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.

Computational Investigations of the Transmembrane Italian-Mutant (E22K) 3A\(\beta_{11 - 40}\) in Aqueous Solution

2018 ◽  
Vol 28 (3) ◽  
pp. 265 ◽  
Author(s):  
Son Tung Ngo
Keyword(s):  
Structural Changes ◽  
Replica Exchange ◽  
Aβ Oligomers ◽  
Replica Exchange Molecular Dynamics ◽  
Charged Residue ◽  
Intermolecular Contacts ◽  
Structural Details ◽  
Positively Charged ◽  
Dynamic Fluctuation ◽  
Good Agreement

The Amyloid beta (Aβ) oligomers are characterized as critical cytotoxic materials in Alzheimer’s disease (AD) pathogenesis. Structural details of transmembrane oligomers are inevitably necessary to design/search potential inhibitor due to treat AD. However, the experimental detections for structural modify of low-order Aβ oligomers are precluded due to the extremely dynamic fluctuation of the oligomers. In this project, the transmembrane Italian-mutant (E22K) 3Aβ11-40 (tmE22K 3Aβ11-40) was extensively investigated upon the temperature replica exchange molecular dynamics (REMD) simulations. The structural changes of the trimer when replacing the negative charged residue E22 by a positively charged residue K were monitored over simulation intervals. The oligomer size was turned to be larger and the increase of β-content was recorded. The momentous gain of intermolecular contacts with DPPC molecules implies that tmE22K 3Aβ11-40 easier self-inserts into the membrane than the WT one. Furthermore, the tighter interaction between constituting monomers was indicated implying that the E22K mutation probably enhances the Aβ fibril formation. The results are in good agreement with experiments that E22K amyloid is self-aggregate faster than the WT form. Details information of tmE22K trimer structure and kinetics probably yield the understanding of AD mechanism.

Rare event simulation

2017 ◽  
Author(s):  
Michael P. Allen ◽  
Dominic J. Tildesley
Keyword(s):  
Rare Event ◽  
Path Sampling ◽  
Rapid Progress ◽  
Computationally Efficient ◽  
Transition Path ◽  
Transition Path Sampling ◽  
Event Simulation ◽  
Reaction Coordinates ◽  
Simulation Techniques ◽  
Transition Interface

The development of techniques to simulate infrequent events has been an area of rapid progress in recent years. In this chapter, we shall discuss some of the simulation techniques developed to study the dynamics of rare events. A basic summary of the statistical mechanics of barrier crossing is followed by a discussion of approaches based on the identification of reaction coordinates, and those which seek to avoid prior assumptions about the transition path. The demanding technique of transition path sampling is introduced and forward flux sampling and transition interface sampling are considered as rigorous but computationally efficient approaches.

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