scholarly journals Erratum: “Multi-particle collision dynamics for a coarse-grained model of soft colloids” [J. Chem. Phys. 151, 074902 (2019)]

2021 ◽  
Vol 154 (7) ◽  
pp. 079901
Author(s):  
José Ruiz-Franco ◽  
Diego Jaramillo-Cano ◽  
Manuel Camargo ◽  
Christos N. Likos ◽  
Emanuela Zaccarelli
Keyword(s):  
Chem Phys ◽  
Coarse Grained ◽  
Particle Collision ◽  
Collision Dynamics ◽  
Coarse Grained Model ◽  
Soft Colloids

scholarly journals Multi-particle collision dynamics for a coarse-grained model of soft colloids

2019 ◽  
Vol 151 (7) ◽  
pp. 074902 ◽  
Author(s):  
José Ruiz-Franco ◽  
Diego Jaramillo-Cano ◽  
Manuel Camargo ◽  
Christos N. Likos ◽  
Emanuela Zaccarelli
Keyword(s):  
Coarse Grained ◽  
Particle Collision ◽  
Collision Dynamics ◽  
Coarse Grained Model ◽  
Soft Colloids

scholarly journals Thermodynamics of adaptive molecular resolution

2016 ◽  
Vol 374 (2080) ◽  
pp. 20160152 ◽  
Author(s):  
R. Delgado-Buscalioni
Keyword(s):  
Free Energy ◽  
Potential Energy ◽  
Local Thermodynamic Equilibrium ◽  
Thermodynamic Formalism ◽  
Energy Difference ◽  
Chem Phys ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Thermodynamic Potentials ◽  
Energy Compensation

A relatively general thermodynamic formalism for adaptive molecular resolution (AMR) is presented. The description is based on the approximation of local thermodynamic equilibrium and considers the alchemic parameter λ as the conjugate variable of the potential energy difference between the atomistic and coarse-grained model Φ = U (1) − U (0) . The thermodynamic formalism recovers the relations obtained from statistical mechanics of H-AdResS (Español et al ., J. Chem. Phys. 142 , 064115, 2015 ( doi:10.1063/1.4907006 )) and provides relations between the free energy compensation and thermodynamic potentials. Inspired by this thermodynamic analogy, several generalizations of AMR are proposed, such as the exploration of new Maxwell relations and how to treat λ and Φ as ‘real’ thermodynamic variables . This article is part of the themed issue ‘Multiscale modelling at the physics–chemistry–biology interface’.

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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