implementation of dissipative particle dynamics that is free of the inconsistencies that plagued earlier algorithms is proposed, and the present algorithm satisfies a form of microscopic reversibility and recovers the correct equilibrium properties.

On the numerical treatment of dissipative particle dynamics and related systems

How would you integrate the equations of motion in dissipative particle dynamics simulations ?

In this work we assess the quality and performance of several novel dissipative particle dynamics integration sche have not previously been tested independently. Based on a thorough comparison we

Compiling and Optimizing Java 8 Programs for GPU Execution

A just-in-time (JIT) compiler that can generate and optimize GPU code from a pure Java program written using lambda expressions with the new parallel streams APIs in Java 8 by automatically leveraging the computational capability of GPUs is presented.