Statistical Mechanical Model of Topological Fluctuations and the Intermediate Phase in Binary Phosphate Glasses

2019 ◽  
Vol 123 (35) ◽  
pp. 7640-7648 ◽  
Author(s):  
Katelyn A. Kirchner ◽  
Mikkel S. Bødker ◽  
Morten M. Smedskjaer ◽  
Seong H. Kim ◽  
John C. Mauro
Keyword(s):  
Mechanical Model ◽  
Intermediate Phase ◽  
Phosphate Glasses ◽  
Statistical Mechanical Model ◽  
Statistical Mechanical ◽  
Topological Fluctuations

A statistical mechanical model for inverse melting

2003 ◽  
Vol 119 (8) ◽  
pp. 4582-4591 ◽  
Author(s):  
Melissa R. Feeney ◽  
Pablo G. Debenedetti ◽  
Frank H. Stillinger
Keyword(s):  
Mechanical Model ◽  
Statistical Mechanical Model ◽  
Statistical Mechanical

scholarly journals Cooperativity and modularity in protein folding

2016 ◽  
Author(s):  
Masaki Sasai ◽  
George Chikenji ◽  
Tomoki P. Terada
Keyword(s):  
Protein Folding ◽  
Mechanical Model ◽  
Energy Landscape ◽  
Native Conformation ◽  
Folding Nucleus ◽  
Modern Methods ◽  
Complex Topology ◽  
Statistical Mechanical Model ◽  
Statistical Mechanical ◽  
Dynamical Features

AbstractA simple statistical mechanical model proposed by Wako and Saitô has explained the aspects of protein folding surprisingly well. This model was systematically applied to multiple proteins by Muñoz and Eaton and has since been referred to as the Wako-Saitô-Muñoz-Eaton (WSME) model. The success of the WSME model in explaining the folding of many proteins has verified the hypothesis that the folding is dominated by native interactions, which makes the energy landscape globally biased toward native conformation. Using the WSME and other related models, Saitô emphasized the importance of the hierarchical pathway in protein folding; folding starts with the creation of contiguous segments having a native-like configuration and proceeds as growth and coalescence of these segments. The ϕ-values calculated for barnase with the WSME model suggested that segments contributing to the folding nucleus are similar to the structural modules defined by the pattern of native atomic contacts. The WSME model was extended to explain folding of multi-domain proteins having a complex topology, which opened the way to comprehensively understanding the folding process of multi-domain proteins. The WSME model was also extended to describe allosteric transitions, indicating that the allosteric structural movement does not occur as a deterministic sequential change between two conformations but as a stochastic diffusive motion over the dynamically changing energy landscape. Statistical mechanical viewpoint on folding, as highlighted by the WSME model, has been renovated in the context of modern methods and ideas, and will continue to provide insights on equilibrium and dynamical features of proteins.

scholarly journals Statistical Mechanical Model of Gas Adsorption in a Metal-Organic Framework Harboring a Rotaxane Molecular Shuttle

2020 ◽  
Author(s):  
Jonathan Carney ◽  
David Roundy ◽  
Cory M. Simon
Keyword(s):  
Mechanical Model ◽  
Gas Adsorption ◽  
Adsorption Properties ◽  
Temperature Sensitive ◽  
Adsorption Model ◽  
Adsorption Sites ◽  
Statistical Mechanical Model ◽  
Metal Organic ◽  
Statistical Mechanical ◽  
Molecular Shuttle

Metal-organic frameworks (MOFs) are modular and tunable nano-porous materials with applications in gas storage, separations, and sensing. Flexible/dynamic components that respond to adsorbed gas can give MOFs unique or enhanced adsorption properties. Here, we explore the adsorption properties that could be imparted to a MOF by a rotaxane molecular shuttle (RMS) in its pores. In the unit cell of an RMS-MOF, a macrocyclic wheel is mechanically interlocked with a strut of the MOF scaffold. The wheel shuttles between stations on the strut that are also gas adsorption sites. At a level of abstraction similar to the seminal Langmuir adsorption model, we pose and analyze a simple statistical mechanical model of gas adsorption in an RMS-MOF that accounts for (i) wheel/gas competition for sites on the strut and (ii) gas-induced changes in the configurational entropy of the shuttling wheel. We determine how the amount of gas adsorbed, position of the wheel, and differential energy of adsorption depend on temperature, pressure, and the interactions of the gas/wheel with the stations. Our model reveals that, compared to a rigid, Langmuir material, the chemistry of the RMS-MOF can be tuned to render gas adsorption more or less temperature-sensitive and to release more or less heat upon adsorption. The model also uncovers a non-monotonic relationship between the temperature and the position of the wheel if gas out-competes the wheel for its preferable station.

DNA CURVATURE OF (CCTG)n · (CAGG)n AND (ATTCT)n · (AGAAT)n REPEATS SEQUENCES

2005 ◽  
Vol 19 (15n17) ◽  
pp. 2921-2926
Author(s):  
Lu CAI
Keyword(s):  
Experimental Data ◽  
Theoretical Prediction ◽  
Mechanical Model ◽  
Polyacrylamide Gel ◽  
Human Diseases ◽  
Dna Curvature ◽  
Statistical Mechanical Model ◽  
Statistical Mechanical

A statistical mechanical model was used to calculate the curvature of the 5 chemically synthesized DNAs which contain repeats sequences ( CCTG )n · ( CAGG )n and ( ATTCT )n · ( AGAAT )n associated with human diseases. 8% polyacrylamide gel analyses were also performed for these 5 DNAs. The results indicate the curvature of the sequences CCTG/bend and ATTCT/bend are larger than that of the sequences CCTG/straight and ATTCT/straight. The curvature of straight/bend is larger than that of CCTG/straight and ATTCT/straight, and smaller than that of CCTG/bend and ATTCT/bend. There exists good consistent between theoretical prediction and experimental data.

scholarly journals Structural Characterization and Statistical-Mechanical Model of Epidermal Patterns

2016 ◽  
Vol 111 (11) ◽  
pp. 2534-2545 ◽  
Author(s):  
Duyu Chen ◽  
Wen Yih Aw ◽  
Danelle Devenport ◽  
Salvatore Torquato
Keyword(s):  
Structural Characterization ◽  
Mechanical Model ◽  
Statistical Mechanical Model ◽  
Statistical Mechanical

Statistical mechanical model for the formation of octahedral silicon in phosphosilicate glasses

2021 ◽  
Author(s):  
Mikkel L. Bødker ◽  
Johan B. Pedersen ◽  
Francisco Muñoz ◽  
John C. Mauro ◽  
Morten M. Smedskjaer
Keyword(s):  
Mechanical Model ◽  
Statistical Mechanical Model ◽  
Statistical Mechanical
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