Influence of the Molecular Surface Characteristics of the Diastereoisomers of a Quartet Molecule on their Physicochemical Properties: A Linear Solvation Free-Energy Study

1999 ◽  
Vol 5 (12) ◽  
pp. 3533-3548 ◽  
Author(s):  
Nora Ventosa ◽  
Daniel Ruiz-Molina ◽  
Josep Sedó ◽  
Concepció Rovira ◽  
Xavier Tomas ◽  
...  
Keyword(s):  
Free Energy ◽  
Physicochemical Properties ◽  
Surface Characteristics ◽  
Solvation Free Energy ◽  
Molecular Surface ◽  
Linear Solvation

GPU-Accelerated Computation of Solvation Free Energy for Kinetostatic Protein Folding Simulation

2013 ◽  
Author(s):  
Morad Behandish ◽  
Pouya Tavousi ◽  
Horea T. Ilieş ◽  
Kazem Kazerounian
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Graphics Processing Units ◽  
Solvation Free Energy ◽  
Van Der Waals Interactions ◽  
Molecular Surface ◽  
Efficient Computation ◽  
Performance Improvements ◽  
Folding Simulation ◽  
Computational Bottleneck

A realistic computer simulation of protein folding requires a comprehensive account of interaction energetics, placing a substantial demand on processing power. This paper presents an improved computational framework for protein folding software package PROTOFOLD, that enables efficient computation of solvation free energy effects in addition to Coulombic and van der Waals interactions. Efficient data structures have been utilized to speed-up the sequential running times from O(n2) to O(n), n being the number of atoms. It turns out, however, that an accurate evaluation of molecular surface areas characterizing the solvation effects imposes a computational bottleneck to the entire simulation. Massive computational power offered by Graphics Processing Units (GPU) was exploited to develop a simple and efficient Single-Instruction Multiple-Thread (SIMT) algorithm for the latter step. The running times were monitored for different steps of the folding simulation for different molecular sizes. Significant performance improvements were observed, yielding promising results where numerous iterative runs are needed.

A Linear Solvation Free Energy Relationship Analysis of Solubilization in Mixed Cationic−Nonionic Micelles

Langmuir ◽  
1999 ◽  
Vol 15 (20) ◽  
pp. 6770-6774 ◽  
Author(s):  
Magali A. Rodrigues ◽  
Elena O. Alonso ◽  
Chang Yihwa ◽  
João P. S. Farah ◽  
Frank H. Quina
Keyword(s):  
Free Energy ◽  
Solvation Free Energy ◽  
Relationship Analysis ◽  
Linear Solvation

To the fast calculation of the solvation free energy. Combining expanded ensembles with L2MC

2021 ◽  
Vol 42 (11) ◽  
pp. 787-792
Author(s):  
Alexei Nikitin ◽  
Vladislava Milchevskaya ◽  
Alexander Lyubartsev
Keyword(s):  
Free Energy ◽  
Solvation Free Energy ◽  
Fast Calculation

scholarly journals Application of reference-modified density functional theory: Temperature and pressure dependences of solvation free energy

2017 ◽  
Vol 39 (4) ◽  
pp. 202-217 ◽  
Author(s):  
Tomonari Sumi ◽  
Yutaka Maruyama ◽  
Ayori Mitsutake ◽  
Kenji Mochizuki ◽  
Kenichiro Koga
Keyword(s):  
Density Functional Theory ◽  
Free Energy ◽  
Density Functional ◽  
Solvation Free Energy ◽  
Functional Theory ◽  
Temperature And Pressure
Sign in / Sign up

Export Citation Format

Share Document