Modeling chemical reactions in classical molecular dynamics simulations

Gissinger, Jacob R.; Jensen, Benjamin D.; Wise, Kristopher E.

doi:10.1016/j.polymer.2017.09.038

Cited by 146 publications

(142 citation statements)

References 21 publications

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“…In addition to the aforementioned molecular dynamics simulation plans for the standard GARD model, whereby all catalysis event are non-covalent, we should lay the foundations for analyzing the behavior of the new metabolic GARD model [8,97]. For this, molecular dynamics versions capable of simulating the formation and breakage of covalent bonds as described in [23,98,99] is essential. In a typical example, covalent non-enzymatic catalysis is exerted by one lipid molecule in a lipid assembly, enhancing the rate of covalent modification of the head group of a neighboring lipid as described in the realm of the GARD model [84], as well as experimentally [45,78].…”

Section: Roadmap For Gard Evidence Via Molecular Dynamicsmentioning

confidence: 99%

Protobiotic Systems Chemistry Analyzed by Molecular Dynamics

Kahana

Lancet

2019

Life

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Systems chemistry has been a key component of origin of life research, invoking models of life’s inception based on evolving molecular networks. One such model is the graded autocatalysis replication domain (GARD) formalism embodied in a lipid world scenario, which offers rigorous computer simulation based on defined chemical kinetics equations. GARD suggests that the first pre-RNA life-like entities could have been homeostatically-growing assemblies of amphiphiles, undergoing compositional replication and mutations, as well as rudimentary selection and evolution. Recent progress in molecular dynamics has provided an experimental tool to study complex biological phenomena such as protein folding, ligand-receptor interactions, and micellar formation, growth, and fission. The detailed molecular definition of GARD and its inter-molecular catalytic interactions make it highly compatible with molecular dynamics analyses. We present a roadmap for simulating GARD’s kinetic and thermodynamic behavior using various molecular dynamics methodologies. We review different approaches for testing the validity of the GARD model by following micellar accretion and fission events and examining compositional changes over time. Near-future computational advances could provide empirical delineation for further system complexification, from simple compositional non-covalent assemblies towards more life-like protocellular entities with covalent chemistry that underlies metabolism and genetic encoding.

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Section: Roadmap For Gard Evidence Via Molecular Dynamicsmentioning

confidence: 99%

Protobiotic Systems Chemistry Analyzed by Molecular Dynamics

Kahana

Lancet

2019

Life

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“…The cubic volumes in these simulations are around 4 nm long. More efficient polymer-specific schemes such as Polymatic 22 and template-based polymerization 23 have been devised to tackle the issue of high computational cost of atomistic reaction modelling. Both of these models generated crosslinked networks of hundreds of reactive units where system sizes reach a few nm, but these length-scales are far from the experimentally relevant length-scales (100's to 1000's of nm).…”

Section: Introductionmentioning

confidence: 99%

Routine million-particle simulations of epoxy curing with dissipative particle dynamics

Thomas

Alberts

Henry

et al. 2018

J. Theor. Comput. Chem.

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Mesoscale simulation techniques have helped to bridge the length scales and time scales needed to predict the microstructures of cured epoxies, but gaps in computational cost and experimental relevance have limited their impact. In this work, we develop an open-source plugin epoxpy for HOOMD-Blue that enables epoxy crosslinking simulations of millions of particles to be routinely performed on a single modern graphics card. We demonstrate the first implementation of custom temperature-time curing profiles with dissipative particle dynamics and show that reaction kinetics depend sensitively on the stochastic bonding rates. We provide guidelines for modeling first-order reaction dynamics in a classic epoxy/hardener/toughener system and show structural sensitivity to the temperature-time profile during cure. We conclude with a discussion of how these efficient large-scale simulations can be used to evaluate ensembles of epoxy processing protocols to quantify the sensitivity of microstructure on processing.

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“…In the most popular and well-studied applications, such as the MARTINI model, this ideal of reproducibility is achieved, however, for new methods, developers often are required to build code from scratch to explore hypotheses, and the resultant code is often domain-specific and not written for Future Directions. LAMMPS currently has the ability to create and destroy bonds during a simulation and modify particle types [24], although the file format is complex and difficult to master. We are currently developing a user-friendly method to control these simulations using only a few lines of moltemplate code (https://github.com/jewettaij/lammps_mca_examples).…”

Section: Discussionmentioning

confidence: 99%

“…Coarse-grained representations often present an additional challenge: they may include custom particle attributes and/or move under the influence of unconventional forces, such as the manybody "mW" water particle used in Figure 2b [23], as well as forces that drive the system out of equilibrium. A diverse and growing list of methods exist for running non-equilibrium simulations in LAMMPS, such as time-varying external forces, motors used to twist DNA in Figure 1ab (explained in the supplemental data), the collective motion of self-propelled colloidal particles (https://lammps.sandia.gov/doc/fix_propel_self.html), and chemical reactions [24]. The data required to characterize these non-standard forces is often encoded in domain-specific file formats that are not supported in traditional molecule builder software.…”

Section: Methodsmentioning

confidence: 99%

Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics

Jewett

Stelter

Lambert

et al. 2021

Journal of Molecular Biology

256

144

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This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

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Modeling chemical reactions in classical molecular dynamics simulations

Cited by 146 publications

References 21 publications

Protobiotic Systems Chemistry Analyzed by Molecular Dynamics

Protobiotic Systems Chemistry Analyzed by Molecular Dynamics

Routine million-particle simulations of epoxy curing with dissipative particle dynamics

Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics

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