1
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Boulougouris GC. Event horizon kinetic Monte Carlo. J Chem Phys 2024; 161:044109. [PMID: 39046345 DOI: 10.1063/5.0220945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 07/05/2024] [Indexed: 07/25/2024] Open
Abstract
In this study, we present a novel approach for modeling the dynamics of stochastic processes. The fundamental concept involves constructing a stochastic Markov chain comprising states separated by more than one stochastic event. Initially, the method explores the network of neighboring states connected by stochastic events. This exploration results in a "horizon" of events leading to a set of "boundary" states at the periphery of each local network. Subsequently, the next member in the Markov chain is selected from the "boundary" states based on the probability of reaching each of the "boundary" states for the first time. Meanwhile, the simulation clock is updated according to the time required to reach the boundary for the first time. This can be achieved using an analytical approach, where the probability of reaching each boundary state for the first time is estimated using absorbing conditions for all boundary states in the analytical solution of a master equation describing the local network of states around each current state. The proposed method is demonstrated in modeling the dynamics in networks of stochastic reactions but can be easily applied in any stochastic system whose dynamics can be expressed via the solution of a master equation. It is expected to enhance the efficiency of event-driven Monte Carlo simulations, originally introduced by Gillespie and widely regarded as the gold standard in the field, especially in cases where the presence of events is characterized by different timescales.
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Affiliation(s)
- Georgios C Boulougouris
- Laboratory of Computational Physical Chemistry, Department of Molecular Biology and Genetics, University of Thrace, GR-68100 Alexandroupoulis, Greece
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2
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Boulougouris GC. Accessible Molecular System Creator: Building Molecular Configurations Based on the Inaccessible Molecular Volume and Accessible Molecular Surface via Static Monte Carlo Sampling. J Phys Chem B 2023; 127:9520-9531. [PMID: 37883744 DOI: 10.1021/acs.jpcb.3c03670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Monte Carlo (MC) stochastic sampling is a powerful tool in classical molecular simulations that directly connects the observable macroscopic properties of matter and the underlying atomistic interactions. This connection operates within the framework of the statistical mechanics proposed by Gibbs. Most MC simulations are "dynamic," creating statistical ensembles of microstates via a Markovian chain, where each microstate in the ensemble depends only on its previous microstate. Herein, we re-examine an alternative form of MC that generates ensemble members through a "static" approach, building molecular systems stepwise. The basic theory for such an approach traces back to Rosenbluth and Rosenbluth, who proposed "static" stepwise sampling of a polymeric chain. It is almost as old as the Metropolis importance sampling approach used in dynamic MC, although the latter has been considerably more popular than the former. Herein, we address the main obstacle in static MC that has hindered the widespread adoption of Rosenbluth-based approaches in atomistic simulations. The obstacle lies in mapping the molecular accessible volume for adding a molecule in a Rosenbluth-like static sampling of atomistic configurations. We demonstrate a breakthrough by leveraging the ability to analytically map the inaccessible molecular volume and the accessible molecular surface owing to interatomically excluded volume interactions. This advance substantially enhances the ability to create molecular samples using a Rosenbluth-like static building process. The proposed approach can be used as a tool for creating initial configurations in MC or molecular dynamics simulations─a field where Rosenbluth-like static building has been applied. Additionally, this approach can be used as the first step in a perturbation scheme that accurately estimates free energy differences by estimating the chemical work related to molecule addition, removal, or reinsertion within the context of free energy perturbation schemes employed in molecular simulations.
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Affiliation(s)
- Georgios C Boulougouris
- Laboratory of Computational Physical Chemistry, Department of Molecular Biology and Genetics, University of Thrace, GR 681 00 Alexandroupoulis, Greece
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3
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Koskin V, Kells A, Clayton J, Hartmann AK, Annibale A, Rosta E. Variational kinetic clustering of complex networks. J Chem Phys 2023; 158:104112. [PMID: 36922127 DOI: 10.1063/5.0105099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Efficiently identifying the most important communities and key transition nodes in weighted and unweighted networks is a prevalent problem in a wide range of disciplines. Here, we focus on the optimal clustering using variational kinetic parameters, linked to Markov processes defined on the underlying networks, namely, the slowest relaxation time and the Kemeny constant. We derive novel relations in terms of mean first passage times for optimizing clustering via the Kemeny constant and show that the optimal clustering boundaries have equal round-trip times to the clusters they separate. We also propose an efficient method that first projects the network nodes onto a 1D reaction coordinate and subsequently performs a variational boundary search using a parallel tempering algorithm, where the variational kinetic parameters act as an energy function to be extremized. We find that maximization of the Kemeny constant is effective in detecting communities, while the slowest relaxation time allows for detection of transition nodes. We demonstrate the validity of our method on several test systems, including synthetic networks generated from the stochastic block model and real world networks (Santa Fe Institute collaboration network, a network of co-purchased political books, and a street network of multiple cities in Luxembourg). Our approach is compared with existing clustering algorithms based on modularity and the robust Perron cluster analysis, and the identified transition nodes are compared with different notions of node centrality.
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Affiliation(s)
- Vladimir Koskin
- Department of Chemistry, King's College London, SE1 1DB London, United Kingdom
| | - Adam Kells
- Department of Chemistry, King's College London, SE1 1DB London, United Kingdom
| | - Joe Clayton
- Department of Physics and Astronomy, University College London, WC1E 6BT London, United Kingdom
| | | | - Alessia Annibale
- Department of Mathematics, King's College London, SE11 6NJ London, United Kingdom
| | - Edina Rosta
- Department of Physics and Astronomy, University College London, WC1E 6BT London, United Kingdom
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4
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Sharpe DJ, Wales DJ. Efficient and exact sampling of transition path ensembles on Markovian networks. J Chem Phys 2020; 153:024121. [DOI: 10.1063/5.0012128] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Daniel J. Sharpe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David J. Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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5
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Swinburne TD, Wales DJ. Defining, Calculating, and Converging Observables of a Kinetic Transition Network. J Chem Theory Comput 2020; 16:2661-2679. [PMID: 32155072 DOI: 10.1021/acs.jctc.9b01211] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Kinetic transition networks (KTNs) of local minima and transition states are able to capture the dynamics of numerous systems in chemistry, biology, and materials science. However, extracting observables is numerically challenging for large networks and generally will be sensitive to additional computational discovery. To have any measure of convergence for observables, these sensitivities must be regularly calculated. We present a matrix formulation of the discrete path sampling framework for KTNs, deriving expressions for branching probabilities, transition rates, and waiting times. Using the concept of the quasi-stationary distribution, a clear hierarchy of expressions for network observables is established, from exact results to steady-state approximations. We use these results in combination with the graph transformation method to derive the sensitivity, with respect to perturbations of the known KTN, giving explicit terms for the pairwise sensitivity and discussing the pathwise sensitivity. These results provide guidelines for converging the network, with respect to additional sampling, focusing on the estimates obtained for the overall rate coefficients between product and reactant states. We demonstrate this procedure for transitions in the double-funnel landscape of the 38-atom Lennard-Jones cluster.
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Affiliation(s)
- Thomas D Swinburne
- Aix-Marseille Université, CNRS, CINaM UMR 7325, Campus de Luminy, 13288 Marseille, France
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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6
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Vogiatzis GG, van Breemen LCA, Hütter M. Network Topology of the States Probed by a Glassy Polymer during Physical Aging. MACROMOL THEOR SIMUL 2019. [DOI: 10.1002/mats.201900036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Georgios Grigorios Vogiatzis
- Polymer TechnologyDepartment of Mechanical EngineeringEindhoven University of Technology PO Box 513 5600 MB Eindhoven The Netherlands
- Dutch Polymer Institute PO Box 902 5600 AX Eindhoven The Netherlands
| | - Lambèrt Cécile Angelo van Breemen
- Polymer TechnologyDepartment of Mechanical EngineeringEindhoven University of Technology PO Box 513 5600 MB Eindhoven The Netherlands
| | - Markus Hütter
- Polymer TechnologyDepartment of Mechanical EngineeringEindhoven University of Technology PO Box 513 5600 MB Eindhoven The Netherlands
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7
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Raza Z, Alling B, Abrikosov IA. Computer simulations of glasses: the potential energy landscape. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:293201. [PMID: 26139691 DOI: 10.1088/0953-8984/27/29/293201] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We review the current state of research on glasses, discussing the theoretical background and computational models employed to describe them. This article focuses on the use of the potential energy landscape (PEL) paradigm to account for the phenomenology of glassy systems, and the way in which it can be applied in simulations and the interpretation of their results. This article provides a broad overview of the rich phenomenology of glasses, followed by a summary of the theoretical frameworks developed to describe this phenomonology. We discuss the background of the PEL in detail, the onerous task of how to generate computer models of glasses, various methods of analysing numerical simulations, and the literature on the most commonly used model systems. Finally, we tackle the problem of how to distinguish a good glass former from a good crystal former from an analysis of the PEL. In summarising the state of the potential energy landscape picture, we develop the foundations for new theoretical methods that allow the ab initio prediction of the glass-forming ability of new materials by analysis of the PEL.
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Affiliation(s)
- Zamaan Raza
- Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83, Linköping, Sweden
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8
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Mehta D, Chen T, Morgan JWR, Wales DJ. Exploring the potential energy landscape of the Thomson problem via Newton homotopies. J Chem Phys 2015; 142:194113. [PMID: 26001453 DOI: 10.1063/1.4921163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Locating the stationary points of a real-valued multivariate potential energy function is an important problem in many areas of science. This task generally amounts to solving simultaneous nonlinear systems of equations. While there are several numerical methods that can find many or all stationary points, they each exhibit characteristic problems. Moreover, traditional methods tend to perform poorly near degenerate stationary points with additional zero Hessian eigenvalues. We propose an efficient and robust implementation of the Newton homotopy method, which is capable of quickly sampling a large number of stationary points of a wide range of indices, as well as degenerate stationary points. We demonstrate our approach by applying it to the Thomson problem. We also briefly discuss a possible connection between the present work and Smale's 7th problem.
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Affiliation(s)
- Dhagash Mehta
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Tianran Chen
- Department of Mathematics, Michigan State University, East Lansing, Michigan 48823, USA
| | - John W R Morgan
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David J Wales
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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9
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Wales DJ. Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape. J Chem Phys 2015; 142:130901. [DOI: 10.1063/1.4916307] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- D. J. Wales
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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10
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Athènes M, Bulatov VV. Path factorization approach to stochastic simulations. PHYSICAL REVIEW LETTERS 2014; 113:230601. [PMID: 25526107 DOI: 10.1103/physrevlett.113.230601] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Indexed: 06/04/2023]
Abstract
The computational efficiency of stochastic simulation algorithms is notoriously limited by the kinetic trapping of the simulated trajectories within low energy basins. Here we present a new method that overcomes kinetic trapping while still preserving exact statistics of escape paths from the trapping basins. The method is based on path factorization of the evolution operator and requires no prior knowledge of the underlying energy landscape. The efficiency of the new method is demonstrated in simulations of anomalous diffusion and phase separation in a binary alloy, two stochastic models presenting severe kinetic trapping.
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Affiliation(s)
- Manuel Athènes
- CEA, DEN, Service de Recherches de Métallurgie Physique, F-91191 Gif-sur-Yvette, France
| | - Vasily V Bulatov
- Lawrence Livermore National Laboratory, Livermore, California 94551, USA
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11
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Mehta D, Chen T, Hauenstein JD, Wales DJ. Communication: Newton homotopies for sampling stationary points of potential energy landscapes. J Chem Phys 2014; 141:121104. [DOI: 10.1063/1.4896657] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Dhagash Mehta
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, Indiana 46556, USA
- University Chemical Laboratory, The University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Tianran Chen
- Department of Mathematics, Michigan State University, East Lansing, Michigan 48823, USA
| | - Jonathan D. Hauenstein
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - David J. Wales
- University Chemical Laboratory, The University of Cambridge, Cambridge CB2 1EW, United Kingdom
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12
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Hughes C, Mehta D, Wales DJ. An inversion-relaxation approach for sampling stationary points of spin model Hamiltonians. J Chem Phys 2014; 140:194104. [PMID: 24852527 DOI: 10.1063/1.4875697] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Sampling the stationary points of a complicated potential energy landscape is a challenging problem. Here, we introduce a sampling method based on relaxation from stationary points of the highest index of the Hessian matrix. We illustrate how this approach can find all the stationary points for potentials or Hamiltonians bounded from above, which includes a large class of important spin models, and we show that it is far more efficient than previous methods. For potentials unbounded from above, the relaxation part of the method is still efficient in finding minima and transition states, which are usually the primary focus of attention for atomistic systems.
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Affiliation(s)
- Ciaran Hughes
- The Department of Applied Mathematics and Theoretical Physics, The University of Cambridge, Clarkson Road, Cambridge CB3 0EH, United Kingdom
| | - Dhagash Mehta
- Department of Mathematics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - David J Wales
- Department of Chemistry, The University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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13
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Lempesis N, Vogiatzis GG, Boulougouris GC, van Breemen LC, Hütter M, Theodorou DN. Tracking a glassy polymer on its energy landscape in the course of elastic deformation. Mol Phys 2013. [DOI: 10.1080/00268976.2013.825018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Lempesis N, Boulougouris GC, Theodorou DN. Temporal disconnectivity of the energy landscape in glassy systems. J Chem Phys 2013; 138:12A545. [PMID: 23556796 DOI: 10.1063/1.4792363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
An alternative graphical representation of the potential energy landscape (PEL) has been developed and applied to a binary Lennard-Jones glassy system, providing insight into the unique topology of the system's potential energy hypersurface. With the help of this representation one is able to monitor the different explored basins of the PEL, as well as how--and mainly when--subsets of basins communicate with each other via transitions in such a way that details of the prior temporal history have been erased, i.e., local equilibration between the basins in each subset has been achieved. In this way, apart from detailed information about the structure of the PEL, the system's temporal evolution on the PEL is described. In order to gather all necessary information about the identities of two or more basins that are connected with each other, we consider two different approaches. The first one is based on consideration of the time needed for two basins to mutually equilibrate their populations according to the transition rate between them, in the absence of any effect induced by the rest of the landscape. The second approach is based on an analytical solution of the master equation that explicitly takes into account the entire explored landscape. It is shown that both approaches lead to the same result concerning the topology of the PEL and dynamical evolution on it. Moreover, a "temporal disconnectivity graph" is introduced to represent a lumped system stemming from the initial one. The lumped system is obtained via a specially designed algorithm [N. Lempesis, D. G. Tsalikis, G. C. Boulougouris, and D. N. Theodorou, J. Chem. Phys. 135, 204507 (2011)]. The temporal disconnectivity graph provides useful information about both the lumped and the initial systems, including the definition of "metabasins" as collections of basins that communicate with each other via transitions that are fast relative to the observation time. Finally, the two examined approaches are compared to an "on the fly" molecular dynamics-based algorithm [D. G. Tsalikis, N. Lempesis, G. C. Boulougouris, and D. N. Theodorou, J. Chem. Theory Comput. 6, 1307 (2010)].
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Affiliation(s)
- Nikolaos Lempesis
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780 Athens, Greece
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15
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Boulougouris GC. On the Estimation of the Free Energy, From a Single Equilibrium Statistical Ensemble, via Particle Reinsertion. J Phys Chem B 2012; 116:997-1006. [DOI: 10.1021/jp2036185] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Georgios C. Boulougouris
- Department of Molecular Biology and Genetics, Democritius University, 68100, Alexandroupolis, Greece, and Scienomics SARL, 17, Square Edouard VII, 75009 Paris, France
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16
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Lempesis N, Tsalikis DG, Boulougouris GC, Theodorou DN. Lumping analysis for the prediction of long-time dynamics: From monomolecular reaction systems to inherent structure dynamics of glassy materials. J Chem Phys 2011; 135:204507. [DOI: 10.1063/1.3663207] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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17
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Scott A, Watier F. Goal achieving probabilities of constrained mean-variance strategies. Stat Probab Lett 2011. [DOI: 10.1016/j.spl.2011.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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18
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Predicting fluid phase equilibrium via histogram reweighting with Gibbs ensemble Monte Carlo simulations. J Supercrit Fluids 2010. [DOI: 10.1016/j.supflu.2010.09.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Tsalikis DG, Lempesis N, Boulougouris GC, Theodorou DN. Temperature Accelerated Dynamics in Glass-Forming Materials. J Phys Chem B 2010; 114:7844-53. [DOI: 10.1021/jp908975d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Dimitrios G. Tsalikis
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780 Athens, Greece, Engineering Informatics and Telecommunications, University of Western Macedonia, Konstantinou Karamanli 55,GR-50100 Kozani, Greece, Department of Chemical Engineering, University of Patras, GR-26500 Patras, Greece, and Scienomics SARL, 17, Square Edouard VII, 75009 Paris
| | - Nikolaos Lempesis
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780 Athens, Greece, Engineering Informatics and Telecommunications, University of Western Macedonia, Konstantinou Karamanli 55,GR-50100 Kozani, Greece, Department of Chemical Engineering, University of Patras, GR-26500 Patras, Greece, and Scienomics SARL, 17, Square Edouard VII, 75009 Paris
| | - Georgios C. Boulougouris
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780 Athens, Greece, Engineering Informatics and Telecommunications, University of Western Macedonia, Konstantinou Karamanli 55,GR-50100 Kozani, Greece, Department of Chemical Engineering, University of Patras, GR-26500 Patras, Greece, and Scienomics SARL, 17, Square Edouard VII, 75009 Paris
| | - Doros N. Theodorou
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780 Athens, Greece, Engineering Informatics and Telecommunications, University of Western Macedonia, Konstantinou Karamanli 55,GR-50100 Kozani, Greece, Department of Chemical Engineering, University of Patras, GR-26500 Patras, Greece, and Scienomics SARL, 17, Square Edouard VII, 75009 Paris
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20
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Tsalikis DG, Lempesis N, Boulougouris GC, Theodorou DN. Efficient Parallel Decomposition of Dynamical Sampling in Glass-Forming Materials Based on an “On the Fly” Definition of Metabasins. J Chem Theory Comput 2010. [DOI: 10.1021/ct9004245] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Dimitrios G. Tsalikis
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780 Athens, Greece, Engineering Informatics and Telecommunications, University of Western Macedonia, Konstantinou Karamanli 55, GR-50100 Kozani, Greece, Department of Chemical Engineering, University of Patras, GR-26500 Patras, Greece, and Scienomics SARL, 17, Square Edouard VII, 75009 Paris
| | - Nikolaos Lempesis
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780 Athens, Greece, Engineering Informatics and Telecommunications, University of Western Macedonia, Konstantinou Karamanli 55, GR-50100 Kozani, Greece, Department of Chemical Engineering, University of Patras, GR-26500 Patras, Greece, and Scienomics SARL, 17, Square Edouard VII, 75009 Paris
| | - Georgios C. Boulougouris
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780 Athens, Greece, Engineering Informatics and Telecommunications, University of Western Macedonia, Konstantinou Karamanli 55, GR-50100 Kozani, Greece, Department of Chemical Engineering, University of Patras, GR-26500 Patras, Greece, and Scienomics SARL, 17, Square Edouard VII, 75009 Paris
| | - Doros N. Theodorou
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780 Athens, Greece, Engineering Informatics and Telecommunications, University of Western Macedonia, Konstantinou Karamanli 55, GR-50100 Kozani, Greece, Department of Chemical Engineering, University of Patras, GR-26500 Patras, Greece, and Scienomics SARL, 17, Square Edouard VII, 75009 Paris
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21
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Wales DJ. Calculating rate constants and committor probabilities for transition networks by graph transformation. J Chem Phys 2009; 130:204111. [DOI: 10.1063/1.3133782] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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22
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Spyriouni T, Boulougouris GC, Theodorou DN. Prediction of Sorption of CO2 in Glassy Atactic Polystyrene at Elevated Pressures Through a New Computational Scheme. Macromolecules 2009. [DOI: 10.1021/ma8015294] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Theodora Spyriouni
- Institute of Physical Chemistry, NCSR “Demokritos”, Aghia Paraskevi Attikis, 153 10 Athens, Greece, Scienomics SARL, 17, Square Eduard VII, 75009 Paris, France, and Department of Materials Science and Engineering, School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou, Zografou Campus, Athens 15780, Greece
| | - Georgios C. Boulougouris
- Institute of Physical Chemistry, NCSR “Demokritos”, Aghia Paraskevi Attikis, 153 10 Athens, Greece, Scienomics SARL, 17, Square Eduard VII, 75009 Paris, France, and Department of Materials Science and Engineering, School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou, Zografou Campus, Athens 15780, Greece
| | - Doros N. Theodorou
- Institute of Physical Chemistry, NCSR “Demokritos”, Aghia Paraskevi Attikis, 153 10 Athens, Greece, Scienomics SARL, 17, Square Eduard VII, 75009 Paris, France, and Department of Materials Science and Engineering, School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou, Zografou Campus, Athens 15780, Greece
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23
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Boulougouris GC, Theodorou DN. Probing subglass relaxation in polymers via a geometric representation of probabilities, observables, and relaxation modes for discrete stochastic systems. J Chem Phys 2009; 130:044905. [DOI: 10.1063/1.3063118] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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24
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Carr JM, Wales DJ. Refined kinetic transition networks for the GB1 hairpin peptide. Phys Chem Chem Phys 2009; 11:3341-54. [DOI: 10.1039/b820649j] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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25
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Tsalikis DG, Lempesis N, Boulougouris GC, Theodorou DN. On the Role of Inherent Structures in Glass-Forming Materials: I. The Vitrification Process. J Phys Chem B 2008; 112:10619-27. [DOI: 10.1021/jp801296k] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dimitrios G. Tsalikis
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780 Athens, Greece, and Scienomics, 17, Square Eduard VII, 75009 Paris, France
| | - Nikolaos Lempesis
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780 Athens, Greece, and Scienomics, 17, Square Eduard VII, 75009 Paris, France
| | - Georgios C. Boulougouris
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780 Athens, Greece, and Scienomics, 17, Square Eduard VII, 75009 Paris, France
| | - Doros N. Theodorou
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780 Athens, Greece, and Scienomics, 17, Square Eduard VII, 75009 Paris, France
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Tsalikis D, Lempesis N, Boulougouris GC, Theodorou DN. On the Role of Inherent Structures in Glass-forming Materials: II. Reconstruction of the Mean Square Displacement by Rigorous Lifting of the Inherent Structure Dynamics. J Phys Chem B 2008; 112:10628-37. [DOI: 10.1021/jp8013223] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dimitrios Tsalikis
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780 Athens, Greece, and Scienomics, 17, Square Edouard VII, 75009 Paris
| | - Nikolaos Lempesis
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780 Athens, Greece, and Scienomics, 17, Square Edouard VII, 75009 Paris
| | - Georgios C. Boulougouris
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780 Athens, Greece, and Scienomics, 17, Square Edouard VII, 75009 Paris
| | - Doros N. Theodorou
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR-15780 Athens, Greece, and Scienomics, 17, Square Edouard VII, 75009 Paris
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