Conformation of Polyalanine and Polyglycine Dications in the Gas Phase: Insight from Ion Mobility Spectrometry and Replica-Exchange Molecular Dynamics

2010 ◽  
Vol 114 (25) ◽  
pp. 6888-6896 ◽  
Author(s):  
Florian Albrieux ◽  
Florent Calvo ◽  
Fabien Chirot ◽  
Aleksey Vorobyev ◽  
Yury O. Tsybin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Gas Phase ◽  
Ion Mobility Spectrometry ◽  
Ion Mobility ◽  
Replica Exchange ◽  
Replica Exchange Molecular Dynamics

scholarly journals Statistical Analysis of Ion Mobility Spectrometry. I. Unbiased and Guided Replica-Exchange Molecular Dynamics

2011 ◽  
Vol 23 (2) ◽  
pp. 386-396 ◽  
Author(s):  
Fabien Chirot ◽  
Florent Calvo ◽  
Florian Albrieux ◽  
Jérôme Lemoine ◽  
Yury O. Tsybin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Statistical Analysis ◽  
Ion Mobility Spectrometry ◽  
Ion Mobility ◽  
Replica Exchange ◽  
Replica Exchange Molecular Dynamics

Effects of electrospray mechanisms and structural relaxation on polylactide ion conformations in the gas phase: insights from ion mobility spectrometry and molecular dynamics simulations

2020 ◽  
Vol 22 (7) ◽  
pp. 4193-4204 ◽  
Author(s):  
Quentin Duez ◽  
Haidy Metwally ◽  
Sébastien Hoyas ◽  
Vincent Lemaur ◽  
Jérôme Cornil ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Gas Phase ◽  
Ion Mobility Spectrometry ◽  
Ion Mobility ◽  
Structural Relaxation ◽  
Structural Features ◽  
Formation Mechanisms ◽  
Dynamics Simulations

Gas-phase polymer ions may retain structural features associated with their electrospray formation mechanisms.

Solution Study of Engineered Quartz Binding Peptides Using Replica Exchange Molecular Dynamics

2010 ◽  
Vol 11 (12) ◽  
pp. 3266-3274 ◽  
Author(s):  
Rebecca Notman ◽  
E. Emre Oren ◽  
Candan Tamerler ◽  
Mehmet Sarikaya ◽  
Ram Samudrala ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Replica Exchange ◽  
Replica Exchange Molecular Dynamics ◽  
Solution Study ◽  
Binding Peptides

scholarly journals Insights into the Folding and Unfolding Processes of Wild-Type and Mutated SH3 Domain by Molecular Dynamics and Replica Exchange Molecular Dynamics Simulations

PLoS ONE ◽  
2013 ◽  
Vol 8 (5) ◽  
pp. e64886 ◽  
Author(s):  
Wen-Ting Chu ◽  
Ji-Long Zhang ◽  
Qing-Chuan Zheng ◽  
Lin Chen ◽  
Hong-Xing Zhang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Sh3 Domain ◽  
Replica Exchange ◽  
Wild Type ◽  
Replica Exchange Molecular Dynamics ◽  
Dynamics Simulations

Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent

2016 ◽  
Vol 18 (18) ◽  
pp. 13052-13065 ◽  
Author(s):  
Emanuel K. Peter ◽  
Joan-Emma Shea ◽  
Igor V. Pivkin
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Protein Folding ◽  
Kinetic Monte Carlo ◽  
Replica Exchange ◽  
Replica Exchange Molecular Dynamics ◽  
Accelerated Simulation ◽  
Explicit Solvent ◽  
Exchange Algorithms

In this paper, we present a coarse replica exchange molecular dynamics (REMD) approach, based on kinetic Monte Carlo (kMC).

Sign in / Sign up

Export Citation Format

Share Document