Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study

2003 ◽  
Vol 24 (12) ◽  
pp. 1432-1436 ◽  
Author(s):  
Bojan Zagrovic ◽  
Vijay Pande
Keyword(s):  
Distributed Computing ◽  
Folding Rate ◽  
Small Protein ◽  
Solvent Viscosity ◽  
Viscosity Dependence

scholarly journals Frictional effects on RNA folding: Speed limit and Kramers turnover

2018 ◽  
Author(s):  
Naoto Hori ◽  
Natalia A. Denesyuk ◽  
D. Thirumalai
Keyword(s):  
Single Molecule ◽  
Rna Folding ◽  
Theoretical Estimate ◽  
Speed Limit ◽  
Free Energy Barrier ◽  
Folding Rate ◽  
Solvent Viscosity ◽  
Folding Rates ◽  
Friction Regime ◽  
Frictional Effects

AbstractWe investigated frictional effects on the folding rates of a human Telomerase hairpin (hTR HP) and H-type pseudoknot from the Beet Western Yellow Virus (BWYV PK) using simulations of the Three Interaction Site (TIS) model for RNA. The heat capacity from TIS model simulations, calculated using temperature replica exchange simulations, reproduces nearly quantitatively the available experimental data for the hTR HP. The corresponding results for BWYV PK serve as predictions. We calculated the folding rates (kFs) from more than 100 folding trajectories for each value of the solvent viscosity (η) at a fixed salt concentration of 200 mM. Using the theoretical estimate ( where N is number of nucleotides) for folding free energy barrier, kF data for both the RNAs are quantitatively fit using one dimensional Kramers’ theory with two parameters specifying the curvatures in the unfolded basin and the barrier top. In the high-friction regime (η ≳ 10−5 Pa·s), for both HP and PK, kFs decrease as 1/η whereas in the low friction regime kFs increase as η increases, leading to a maximum folding rate at a moderate viscosity (~ 10−6 Pa·s), which is the Kramers turnover. From the fits, we find that the speed limit to RNA folding at water viscosity is between (1 − 4)μs, which is in accord with our previous theoretical prediction as well as results from several single molecule experiments. Both the RNA constructs fold by parallel pathways. Surprisingly, we find that the flux through the pathways could be altered by changing solvent viscosity, a prediction that is more easily testable in RNA than proteins.

Power Consumption Evaluation of Distributed Computing Network Considering Traffic Locality

2012 ◽  
Vol E95.B (8) ◽  
pp. 2538-2548
Author(s):  
Yukio OGAWA ◽  
Go HASEGAWA ◽  
Masayuki MURATA
Keyword(s):  
Distributed Computing ◽  
Power Consumption

Matlab and Parallel Computing

2012 ◽  
Vol 17 (4) ◽  
pp. 207-216 ◽  
Author(s):  
Magdalena Szymczyk ◽  
Piotr Szymczyk
Keyword(s):  
Image Processing ◽  
Signal Processing ◽  
Parallel Computing ◽  
Distributed Computing ◽  
Control Systems ◽  
High Performance ◽  
Parallel Applications ◽  
Process Simulations ◽  
Key Features ◽  
Financial Process

Abstract The MATLAB is a technical computing language used in a variety of fields, such as control systems, image and signal processing, visualization, financial process simulations in an easy-to-use environment. MATLAB offers "toolboxes" which are specialized libraries for variety scientific domains, and a simplified interface to high-performance libraries (LAPACK, BLAS, FFTW too). Now MATLAB is enriched by the possibility of parallel computing with the Parallel Computing ToolboxTM and MATLAB Distributed Computing ServerTM. In this article we present some of the key features of MATLAB parallel applications focused on using GPU processors for image processing.

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