ESPResSo++ 2.0: Advanced methods for multiscale molecular simulation

Guzman, Horacio V.; Tretyakov, Nikita; Kobayashi, Hideki; Fogarty, Aoife C.; Kreis, Karsten; Krajniak, Jakub; Junghans, Christoph; Kremer, Kurt; Stuehn, Torsten

doi:10.1016/j.cpc.2018.12.017

Cited by 38 publications

(33 citation statements)

References 104 publications

(185 reference statements)

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“…Molecular dynamics simulations are performed using the ESPResSo++ package [34,35]. Starting with the equilibrated systems our simulation procedure consists of three steps:…”

Section: Simulation Proceduresmentioning

confidence: 99%

Investigation of Crystallization and Relaxation Effects in Coarse-Grained Polyethylene Systems after Uniaxial Stretching

et al. 2021

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In this study, we investigate the thermo-mechanical relaxation and crystallization behavior of polyethylene using mesoscale molecular dynamics simulations. Our models specifically mimic constraints that occur in real-life polymer processing: After strong uniaxial stretching of the melt, we quench and release the polymer chains at different loading conditions. These conditions allow for free or hindered shrinkage, respectively. We present the shrinkage and swelling behavior as well as the crystallization kinetics over up to 600 ns simulation time. We are able to precisely evaluate how the interplay of chain length, temperature, local entanglements and orientation of chain segments influences crystallization and relaxation behavior. From our models, we determine the temperature dependent crystallization rate of polyethylene, including crystallization onset temperature.

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“…Molecular dynamics simulations are performed using the ESPResSo++ package [34,35]. Starting with the equilibrated systems our simulation procedure consists of three steps:…”

Section: Simulation Proceduresmentioning

confidence: 99%

Investigation of Crystallization and Relaxation Effects in Coarse-Grained Polyethylene Systems after Uniaxial Stretching

et al. 2021

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“…The SPlit and conQueR model (SPQR) is a coarse-grained representation [ 36 ] of RNA, originally designed for structure prediction [ 37 ]. Under this scheme, each nucleotide is treated as an anisotropic particle and a spherical bead, which stand for the nucleoside and the phosphate group respectively.…”

Section: Methodsmentioning

confidence: 99%

Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models

Poblete

Guzman

2021

Viruses

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Three-dimensional RNA domain reconstruction is important for the assembly, disassembly and delivery functionalities of a packed proteinaceus capsid. However, to date, the self-association of RNA molecules is still an open problem. Recent chemical probing reports provide, with high reliability, the secondary structure of diverse RNA ensembles, such as those of viral genomes. Here, we present a method for reconstructing the complete 3D structure of RNA genomes, which combines a coarse-grained model with a subdomain composition scheme to obtain the entire genome inside proteinaceus capsids based on secondary structures from experimental techniques. Despite the amount of sampling involved in the folded and also unfolded RNA molecules, advanced microscope techniques can provide points of anchoring, which enhance our model to include interactions between capsid pentamers and RNA subdomains. To test our method, we tackle the satellite tobacco mosaic virus (STMV) genome, which has been widely studied by both experimental and computational communities. We provide not only a methodology to structurally analyze the tertiary conformations of the RNA genome inside capsids, but a flexible platform that allows the easy implementation of features/descriptors coming from both theoretical and experimental approaches.

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“…For instance, Molecular Dynamics (MD) simulations [ 5 ] can examine protein dynamics up to the microsecond level though they are still not fast enough to capture conformational transitions that take place over larger timescales-milliseconds or more. Methods such as targeted, biased, or steered MD, umbrella sampling, replica exchange, activation relaxation, conformational flooding, swarm methods, and others attempt to lower the computational demands of MD-based approaches [ 6 , 7 , 8 , 9 ], and Multiscale Molecular Dynamics Simulation methods [ 10 ]. Some methods focus on deforming a trivial conformational path (obtained, for instance, through morphing) to improve its energy profile.…”

Section: Introductionmentioning

confidence: 99%

Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC

2021

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To understand how proteins function on a cellular level, it is of paramount importance to understand their structures and dynamics, including the conformational changes they undergo to carry out their function. For the aforementioned reasons, the study of large conformational changes in proteins has been an interest to researchers for years. However, since some proteins experience rapid and transient conformational changes, it is hard to experimentally capture the intermediate structures. Additionally, computational brute force methods are computationally intractable, which makes it impossible to find these pathways which require a search in a high-dimensional, complex space. In our previous work, we implemented a hybrid algorithm that combines Monte-Carlo (MC) sampling and RRT*, a version of the Rapidly Exploring Random Trees (RRT) robotics-based method, to make the conformational exploration more accurate and efficient, and produce smooth conformational pathways. In this work, we integrated the rigidity analysis of proteins into our algorithm to guide the search to explore flexible regions. We demonstrate that rigidity analysis dramatically reduces the run time and accelerates convergence.

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ESPResSo++ 2.0: Advanced methods for multiscale molecular simulation

Cited by 38 publications

References 104 publications

Investigation of Crystallization and Relaxation Effects in Coarse-Grained Polyethylene Systems after Uniaxial Stretching

Investigation of Crystallization and Relaxation Effects in Coarse-Grained Polyethylene Systems after Uniaxial Stretching

Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models

Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC

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