ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics

PLoS Computational Biology
Moritz HoffmannFrank Noé

Abstract

Interacting-particle reaction dynamics (iPRD) combines the simulation of dynamical trajectories of interacting particles as in molecular dynamics (MD) simulations with reaction kinetics, in which particles appear, disappear, or change their type and interactions based on a set of reaction rules. This combination facilitates the simulation of reaction kinetics in crowded environments, involving complex molecular geometries such as polymers, and employing complex reaction mechanisms such as breaking and fusion of polymers. iPRD simulations are ideal to simulate the detailed spatiotemporal reaction mechanism in complex and dense environments, such as in signalling processes at cellular membranes, or in nano- to microscale chemical reactors. Here we introduce the iPRD software ReaDDy 2, which provides a Python interface in which the simulation environment, particle interactions and reaction rules can be conveniently defined and the simulation can be run, stored and analyzed. A C++ interface is available to enable deeper and more flexible interactions with the framework. The main computational work of ReaDDy 2 is done in hardware-specific simulation kernels. While the version introduced here provides single- and multi-threading CPU ...Continue Reading

References

Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
May 1, 1997·Biophysical Journal·R R Gabdoulline, R C Wade
May 8, 1998·Methods : a Companion to Methods in Enzymology·R R Gabdoulline, R C Wade
Sep 5, 2002·Nature Reviews. Molecular Cell Biology·Joseph A Beavo, Laurence L Brunton
Jul 23, 2003·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·Steven Chu
Oct 7, 2003·Proceedings of the National Academy of Sciences of the United States of America·Bertil Halle, Monika Davidovic
Feb 20, 2004·Cancer Research·Rinat AbramovitchAlik Honigman
Apr 9, 2005·Bioinformatics·Johan HattneJohan Elf
May 21, 2005·Physical Review Letters·Jeroen S van Zon, Pieter Rein ten Wolde
Jan 6, 2006·The Journal of Chemical Physics·Jeroen S van Zon, Pieter Rein ten Wolde
Oct 14, 2006·Bioinformatics·Chris SanfordJohn Parkinson
Apr 8, 2009·Thrombosis and Haemostasis·Duska DragunBjörn Hegner
Aug 25, 2009·Physical Biology·Radek Erban, S Jonathan Chapman
Oct 30, 2009·Trends in Biochemical Sciences·Miles D Houslay
Feb 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Koichi TakahashiPieter Rein ten Wolde
Oct 13, 2008·SIAM Journal on Scientific Computing : a Publication of the Society for Industrial and Applied Mathematics·Rex A KerrJoel R Stiles
Jun 10, 2010·BMC Bioinformatics·Gerd GruenertPeter Dittrich
Jan 21, 2011·Nature Reviews. Neuroscience·Amantha Thathiah, Bart De Strooper
Mar 23, 2011·PLoS Computational Biology·Elijah RobertsZaida Luthey-Schulten
Mar 18, 2009·Journal of Physics. Condensed Matter : an Institute of Physics Journal·A AyadimS Amokrane
Feb 4, 2012·Current Medicinal Chemistry·B TrzaskowskiS Filipek
Aug 22, 2012·Proceedings of the National Academy of Sciences of the United States of America·Emanuel SchneckRoland R Netz
Sep 26, 2012·Journal of Computational Chemistry·Elijah RobertsZaida Luthey-Schulten
Mar 14, 2013·Reports on Progress in Physics·Felix Höfling, Thomas Franosch
Aug 10, 2013·The Journal of Chemical Physics·Samuel A Isaacson
May 17, 2014·The Journal of Chemical Physics·Heinrich C R Klein, Ulrich S Schwarz
Sep 5, 2014·Biophysical Journal·Johannes SchönebergFrank Noé
Jan 1, 2014·BMC Biophysics·Johannes SchönebergFrank Noé
Jul 1, 2015·Journal of Computational Chemistry·Michael MartinezRebecca C Wade
Sep 15, 2015·PLoS Computational Biology·Alexander UllrichFrank Noé
Dec 10, 2015·The Journal of Chemical Physics·Adithya VijaykumarPieter Rein Ten Wolde
Jan 23, 2016·Scientific Reports·Shailesh R AgarwalRobert D Harvey
Feb 4, 2016·Biophysical Journal·Paul J Michalski, Leslie M Loew
Mar 24, 2017·The Journal of Chemical Physics·Adithya VijaykumarPeter G Bolhuis
Nov 17, 2017·The Journal of Chemical Physics·Luigi Sbailò, Frank Noé

❮ Previous
Next ❯

Citations

Nov 5, 2019·The Journal of Chemical Physics·Manuel DibakFelix Höfling
Jan 31, 2020·BMC Bioinformatics·Satya N V ArjunanKoichi Takahashi
Jun 17, 2020·Nature Chemical Biology·Jan MöllerMartin J Lohse
Jun 17, 2020·Soft Matter·Pritam Kumar Jana, Bortolo Matteo Mognetti
May 22, 2019·Physical Review. E·Wei-Xiang ChewSatya N V Arjunan
Jan 3, 2020·The Journal of Chemical Physics·Á Ruiz-MartínezD M Tartakovsky
Mar 1, 2020·Current Opinion in Structural Biology·Benjamin R JaggerAdrian J Mulholland
May 30, 2020·Biophysical Journal·Matthew J VargaMargaret E Johnson
Mar 7, 2021·Biophysical Journal·Wylie Stroberg, Santiago Schnell
May 14, 2021·PLoS Computational Biology·Jasia KingAurélie Carlier
May 27, 2020·ACS Omega·Emiko Zumbro, Alfredo Alexander-Katz
Oct 15, 2021·Proceedings of the National Academy of Sciences of the United States of America·Anna LappalaKarissa Y Sanbonmatsu
Oct 23, 2021·The Journal of Physical Chemistry Letters·Mohsen Sadeghi, Frank Noé

❮ Previous
Next ❯

Software Mentioned

conda
Lattice Microbes
VMD viewer
spatiocyte
eGFRD
MCell
LAMMPS
ReaDDy
Smoldyn
readdy ReactionDiffusionSystem

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.