The multiscale coarse-graining method. VII. Free energy decomposition of coarse-grained effective potentials

2011 ◽  
Vol 134 (22) ◽  
pp. 224107 ◽  
Author(s):  
Lanyuan Lu ◽  
Gregory A. Voth
Keyword(s):  
Free Energy ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Energy Decomposition ◽  
Effective Potentials ◽  
Free Energy Decomposition

scholarly journals Effect of double mutations T790M/L858R on conformation and drug-resistant mechanism of epidermal growth factor receptor explored by molecular dynamics simulations

RSC Advances ◽  
2018 ◽  
Vol 8 (70) ◽  
pp. 39797-39810 ◽  
Author(s):  
Fangfang Yan ◽  
Xinguo Liu ◽  
Shaolong Zhang ◽  
Jing Su ◽  
Qinggang Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Epidermal Growth Factor Receptor ◽  
Decomposition Method ◽  
Growth Factor Receptor ◽  
Drug Resistant ◽  
Energy Decomposition ◽  
Free Energy Decomposition ◽  
Epidermal Growth ◽  
Dynamics Simulations

The MM-GBSA method coupled with residue-based free energy decomposition method was performed to explore drug-resistant mechanisms of the mutated EGFR.

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.

Do all pieces make a whole? Thiele cumulants and the free energy decomposition

2007 ◽  
Vol 117 (4) ◽  
pp. 535-540 ◽  
Author(s):  
Matevž Bren ◽  
Jan Florián ◽  
Janez Mavri ◽  
Urban Bren
Keyword(s):  
Free Energy ◽  
Energy Decomposition ◽  
Free Energy Decomposition
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