Permeation Rates of Oxygen through a Lipid Bilayer Using Replica Exchange Transition Interface Sampling

2020 ◽  
Author(s):  
Enrico Riccardi ◽  
Andreas Krämer ◽  
Titus S. van Erp ◽  
An Ghysels
Keyword(s):  
Lipid Bilayer ◽  
Replica Exchange ◽  
Transition Interface

scholarly journals Foundations and latest advances in replica exchange transition interface sampling

2017 ◽  
Vol 147 (15) ◽  
pp. 152722 ◽  
Author(s):  
Raffaela Cabriolu ◽  
Kristin M. Skjelbred Refsnes ◽  
Peter G. Bolhuis ◽  
Titus S. van Erp
Keyword(s):  
Replica Exchange ◽  
Transition Interface

scholarly journals OpenPathSampling: A Python framework for path sampling simulations. II. Building and customizing path ensembles and sample schemes

2018 ◽  
Author(s):  
David W.H. Swenson ◽  
Jan-Hendrik Prinz ◽  
Frank Noe ◽  
John D. Chodera ◽  
Peter G. Bolhuis
Keyword(s):  
Companion Paper ◽  
Replica Exchange ◽  
Path Sampling ◽  
Transition Path ◽  
Transition Path Sampling ◽  
Molecular Systems ◽  
Sampling Algorithms ◽  
Basic Concepts ◽  
Transition Interface ◽  
Theoretical Developments

The OpenPathSampling (OPS) package provides an easy-to-use framework to apply transition path sampling methodologies to complex molecular systems with a minimum of effort. Yet, the extensibility of OPS allows for the exploration of new path sampling algorithms by building on a variety of basic operations. In a companion paper [Swenson et al 2018] we introduced the basic concepts and the structure of the OPS package, and how it can be employed to perform standard transition path sampling and (replica exchange) transition interface sampling. In this paper, we elaborate on two theoretical developments that went into the design of OPS. The first development relates to the construction of path ensembles, the what is being sampled. We introduce a novel set-based notation forthepath ensemble, which provides an alternative paradigm for constructing path ensembles, and allows building arbitrarily complex path ensembles from fundamental ones. The second fundamental development is the structure for the customisation of Monte Carlo procedures; how path ensembles are being sampled. We describe in detail the OPS objects that implement this approach to customization, the MoveScheme and the PathMover, and provide tools to create and manipulate these objects. We illustrate both the path ensemble building and sampling scheme customization with several examples. OPS thus facilitates both standard path sampling application in complex systems as well as the development of new path sampling methodology, beyond the default.

scholarly journals Rare event simulations reveal subtle key steps in aqueous silicate condensation

2017 ◽  
Vol 19 (20) ◽  
pp. 13361-13371 ◽  
Author(s):  
Mahmoud Moqadam ◽  
Enrico Riccardi ◽  
Thuat T. Trinh ◽  
Anders Lervik ◽  
Titus S. van Erp
Keyword(s):  
Molecular Dynamics ◽  
Rare Event ◽  
Replica Exchange ◽  
Condensation Process ◽  
Early Stages ◽  
Key Steps ◽  
Rare Event Simulations ◽  
Event Simulations ◽  
Transition Interface

A replica exchange transition interface sampling (RETIS) study combined with Born–Oppenheimer molecular dynamics (BOMD) is used to investigate the dynamics, thermodynamics and the mechanism of the early stages of the silicate condensation process.

Nano-pore Lipid Bilayer Formed by Self-spreading Method

2019 ◽  
Vol 139 (10) ◽  
pp. 1146-1152
Author(s):  
Zugui Peng ◽  
Kenta Shimba ◽  
Yoshitaka Miyamoto ◽  
Tohru Yagi
Keyword(s):  
Lipid Bilayer
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