Mesoscale modeling of cement matrix using the concept of building block

2015 ◽  
Vol 1759 ◽  
Author(s):  
Denvid Lau ◽  
Zechuan Yu ◽  
Oral Buyukozturk
Keyword(s):  
Cement Paste ◽  
Building Block ◽  
Time Scale ◽  
Modeling Technique ◽  
Coarse Grained ◽  
Cement Matrix ◽  
Computing Power ◽  
Coarse Grained Model ◽  
Atomistic Models ◽  
Extended Length

ABSTRACTCalcium silicate hydrate (C-S-H) gel is the cohesive phase in cement paste and critically controls the cement hydration. Atomistic models can reproduce reasonable structural and mechanical properties of C-S-H gel at the nano scale. However, the length and time scale of such all-atom modeling technique are restrained by limited computing power. Under this context, coarse-grained modeling technique emerges as a useful alternative for investigating cement paste at extended length and time scale. Here, we regard the building block of cement as ellipsoid and develop a coarse-grained model of cement matrix based on the Gay-Berne (GB) potential. Emphasis of the present paper is on the parameterization and interpretation of the GB potential formula.

Parameterization of a coarse-grained model with short-ranged interactions for modeling fuel cell membranes with controlled water uptake

2017 ◽  
Vol 19 (27) ◽  
pp. 17698-17707 ◽  
Author(s):  
Jibao Lu ◽  
Chance Miller ◽  
Valeria Molinero
Keyword(s):  
Fuel Cell ◽  
Activity Coefficient ◽  
Water Uptake ◽  
Coarse Grained ◽  
Fuel Cell Membranes ◽  
Coarse Grained Model ◽  
Experimental Activity ◽  
Tetramethylammonium Chloride ◽  
Atomistic Models ◽  
Wide Range

The coarse-grained model FFpvap reproduces the experimental activity coefficient of water in tetramethylammonium chloride solutions over a wide range of concentrations, with a hundred-fold gain in computing efficiency with respect to atomistic models.

scholarly journals Single-molecule biophysics experiments in silico: Towards a physical model of a replisome

2021 ◽  
Author(s):  
Christopher Maffeo ◽  
Han-Yi Chou ◽  
Aleksei Aksimentiev
Keyword(s):  
Single Molecule ◽  
In Silico ◽  
Computational Models ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Test Bed ◽  
Computing Power ◽  
Coarse Grained Model ◽  
Biomolecular Dynamics ◽  
Single Molecule Studies

AbstractThe interpretation of single-molecule experiments is frequently aided by computational modeling of biomolecular dynamics. The growth of computing power and ongoing validation of computational models suggest that it soon may be possible to replace some experiments out-right with computational mimics. Here we offer a blueprint for performing single-molecule studies in silico using a DNA binding protein as a test bed. We demonstrate how atomistic simulations, typically limited to sub-millisecond durations and zeptoliter volumes, can guide development of a coarse-grained model for use in simulations that mimic experimental assays. We show that, after initially correcting excess attraction between the DNA and protein, qualitative consistency between several experiments and their computational equivalents is achieved, while additionally providing a detailed portrait of the underlying mechanics. Finally the model is used to simulate the trombone loop of a replication fork, a large complex of proteins and DNA.

scholarly journals Coarse-Grained Model of the SNARE Complex Shows that Quick Zippering Requires Partial Assembly

2018 ◽  
Author(s):  
N. Fortoul ◽  
M. Bykhovskaia ◽  
A. Jagota
Keyword(s):  
Single Molecule ◽  
Time Scale ◽  
Membrane Vesicles ◽  
Vesicle Fusion ◽  
Separation Distance ◽  
Snare Complex ◽  
Coarse Grained ◽  
Complex Needs ◽  
Coarse Grained Model ◽  
Dynamics Simulations

ABSTRACTNeuronal transmitters are released from nerve terminals via the fusion of synaptic vesicles with the presynaptic membrane. Vesicles become attached to the membrane via the SNARE complex. The SNARE complex comprises the vesicle associate protein Synaptobrevin (Syb), the membrane associated protein syntaxin (Syx), and the cytosolic protein SNAP25, which together form a four-helical bundle. The full assembly of Syb onto the core SNARE bundle promotes vesicle fusion. We investigated SNARE assembly using a coarse-grained model of the SNARE complex. The model retains chemical specificity, and was calibrated using single molecule experiments and all-atom molecular dynamics simulations. Steered force-control simulations of SNARE unzippering by peeling off Syb were used to set up initial disassembled states of the SNARE complex. From these states, the assembly process was simulated. We found that if Syb is in helical form, then the SNARE complex assembles rapidly, on a sub-microsecond time-scale. We found that assembly times grow exponentially with separation distance between Syb and Syx C-termni. The formation of helical turns is likely to substantially decelerate the assembly, consistent with single molecule force experiments that show SNARE assembly duration on the time-scale of hundreds of ms. Since synaptic vesicle fusion occurs at a sub-millisecond time-scale, our results indicate that for biologically relevant rapid assembly the SNARE complex needs to be partially zippered and its constituent helices brought into proximity, possibly by means of molecular chaperones.

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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