1
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Vervust W, Zhang DT, Ghysels A, Roet S, van Erp TS, Riccardi E. PyRETIS 3: Conquering rare and slow events without boundaries. J Comput Chem 2024; 45:1224-1234. [PMID: 38345082 DOI: 10.1002/jcc.27319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 04/19/2024]
Abstract
We present and discuss the advancements made in PyRETIS 3, the third instalment of our Python library for an efficient and user-friendly rare event simulation, focused to execute molecular simulations with replica exchange transition interface sampling (RETIS) and its variations. Apart from a general rewiring of the internal code towards a more modular structure, several recently developed sampling strategies have been implemented. These include recently developed Monte Carlo moves to increase path decorrelation and convergence rate, and new ensemble definitions to handle the challenges of long-lived metastable states and transitions with unbounded reactant and product states. Additionally, the post-analysis software PyVisa is now embedded in the main code, allowing fast use of machine-learning algorithms for clustering and visualising collective variables in the simulation data.
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Affiliation(s)
- Wouter Vervust
- IBiTech-BioMMedA Group, Ghent University, Ghent, Belgium
| | - Daniel T Zhang
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
| | - An Ghysels
- IBiTech-BioMMedA Group, Ghent University, Ghent, Belgium
| | - Sander Roet
- Department of Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Titus S van Erp
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
| | - Enrico Riccardi
- Department of Energy Resources, University of Stavanger, Stavanger, Norway
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2
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Vervust W, Zhang DT, van Erp TS, Ghysels A. Path sampling with memory reduction and replica exchange to reach long permeation timescales. Biophys J 2023; 122:2960-2972. [PMID: 36809877 PMCID: PMC10398259 DOI: 10.1016/j.bpj.2023.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/13/2023] [Accepted: 02/15/2023] [Indexed: 02/23/2023] Open
Abstract
Assessing kinetics in biological processes with molecular dynamics simulations remains a computational and conceptual challenge, given the large time and length scales involved. For kinetic transport of biochemical compounds or drug molecules, the permeability through the phospholipid membranes is a key kinetic property, but long timescales are hindering the accurate computation. Technological advances in high-performance computing therefore need to be accompanied by theoretical and methodological developments. In this contribution, the replica exchange transition interface sampling (RETIS) methodology is shown to give perspective toward observing longer permeation pathways. It is first reviewed how RETIS, a path-sampling methodology that gives in principle exact kinetics, can be used to compute membrane permeability. Next, recent and current developments in three RETIS aspects are discussed: several new Monte Carlo moves in the path-sampling algorithm, memory reduction by reducing pathlengths, and exploitation of parallel computing with CPU-imbalanced replicas. Finally, the memory reduction presenting a new replica exchange implementation, coined REPPTIS, is showcased with a permeant needing to pass a membrane with two permeation channels, either representing an entropic or energetic barrier. The REPPTIS results showed clearly that inclusion of some memory and enhancing ergodic sampling via replica exchange moves are both necessary to obtain correct permeability estimates. In an additional example, ibuprofen permeation through a dipalmitoylphosphatidylcholine membrane was modeled. REPPTIS succeeded in estimating the permeability of this amphiphilic drug molecule with metastable states along the permeation pathway. In conclusion, the presented methodological advances allow for deeper insight into membrane biophysics even if the pathways are slow, as RETIS and REPPTIS push the permeability calculations to longer timescales.
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Affiliation(s)
- Wouter Vervust
- IBiTech - Biommeda Research Group, Faculty of Engineering and Architecture, Ghent University, Gent, Belgium
| | - Daniel T Zhang
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
| | - Titus S van Erp
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
| | - An Ghysels
- IBiTech - Biommeda Research Group, Faculty of Engineering and Architecture, Ghent University, Gent, Belgium.
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3
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Zhang DT, Riccardi E, van Erp TS. Enhanced path sampling using subtrajectory Monte Carlo moves. J Chem Phys 2023; 158:024113. [PMID: 36641412 DOI: 10.1063/5.0127249] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Path sampling allows the study of rare events, such as chemical reactions, nucleation, and protein folding, via a Monte Carlo (MC) exploration in path space. Instead of configuration points, this method samples short molecular dynamics (MD) trajectories with specific start- and end-conditions. As in configuration MC, its efficiency highly depends on the types of MC moves. Since the last two decades, the central MC move for path sampling has been the so-called shooting move in which a perturbed phase point of the old path is propagated backward and forward in time to generate a new path. Recently, we proposed the subtrajectory moves, stone-skipping (SS) and web-throwing, that are demonstrably more efficient. However, the one-step crossing requirement makes them somewhat more difficult to implement in combination with external MD programs or when the order parameter determination is expensive. In this article, we present strategies to address the issue. The most generic solution is a new member of subtrajectory moves, wire fencing (WF), that is less thrifty than the SS but more versatile. This makes it easier to link path sampling codes with external MD packages and provides a practical solution for cases where the calculation of the order parameter is expensive or not a simple function of geometry. We demonstrate the WF move in a double-well Langevin model, a thin film breaking transition based on classical force fields, and a smaller ruthenium redox reaction at the ab initio level in which the order parameter explicitly depends on the electron density.
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Affiliation(s)
- Daniel T Zhang
- Norwegian University of Science and Technology, Department of Chemistry, NO-7491 Trondheim, Norway
| | - Enrico Riccardi
- Department of Informatics, UiO, Gaustadalléen 23B, 0373 Oslo, Norway
| | - Titus S van Erp
- Norwegian University of Science and Technology, Department of Chemistry, NO-7491 Trondheim, Norway
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4
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Burgin T, Ellis S, Mayes HB. ATESA: An Automated Aimless Shooting Workflow. J Chem Theory Comput 2023; 19:235-244. [PMID: 36520006 DOI: 10.1021/acs.jctc.2c00543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Transition path sampling methods are powerful tools for studying the dynamics of rare events in molecular simulations. However, these methods are generally restricted to experts with the knowledge and resources to properly set up and analyze the often hundreds of thousands of simulations that constitute a complete study. Aimless Transition Ensemble Sampling and Analysis (ATESA) is a new open-source software program written in Python that automates a full transition path sampling workflow based on the aimless shooting algorithm, streamlining the process and reducing the barrier to use for researchers new to this approach. This introduction to ATESA includes a demonstration of a complete transition path sampling process flow for an example reaction, including finding an initial transition state, sampling with aimless shooting, building a reaction coordinate with inertial likelihood maximization, verifying that coordinate with committor analysis, and measuring the reaction energy profile with umbrella sampling. We also describe our implementation of a termination criterion for aimless shooting based on the Godambe information calculated during model building with likelihood maximization as well as a novel approach to constraining simulations to the desired rare event pathway during umbrella sampling.
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Affiliation(s)
- Tucker Burgin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Samuel Ellis
- The Molecular Sciences Software Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24060, United States.,Department of Chemistry, Virginia Tech University, Blacksburg, Virginia 24061, United States
| | - Heather B Mayes
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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5
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Hall SW, Díaz Leines G, Sarupria S, Rogal J. Practical guide to replica exchange transition interface sampling and forward flux sampling. J Chem Phys 2022; 156:200901. [DOI: 10.1063/5.0080053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Path sampling approaches have become invaluable tools to explore the mechanisms and dynamics of the so-called rare events that are characterized by transitions between metastable states separated by sizable free energy barriers. Their practical application, in particular to ever more complex molecular systems, is, however, not entirely trivial. Focusing on replica exchange transition interface sampling (RETIS) and forward flux sampling (FFS), we discuss a range of analysis tools that can be used to assess the quality and convergence of such simulations, which is crucial to obtain reliable results. The basic ideas of a step-wise evaluation are exemplified for the study of nucleation in several systems with different complexities, providing a general guide for the critical assessment of RETIS and FFS simulations.
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Affiliation(s)
- Steven W. Hall
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Grisell Díaz Leines
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridgeshire CB2 1EW, United Kingdom
| | - Sapna Sarupria
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, USA
| | - Jutta Rogal
- Department of Chemistry, New York University, New York, New York 10003, USA
- Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
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6
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Lervik A, Svenum IH, Wang Z, Cabriolu R, Riccardi E, Andersson S, van Erp TS. The role of pressure and defects in the wurtzite to rock salt transition in cadmium selenide. Phys Chem Chem Phys 2022; 24:8378-8386. [PMID: 35332892 DOI: 10.1039/d1cp05051f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using molecular dynamics and path sampling techniques we investigated the effect of pressure and defects in the wurtzite to rock salt transition in cadmium selenide (CdSe). In the pressure range 2-10 GPa, rate constants of transition are in the order of 10-23 to 105 s-1 for the transformation of a relatively small wurtzite crystal consisting of 1024 atoms with periodic boundary conditions. The transition paths predominantly evolve through an intermediate 5-coordinated structure, as reported before, though its typical lifetime within the transition paths is particularly long in the intermediate pressure range (4-6 GPa). The defects were created by removing Cd-Se pairs from an otherwise perfect crystal. The removals were either selected fully randomized or grouped in clusters (cavity creation). We find that the rate of transition due to the defects increases by several orders of magnitude even for a single pair removal. This is caused by a change in the transition mechanism that no longer proceeds via the intermediate 5-coordinated structure, when defects are present. Further, the cavity creation yields a lower rate than the fully randomized removal.
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Affiliation(s)
- Anders Lervik
- Department of Chemistry, Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway.
| | - Ingeborg-Helene Svenum
- Department of Materials and Nanotechnology, SINTEF Industry, P.O. Box 4760 Torgarden, 7465 Trondheim, Norway
| | - Zhaohui Wang
- Department of Metal Production and Processing, SINTEF Industry, P.O. Box 4760 Torgarden, 7465 Trondheim, Norway
| | - Raffaela Cabriolu
- Department of Chemistry, Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway. .,Department of Physics, Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway
| | - Enrico Riccardi
- Department of Chemistry, Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway. .,Department of Informatics, UiO, Gaustadalléen 23B, 0373 Oslo, Norway
| | - Stefan Andersson
- Department of Metal Production and Processing, SINTEF Industry, P.O. Box 4760 Torgarden, 7465 Trondheim, Norway
| | - Titus S van Erp
- Department of Chemistry, Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway.
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7
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Thin film breakage in oil–in–water emulsions, a multidisciplinary study. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2021.127808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Roet S, Daub CD, Riccardi E. Chemistrees: Data-Driven Identification of Reaction Pathways via Machine Learning. J Chem Theory Comput 2021; 17:6193-6202. [PMID: 34555907 PMCID: PMC8515787 DOI: 10.1021/acs.jctc.1c00458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
We propose to analyze
molecular dynamics (MD) output via a supervised machine
learning (ML) algorithm, the decision tree.
The approach aims to identify the predominant geometric features which
correlate with trajectories that transition between two arbitrarily
defined states. The data-driven algorithm aims to identify these features
without the bias of human “chemical intuition”. We demonstrate
the method by analyzing the proton exchange reactions in formic acid
solvated in small water clusters. The simulations were performed with ab initio MD combined with a method to efficiently sample
the rare event, path sampling. Our ML analysis identified relevant
geometric variables involved in the proton transfer reaction and how
they may change as the number of solvating water molecules changes.
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Affiliation(s)
- Sander Roet
- Department of Chemistry, Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway
| | - Christopher D Daub
- Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Enrico Riccardi
- Department of Informatics, UiO, Gaustadalléen 23B, 0373 Oslo, Norway
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9
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Davoudi S, Ghysels A. Sampling efficiency of the counting method for permeability calculations estimated with the inhomogeneous solubility-diffusion model. J Chem Phys 2021; 154:054106. [PMID: 33557559 DOI: 10.1063/5.0033476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Permeability is a key property in various fields such as membrane technology for chemical separation and transport of substances through cell membranes. At the molecular scale, the counting method uses the number of membrane crossings in a conventional unbiased molecular dynamics simulation to predict the permeability. This contribution investigates under which conditions the counting method has insufficient statistics. An equation is derived for a compartmental model based on the inhomogeneous solubility-diffusion (Smoluchowski) model, giving insight into how the flux correlates with the solubility of permeants. This equation shows that a membrane crossing is a rare event not only when the membrane forms a large free energy barrier but also when the membrane forms a deep free energy well that traps permeants. Such a permeant trap has a high permeability; yet, the counting method suffers from poor statistics. To illustrate this, coarse-grained MD was run for 16 systems of dipalmitoylphosphatidylcholine bilayer membranes with different permeant types. The composition rule for permeability is shown to also hold for fluxes, and it is highlighted that the considered thickness of the membrane causes uncertainty in the permeability calculation of highly permeable membranes. In conclusion, a high permeability in itself is not an effective indicator of the sampling efficiency of the counting method, and caution should be taken for permeants whose solubility varies greatly over the simulation box. A practical consequence relevant in, e.g., drug design is that a drug with high membrane permeability might get trapped by membranes thus reducing its efficacy.
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Affiliation(s)
- Samaneh Davoudi
- IBiTech-BioMMeda Group, Ghent University, Corneel Heymanslaan 10, Block B-entrance 36, 9000 Gent, Belgium
| | - An Ghysels
- IBiTech-BioMMeda Group, Ghent University, Corneel Heymanslaan 10, Block B-entrance 36, 9000 Gent, Belgium
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10
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Mayne CG, Toy W, Carlson KE, Bhatt T, Fanning SW, Greene GL, Katzenellenbogen BS, Chandarlapaty S, Katzenellenbogen JA, Tajkhorshid E. Defining the Energetic Basis for a Conformational Switch Mediating Ligand-Independent Activation of Mutant Estrogen Receptors in Breast Cancer. Mol Cancer Res 2021; 19:1559-1570. [PMID: 34021071 DOI: 10.1158/1541-7786.mcr-20-1017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 04/07/2021] [Accepted: 05/10/2021] [Indexed: 12/25/2022]
Abstract
Although most primary estrogen receptor (ER)-positive breast cancers respond well to endocrine therapies, many relapse later as metastatic disease due to endocrine therapy resistance. Over one third of these are associated with mutations in the ligand-binding domain (LBD) that activate the receptor independent of ligand. We have used an array of advanced computational techniques rooted in molecular dynamics simulations, in concert with and validated by experiments, to characterize the molecular mechanisms by which specific acquired somatic point mutations give rise to ER constitutive activation. By comparing structural and energetic features of constitutively active mutants and ligand-bound forms of ER-LBD with unliganded wild-type (WT) ER, we characterize a spring force originating from strain in the Helix 11-12 loop of WT-ER, opposing folding of Helix 12 into the active conformation and keeping WT-ER off and disordered, with the ligand-binding pocket open for rapid ligand binding. We quantify ways in which this spring force is abrogated by activating mutations that latch (Y537S) or relax (D538G) the folded form of the loop, enabling formation of the active conformation without ligand binding. We also identify a new ligand-mediated hydrogen-bonding network that stabilizes the active, ligand-bound conformation of WT-ER LBD, and similarly stabilizes the active conformation of the ER mutants in the hormone-free state. IMPLICATIONS: Our investigations provide deep insight into the energetic basis for the structural mechanisms of receptor activation through mutation, exemplified here with ER in endocrine-resistant metastatic breast cancers, with potential application to other dysregulated receptor signaling due to driver mutations.
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Affiliation(s)
- Christopher G Mayne
- Department of Biochemistry, University of Illinois at Urbana-Champaign, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Urbana, Illinois
| | - Weiyi Toy
- Memorial Sloan Kettering Cancer Center, Human Oncology and Pathogenesis Program, New York, New York
| | - Kathryn E Carlson
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Trusha Bhatt
- Memorial Sloan Kettering Cancer Center, Human Oncology and Pathogenesis Program, New York, New York
| | - Sean W Fanning
- Ben May Department for Cancer Research, University of Chicago, Chicago, Illinois
| | - Geoffrey L Greene
- Ben May Department for Cancer Research, University of Chicago, Chicago, Illinois
| | - Benita S Katzenellenbogen
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Sarat Chandarlapaty
- Memorial Sloan Kettering Cancer Center, Human Oncology and Pathogenesis Program, New York, New York
| | | | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois at Urbana-Champaign, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Urbana, Illinois. .,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
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11
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Bolhuis PG, Swenson DWH. Transition Path Sampling as Markov Chain Monte Carlo of Trajectories: Recent Algorithms, Software, Applications, and Future Outlook. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202000237] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Peter G. Bolhuis
- Amsterdam Center for Multiscale Modeling van 't Hoff Institute for Molecular Sciences University of Amsterdam PO Box 94157 1090 GD Amsterdam The Netherlands
| | - David W. H. Swenson
- Centre Blaise Pascal Ecole Normale Superieure 46, allée d'Italie 69364 Lyon Cedex 07 France
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12
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Aarøen O, Riccardi E, Sletmoen M. Exploring the effects of approach velocity on depletion force and coalescence in oil-in-water emulsions. RSC Adv 2021; 11:8730-8740. [PMID: 35423378 PMCID: PMC8695179 DOI: 10.1039/d1ra00661d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 02/18/2021] [Indexed: 11/21/2022] Open
Abstract
An emulsion is a thermodynamically unstable system consisting of at least two immiscible liquid phases, one of which is dispersed in the other in the form of droplets of varying size. Most studies on emulsions have focused on the behaviour of emulsion droplets with diameter from ∼50 μm and upwards. However, the properties of smaller droplets may be highly relevant in order to understand the behaviour of emulsions, including their performance in numerous applications within the fields of food, industry, and medical science. The relatively long life-time and small size of these droplets compared to other emulsion droplets, make them suited for optical trapping and micromanipulation technologies. Optical tweezers have previously shown potential in the study of stabilized emulsions. Here we employ optical tweezers to examine unstable oil-in-water emulsions to determine the effects of system parameters on depletion force and coalescence times.
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Affiliation(s)
- Ola Aarøen
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology Høgskoleringen 5 7491 Trondheim Norway
| | - Enrico Riccardi
- Department of Chemistry, Norwegian University of Science and Technology Høgskoleringen 5 7491 Trondheim Norway
- Department of Informatics, UiO Gaustadalléen 23B 0373 Oslo Norway
| | - Marit Sletmoen
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology Høgskoleringen 5 7491 Trondheim Norway
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13
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Riccardi E, Krämer A, van Erp TS, Ghysels A. Permeation Rates of Oxygen through a Lipid Bilayer Using Replica Exchange Transition Interface Sampling. J Phys Chem B 2020; 125:193-201. [DOI: 10.1021/acs.jpcb.0c09947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Enrico Riccardi
- Department of Chemistry, Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway
| | - Andreas Krämer
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Titus S. van Erp
- Department of Chemistry, Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark, Zwijnaarde, Ghent 9000, Belgium
| | - An Ghysels
- IBiTech, Faculty of Engineering and Architecture, Ghent University, Corneel Heymanslaan
10, Block B - entrance 36, 9000 Gent, Belgium
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14
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Aarøen O, Kiær H, Riccardi E. PyVisA
: Visualization and Analysis of path sampling trajectories. J Comput Chem 2020; 42:435-446. [DOI: 10.1002/jcc.26467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/03/2020] [Accepted: 11/26/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Ola Aarøen
- Department of Biotechnology and Food Science Norwegian University of Science and Technology Trondheim Norway
| | - Henrik Kiær
- Department of Chemistry Norwegian University of Science and Technology Trondheim Norway
| | - Enrico Riccardi
- Department of Chemistry Norwegian University of Science and Technology Trondheim Norway
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15
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Lam YH, Abramov Y, Ananthula RS, Elward JM, Hilden LR, Nilsson Lill SO, Norrby PO, Ramirez A, Sherer EC, Mustakis J, Tanoury GJ. Applications of Quantum Chemistry in Pharmaceutical Process Development: Current State and Opportunities. Org Process Res Dev 2020. [DOI: 10.1021/acs.oprd.0c00222] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yu-hong Lam
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yuriy Abramov
- Pfizer Worldwide Research & Development, Groton, Connecticut 06340, United States
| | - Ravi S. Ananthula
- Small Molecule Design and Development, Eli Lilly and Company, Bangalore 560103, India
| | - Jennifer M. Elward
- Molecular Design, Data and Computational Sciences, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Lori R. Hilden
- Small Molecule Design and Development, Eli Lilly and Company, Indianapolis, Indiana 46221, United States
| | - Sten O. Nilsson Lill
- Early Product Development and Manufacturing, Pharmaceutical Sciences, R&D, AstraZeneca Gothenburg, Mölndal 431 50, Sweden
| | - Per-Ola Norrby
- Data Science & Modelling, Pharmaceutical Sciences, R&D, AstraZeneca Gothenburg, Mölndal 431 50 Sweden
| | - Antonio Ramirez
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Edward C. Sherer
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jason Mustakis
- Pfizer Worldwide Research & Development, Groton, Connecticut 06340, United States
| | - Gerald J. Tanoury
- Process Chemistry, Vertex Pharmaceuticals, 50 Northern Avenue, Boston, Massachusetts 02210, United States
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16
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Hussain S, Haji-Akbari A. Studying rare events using forward-flux sampling: Recent breakthroughs and future outlook. J Chem Phys 2020; 152:060901. [DOI: 10.1063/1.5127780] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Sarwar Hussain
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, USA
| | - Amir Haji-Akbari
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, USA
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17
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Daub CD, Riccardi E, Hänninen V, Halonen L. Path sampling for atmospheric reactions: formic acid catalysed conversion of SO3 + H2O to H2SO4. PEERJ PHYSICAL CHEMISTRY 2020. [DOI: 10.7717/peerj-pchem.7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Atmospheric reactions, hitherto studied computationally mainly with static computations in conjunction with transition state theories, can be further described via path sampling calculations. Here we report on an exploratory study of the formic acid catalysed hydrolysis of SO3 to produce H2SO4. We demonstrate that precise measurements of rate coefficients can be obtained in principle for such reactions with an acceptable expenditure of computational resources, and that new insights into the reaction can be obtained by the analysis of the path space explored via path sampling techniques.
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Affiliation(s)
| | - Enrico Riccardi
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
| | - Vesa Hänninen
- Department of Chemistry, University of Helsinki, Helsinki, Finland
| | - Lauri Halonen
- Department of Chemistry, University of Helsinki, Helsinki, Finland
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18
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Riccardi E, Lervik A, Roet S, Aarøen O, Erp TS. PyRETIS 2: An improbability drive for rare events. J Comput Chem 2019; 41:370-377. [DOI: 10.1002/jcc.26112] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 01/27/2023]
Affiliation(s)
- Enrico Riccardi
- Department of ChemistryNorwegian University of Science and Technology Høgskoleringen 5 7491 Trondheim Norway
| | - Anders Lervik
- Department of ChemistryNorwegian University of Science and Technology Høgskoleringen 5 7491 Trondheim Norway
| | - Sander Roet
- Department of ChemistryNorwegian University of Science and Technology Høgskoleringen 5 7491 Trondheim Norway
| | - Ola Aarøen
- Department of Biotechnology and Food ScienceNorwegian University of Science and Technology Høgskoleringen 5 7491 Trondheim Norway
| | - Titus S. Erp
- Department of ChemistryNorwegian University of Science and Technology Høgskoleringen 5 7491 Trondheim Norway
- Center for Molecular Modeling (CMM)Ghent University Technologiepark 903 9052 Zwijnaarde Belgium
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19
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Brotzakis ZF, Bolhuis PG. Approximating free energy and committor landscapes in standard transition path sampling using virtual interface exchange. J Chem Phys 2019; 151:174111. [DOI: 10.1063/1.5119252] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Z. Faidon Brotzakis
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Peter G. Bolhuis
- Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
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20
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Daub CD, Halonen L. Ab Initio Molecular Dynamics Simulations of the Influence of Lithium Bromide Salt on the Deprotonation of Formic Acid in Aqueous Solution. J Phys Chem B 2019; 123:6823-6829. [PMID: 31310529 PMCID: PMC6750841 DOI: 10.1021/acs.jpcb.9b04618] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The deprotonation of formic acid is investigated using metadynamics in tandem with Born-Oppenheimer molecular dynamics simulations. We compare our findings for formic acid in pure water with previous studies before examining formic acid in aqueous solutions of lithium bromide. We carefully consider different definitions for the collective variable(s) used to drive the metadynamics, emphasizing that the variables used must include all of the possible reactive atoms in the system, in this case carboxylate oxygens and water hydrogens. This ensures that all the various possible proton exchange events can be accommodated and the collective variable(s) can distinguish the protonated and deprotonated states, even over rather long ab initio simulation runs (ca. 200-300 ps). Our findings show that the formic acid deprotonation barrier and the free energy of the deprotonated state are higher in concentrated lithium bromide, in agreement with the available experimental data for acids in salt solution. We show that the presence of Br- in proximity to the formic acid hydroxyl group effectively inhibits deprotonation. Our study extends previous work on acid deprotonation in pure water and at air-water interfaces to more complex multicomponent systems of importance in atmospheric and marine chemistry.
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Affiliation(s)
- Christopher D Daub
- Department of Chemistry , University of Helsinki , P.O. Box 55, Helsinki FIN-00014 , Finland
| | - Lauri Halonen
- Department of Chemistry , University of Helsinki , P.O. Box 55, Helsinki FIN-00014 , Finland
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21
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Riccardi E, Tichelkamp T. Calcium ion effects on the water/oil interface in the presence of anionic surfactants. Colloids Surf A Physicochem Eng Asp 2019. [DOI: 10.1016/j.colsurfa.2019.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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Predicting the mechanism and rate of H-NS binding to AT-rich DNA. PLoS Comput Biol 2019; 15:e1006845. [PMID: 30845209 PMCID: PMC6424460 DOI: 10.1371/journal.pcbi.1006845] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 03/19/2019] [Accepted: 02/02/2019] [Indexed: 12/21/2022] Open
Abstract
Bacteria contain several nucleoid-associated proteins that organize their genomic DNA into the nucleoid by bending, wrapping or bridging DNA. The Histone-like Nucleoid Structuring protein H-NS found in many Gram-negative bacteria is a DNA bridging protein and can structure DNA by binding to two separate DNA duplexes or to adjacent sites on the same duplex, depending on external conditions. Several nucleotide sequences have been identified to which H-NS binds with high affinity, indicating H-NS prefers AT-rich DNA. To date, highly detailed structural information of the H-NS DNA complex remains elusive. Molecular simulation can complement experiments by modelling structures and their time evolution in atomistic detail. In this paper we report an exploration of the different binding modes of H-NS to a high affinity nucleotide sequence and an estimate of the associated rate constant. By means of molecular dynamics simulations, we identified three types of binding for H-NS to AT-rich DNA. To further sample the transitions between these binding modes, we performed Replica Exchange Transition Interface Sampling, providing predictions of the mechanism and rate constant of H-NS binding to DNA. H-NS interacts with the DNA through a conserved QGR motif, aided by a conserved arginine at position 93. The QGR motif interacts first with phosphate groups, followed by the formation of hydrogen bonds between acceptors in the DNA minor groove and the sidechains of either Q112 or R114. After R114 inserts into the minor groove, the rest of the QGR motif follows. Full insertion of the QGR motif in the minor groove is stable over several tens of nanoseconds, and involves hydrogen bonds between the bases and both backbone and sidechains of the QGR motif. The rate constant for the process of H-NS binding to AT-rich DNA resulting in full insertion of the QGR motif is in the order of 106 M−1s−1, which is rate limiting compared to the non-specific association of H-NS to the DNA backbone at a rate of 108 M−1s−1. The Histone-like Nucleoid Structuring protein (H-NS) occurs in enterobacteria, such as Salmonella typhimurium and Escherichia coli, and structures DNA by forming filaments along DNA duplexes. Several nucleotide sequences have been identified to which H-NS binds with high affinity. Yet, obtaining highly detailed structural information of the H-NS DNA complex has proven to be a major challenge, which has not been yet resolved. By employing molecular dynamics simulations we were able to provide high resolution insights into the mechanism of DNA binding by H-NS. We identified various ways in which H-NS can bind to DNA. In all binding events, a conserved region in the protein initiates the association of H-NS to DNA. Our results show that H-NS binds in the minor groove of AT-rich DNA via a series of intermediate steps. Using advanced molecular simulation methods we predicted that the process of H-NS binding to the DNA backbone to full insertion into the minor groove occurs in the order of a million times per second, which is slower than the non-specific association of H-NS to the DNA backbone.
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23
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Swenson DWH, Prinz JH, Noe F, Chodera JD, Bolhuis PG. OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics. J Chem Theory Comput 2018; 15:813-836. [PMID: 30336030 PMCID: PMC6374749 DOI: 10.1021/acs.jctc.8b00626] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
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Transition
path sampling techniques allow molecular dynamics simulations of complex
systems to focus on rare dynamical events, providing
insight into mechanisms and the ability to calculate rates inaccessible
by ordinary dynamics simulations. While path sampling algorithms are
conceptually as simple as importance sampling Monte Carlo, the technical
complexity of their implementation has kept these techniques out of
reach of the broad community. Here, we introduce an easy-to-use Python
framework called OpenPathSampling (OPS) that facilitates path sampling
for (bio)molecular systems with minimal effort and yet is still extensible.
Interfaces to OpenMM and an internal dynamics engine for simple models
are provided in the initial release, but new molecular simulation
packages can easily be added. Multiple ready-to-use transition path
sampling methodologies are implemented, including standard transition
path sampling (TPS) between reactant and product states and transition
interface sampling (TIS) and its replica exchange variant (RETIS),
as well as recent multistate and multiset extensions of transition
interface sampling (MSTIS, MISTIS). In addition, tools are provided
to facilitate the implementation of new path sampling schemes built
on basic path sampling components. In this paper, we give an overview
of the design of this framework and illustrate the simplicity of applying
the available path sampling algorithms to a variety of benchmark problems.
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Affiliation(s)
- David W H Swenson
- van 't Hoff Institute for Molecular Sciences , University of Amsterdam , P.O. Box 94157, 1090 GD Amsterdam , The Netherlands.,Computational and Systems Biology Program , Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States
| | - Jan-Hendrik Prinz
- Computational and Systems Biology Program , Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Department of Mathematics and Computer Science, Arnimallee 6 , Freie Universität Berlin , 14195 Berlin , Germany
| | - Frank Noe
- Department of Mathematics and Computer Science, Arnimallee 6 , Freie Universität Berlin , 14195 Berlin , Germany
| | - John D Chodera
- Computational and Systems Biology Program , Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States
| | - Peter G Bolhuis
- van 't Hoff Institute for Molecular Sciences , University of Amsterdam , P.O. Box 94157, 1090 GD Amsterdam , The Netherlands
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24
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Sidky H, Colón YJ, Helfferich J, Sikora BJ, Bezik C, Chu W, Giberti F, Guo AZ, Jiang X, Lequieu J, Li J, Moller J, Quevillon MJ, Rahimi M, Ramezani-Dakhel H, Rathee VS, Reid DR, Sevgen E, Thapar V, Webb MA, Whitmer JK, de Pablo JJ. SSAGES: Software Suite for Advanced General Ensemble Simulations. J Chem Phys 2018; 148:044104. [DOI: 10.1063/1.5008853] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Hythem Sidky
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Yamil J. Colón
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
- Institute for Molecular Engineering and Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Julian Helfferich
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
- Steinbuch Center for Computing, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Benjamin J. Sikora
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Cody Bezik
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Weiwei Chu
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Federico Giberti
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Ashley Z. Guo
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Xikai Jiang
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Joshua Lequieu
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Jiyuan Li
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Joshua Moller
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Michael J. Quevillon
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Mohammad Rahimi
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Hadi Ramezani-Dakhel
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Vikramjit S. Rathee
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Daniel R. Reid
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Emre Sevgen
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Vikram Thapar
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Michael A. Webb
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
- Institute for Molecular Engineering and Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Jonathan K. Whitmer
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Juan J. de Pablo
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
- Institute for Molecular Engineering and Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
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25
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Cabriolu R, Skjelbred Refsnes KM, Bolhuis PG, van Erp TS. Foundations and latest advances in replica exchange transition interface sampling. J Chem Phys 2017; 147:152722. [DOI: 10.1063/1.4989844] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Raffaela Cabriolu
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, 7491 Trondheim, Norway
| | - Kristin M. Skjelbred Refsnes
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, 7491 Trondheim, Norway
| | - Peter G. Bolhuis
- Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Titus S. van Erp
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, 7491 Trondheim, Norway
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