Self-assembling dipeptides: including solvent degrees of freedom in a coarse-grained model

2009 ◽  
Vol 11 (12) ◽  
pp. 2068 ◽  
Author(s):  
Alessandra Villa ◽  
Nico F. A. van der Vegt ◽  
Christine Peter
Keyword(s):  
Degrees Of Freedom ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Self Assembling

Dissipative Particle Dynamics Studies on the Self-Assembling Dynamics of the Peptide Amphiphiles

2008 ◽  
Vol 1135 ◽  
Author(s):  
Taiga Seki ◽  
Noriyoshi Arai ◽  
Taku Ozawa ◽  
Tomoko Shimada ◽  
Kenji Yasuoka ◽  
...  
Keyword(s):  
Self Assembly ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
The Self ◽  
Peptide Amphiphiles ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Self Assembling ◽  
Micro Structures ◽  
Good Agreement

ABSTRACTA coarse-grained model of peptide amphiphiles (PA) dissolved in aqueous solution was presented, where the effects of PA concentration, temperature and shear stress upon the self-assembly of PA were numerically studied by dissipative particle dynamics (DPD) simulation. We technically investigate the repulsion parameter aHW which indicates the repulsion force between the hydrophilic head of PA and water molecules, hence, at the same time, indicating the change in temperature. It was found that aHW played an important role in the self-assembly dynamics and in the resulting micro-structures of PA. By imposing shear strain on the simulation system, the formation of wormlike PA micelles was accelerated. The simulation results were in good agreement with our previous experimental results and the mechanism of shear-induced transition was proposed.

A simple coarse-grained model for self-assembling silk-like protein fibers

2010 ◽  
Vol 144 ◽  
pp. 127-141 ◽  
Author(s):  
Marieke Schor ◽  
Bernd Ensing ◽  
Peter G. Bolhuis
Keyword(s):  
Coarse Grained ◽  
Coarse Grained Model ◽  
Self Assembling ◽  
Protein Fibers

scholarly journals Quantum information probes of charge fractionalization in large-N gauge theories

2021 ◽  
Vol 2021 (5) ◽  
Author(s):  
Brandon S. DiNunno ◽  
Niko Jokela ◽  
Juan F. Pedraza ◽  
Arttu Pönni
Keyword(s):  
Degrees Of Freedom ◽  
Gauge Theories ◽  
Entanglement Entropy ◽  
Coarse Grained ◽  
Strongly Coupled ◽  
Information Theoretic ◽  
Large N ◽  
Wide Range ◽  
Charge Fractionalization ◽  
Electric Flux

Abstract We study in detail various information theoretic quantities with the intent of distinguishing between different charged sectors in fractionalized states of large-N gauge theories. For concreteness, we focus on a simple holographic (2 + 1)-dimensional strongly coupled electron fluid whose charged states organize themselves into fractionalized and coherent patterns at sufficiently low temperatures. However, we expect that our results are quite generic and applicable to a wide range of systems, including non-holographic. The probes we consider include the entanglement entropy, mutual information, entanglement of purification and the butterfly velocity. The latter turns out to be particularly useful, given the universal connection between momentum and charge diffusion in the vicinity of a black hole horizon. The RT surfaces used to compute the above quantities, though, are largely insensitive to the electric flux in the bulk. To address this deficiency, we propose a generalized entanglement functional that is motivated through the Iyer-Wald formalism, applied to a gravity theory coupled to a U(1) gauge field. We argue that this functional gives rise to a coarse grained measure of entanglement in the boundary theory which is obtained by tracing over (part) of the fractionalized and cohesive charge degrees of freedom. Based on the above, we construct a candidate for an entropic c-function that accounts for the existence of bulk charges. We explore some of its general properties and their significance, and discuss how it can be used to efficiently account for charged degrees of freedom across different energy scales.

Insights Into Crowding Effects on Protein Stability From a Coarse-Grained Model

2009 ◽  
Vol 131 (7) ◽  
Author(s):  
Vincent K. Shen ◽  
Jason K. Cheung ◽  
Jeffrey R. Errington ◽  
Thomas M. Truskett
Keyword(s):  
Protein Stability ◽  
Coarse Grained ◽  
Protein Solutions ◽  
Native State ◽  
High Concentration ◽  
Coarse Grained Model ◽  
Excluded Volume Effects ◽  
Thermodynamic Phase ◽  
Broad Interest ◽  
Liquid Liquid Phase Separation

Proteins aggregate and precipitate from high concentration solutions in a wide variety of problems of natural and technological interest. Consequently, there is a broad interest in developing new ways to model the thermodynamic and kinetic aspects of protein stability in these crowded cellular or solution environments. We use a coarse-grained modeling approach to study the effects of different crowding agents on the conformational equilibria of proteins and the thermodynamic phase behavior of their solutions. At low to moderate protein concentrations, we find that crowding species can either stabilize or destabilize the native state, depending on the strength of their attractive interaction with the proteins. At high protein concentrations, crowders tend to stabilize the native state due to excluded volume effects, irrespective of the strength of the crowder-protein attraction. Crowding agents reduce the tendency of protein solutions to undergo a liquid-liquid phase separation driven by strong protein-protein attractions. The aforementioned equilibrium trends represent, to our knowledge, the first simulation predictions for how the properties of crowding species impact the global thermodynamic stability of proteins and their solutions.

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