Systematic study of temperature and density variations in effective potentials for coarse-grained models of molecular liquids

2019 ◽  
Vol 150 (1) ◽  
pp. 014104 ◽  
Author(s):  
Kathryn M. Lebold ◽  
W. G. Noid
Keyword(s):  
Systematic Study ◽  
Coarse Grained ◽  
Molecular Liquids ◽  
Effective Potentials

Coarse-grained simulations for organic molecular liquids based on Gay-Berne and electric multipole potentials

2012 ◽  
Vol 19 (2) ◽  
pp. 551-558 ◽  
Author(s):  
Peijun Xu ◽  
Hujun Shen ◽  
Lu Yang ◽  
Yang Ding ◽  
Beibei Li ◽  
...  
Keyword(s):  
Coarse Grained ◽  
Molecular Liquids ◽  
Coarse Grained Simulations

scholarly journals A multiscale analysis of DNA phase separation: From atomistic to mesoscale level

2018 ◽  
Author(s):  
Tiedong Sun ◽  
Alexander Mirzoev ◽  
Vishal Minhas ◽  
Nikolay Korolev ◽  
Alexander P. Lyubartsev ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Crystalline ◽  
Coarse Graining ◽  
Md Simulations ◽  
Coarse Grained ◽  
Effective Potentials ◽  
Dna Oligonucleotides ◽  
Hexagonally Ordered ◽  
Dna Packing

ABSTRACTDNA condensation and phase separation is of utmost importance for DNA packing in vivo with important applications in medicine, biotechnology and polymer physics. The presence of hexagonally ordered DNA is observed in virus capsids, sperm heads and in dinoflagellates. Rigorous modelling of this process in all-atom MD simulations is presently difficult to achieve due to size and time scale limitations. We used a hierarchical approach for systematic multiscale coarse-grained (CG) simulations of DNA phase separation induced by the three-valent cobalt(III)-hexammine (CoHex3+). Solvent-mediated effective potentials for a CG model of DNA were extracted from all-atom MD simulations. Simulations of several hundred 100-bp-long CG DNA oligonucleotides in the presence of explicit CoHex3+ ions demonstrated aggregation to a liquid crystalline hexagonally ordered phase. Following further coarse-graining and extraction of effective potentials, we conducted modelling at mesoscale level. In agreement with electron microscopy observations, simulations of an 10.2-kbp-long DNA molecule showed phase separation to either a toroid or a fibre with distinct hexagonal DNA packing. The mechanism of toroid formation is analysed in detail. The approach used here is based only on the underlying all-atom force field and uses no adjustable parameters and may be generalized to modelling chromatin up to chromosome size.

On the importance of shear dissipative forces in coarse-grained dynamics of molecular liquids

2015 ◽  
Vol 17 (16) ◽  
pp. 10795-10804 ◽  
Author(s):  
Sergei Izvekov ◽  
Betsy M. Rice
Keyword(s):  
High Resolution ◽  
First Principles ◽  
Dissipative Particle Dynamics ◽  
Coarse Graining ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Molecular Liquids ◽  
Dissipative Forces

In this work we demonstrate from first principles that the shear frictions describing dissipative forces in the direction normal to the vector connecting the coarse-grained (CG) particles in dissipative particle dynamics (DPD) could be dominant for certain real molecular liquids at high-resolution coarse-graining.

Multiscale coarse-grained simulations of ionic liquids: comparison of three approaches to derive effective potentials

2013 ◽  
Vol 15 (20) ◽  
pp. 7701 ◽  
Author(s):  
Yong-Lei Wang ◽  
Alexander Lyubartsev ◽  
Zhong-Yuan Lu ◽  
Aatto Laaksonen
Keyword(s):  
Ionic Liquids ◽  
Coarse Grained ◽  
Effective Potentials ◽  
Coarse Grained Simulations

scholarly journals Effective mechanical potential of cell–cell interaction explains basic structures of three-dimensional morphogenesis

2019 ◽  
Author(s):  
Hiroshi Koyama ◽  
Hisashi Okumura ◽  
Atsushi M. Ito ◽  
Tetsuhisa Otani ◽  
Kazuyuki Nakamura ◽  
...  
Keyword(s):  
Mdck Cells ◽  
Three Dimensional ◽  
Cell Interaction ◽  
Fundamental Principle ◽  
Cell Interactions ◽  
Coarse Grained ◽  
Spherical Particles ◽  
Imaging Data ◽  
Effective Potentials ◽  
Cell Cell

AbstractMechanical properties of cell–cell interactions have been suggested to be critical for the emergence of diverse three-dimensional morphologies of multicellular organisms. Mechanical potential energy of cell–cell interactions has been theoretically assumed, however, whether such potential can be detectable in living systems remains poorly understood. In this study, we developed a novel framework for inferring mechanical forces of cell–cell interactions. First, by analogy to coarse-grained models in molecular and colloidal sciences, cells were approximately assumed to be spherical particles, where microscopic features of cells such as polarities and shapes were not explicitly incorporated and the mean forces (i.e. effective forces) of cell–cell interactions were considered. Then, the forces were statistically inferred from live imaging data, and subsequently, we successfully detected potentials of cell–cell interactions. Finally, computational simulations based on these potentials were performed to test whether these potentials can reproduce the original morphologies. Our results from various systems, including Madin-Darby canine kidney (MDCK) cells, C.elegans early embryos, and mouse blastocysts, suggest that the method can accurately infer the effective potentials and capture the diverse three-dimensional morphologies. Importantly, energy barriers were predicted to exist at the distant regions of the interactions, and this mechanical property of cell–cell interactions was essential for formation of cavities, tubes, cups, and two-dimensional sheets. Collectively, these structures constitute basic structures observed during morphogenesis and organogenesis. We propose that effective potentials of cell– cell interactions are parameters that can be measured from living organisms, and represent a fundamental principle underlying the emergence of diverse three-dimensional morphogenesis.

scholarly journals Coarse-Grained Models Reveal Functional Dynamics – II. Molecular Dynamics Simulation at the Coarse-Grained Level – Theories and Biological Applications

2008 ◽  
Vol 2 ◽  
pp. BBI.S459 ◽  
Author(s):  
Choon-Peng Chng ◽  
Lee-Wei Yang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Conformation ◽  
Conformational Dynamics ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Time Step ◽  
Effective Potentials ◽  
Functional Dynamics ◽  
Indispensable Tool ◽  
Selection Of

Molecular dynamics (MD) simulation has remained the most indispensable tool in studying equilibrium/non-equilibrium conformational dynamics since its advent 30 years ago. With advances in spectroscopy accompanying solved biocomplexes in growing sizes, sampling their dynamics that occur at biologically interesting spatial/temporal scales becomes computationally intractable; this motivated the use of coarse-grained (CG) approaches. CG-MD models are used to study folding and conformational transitions in reduced resolution and can employ enlarged time steps due to the a bsence of some of the fastest motions in the system. The Boltzmann-Inversion technique, heavily used in parameterizing these models, provides a smoothed-out effective potential on which molecular conformation evolves at a faster pace thus stretching simulations into tens of microseconds. As a result, a complete catalytic cycle of HIV-1 protease or the assembly of lipid-protein mixtures could be investigated by CG-MD to gain biological insights. In this review, we survey the theories developed in recent years, which are categorized into Folding-based and Molecular-Mechanics-based. In addition, physical bases in the selection of CG beads/time-step, the choice of effective potentials, representation of solvent, and restoration of molecular representations back to their atomic details are systematically discussed.

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