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

Abstract

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 kernel may be utilized in different simulation environments ranging from flexible scripting solutions up to fully integrated “all-in-one” simulation systems.

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

“…All simulations are carried out with the open DPD environment MFsim [28,29], which utilizes the open Jdpd simulation kernel [3,30]. The sketched electrostatic interactions are implemented in Jdpd classes ParticlePairElectrostaticsDpdPotentialCalculator (for the potential energy between two charged particles) and ParticlePairElectrostaticsDpdForceCon-servativeCalculator (for the electrostatic forces of charged particles) in method calculateParti-clePairInteraction, in which the methods could be easily extended to alternative calculation schemes (e.g., [31]).…”

“…In contrast, coarse-grained mesoscopic simulation techniques such as dissipative particle dynamics (DPD) considerably reduce the necessary number of interacting particles and allow much longer integration time steps on the picosecond scale, as soft particle-particle interactions replace their hard atomistic equivalents. As a result, mesoscopic simulations are orders of magnitude faster, with simulation runs of molecular ensembles representing millions of atoms for microseconds being completed within hours or days on standard multicore workstations [2,3]. Conversely, mesoscopic simulations imply a much lower resolution above the atomic level with only isotropic particle-particle interactions that average nonbonded interactions at the atomic scale-limitations that may prevent an adequate description of the molecular processes in question.…”

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

“…DPD simulations were used to build the microstructures of ROLGs to investigate the drug and ethanol distribution in ROLGs. The coarse-grained bead volume was set at the beginning of the DPD simulation (Bowman et al., 2019 ; Van den Broek et al., 2018 ). One water molecule was considered one DPD bead.…”

MORTAR - A Rich Client Application for in silico Molecule Fragmentation

“…This dates back to Bemis and Murcko's investigation of the diversity of drug molecules known in their time by looking at how many different molecular frameworks can be identified and which of them appear very frequently [21]. A specific application of MORTAR could be the automated generation of adequate fragment molecule sets for mesoscopic simulation approaches of large molecular ensembles to be studied on the nanometer length and microsecond time scales (like "bottomup" Dissipative Particle Dynamics (DPD) [54] supported by the MFsim/Jdpd [55][56] environment).…”