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Molecular Simulation Volume 47, 2021 - Issue 10-11: Recent Developments in Molecular Simulation; Guest Editor: Jerome Delhommelle
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Articles

Finite-size effects of diffusion coefficients computed from molecular dynamics: a review of what we have learned so far

Alper T. Celebia Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The NetherlandsView further author information
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Seyed Hossein Jamalia Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The NetherlandsORCID Iconhttps://orcid.org/0000-0002-4198-0901View further author information
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André Bardowb Energy & Process Systems Engineering, Department of Mechanical and Process Engineering, ETH Zurich, Zürich, SwitzerlandView further author information
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Thijs J. H. Vlugta Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The NetherlandsORCID Iconhttps://orcid.org/0000-0003-3059-8712View further author information
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Othonas A. Moultosa Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The NetherlandsCorrespondence[email protected]
ORCID Iconhttps://orcid.org/0000-0001-7477-9684View further author information
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Pages 831-845 | Received 28 Jun 2020, Accepted 05 Aug 2020, Published online: 01 Sep 2020

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Othonas A. Moultos & Ioannis N. Tsimpanogiannis. (2023) Predictive model for the intra-diffusion coefficients of H2 and O2 in vapour H2O based on data from molecular dynamics simulations. Molecular Physics 121:19-20.
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Shrinjay Sharma, Salvador R. G. Balestra, Richard Baur, Umang Agarwal, Erik Zuidema, Marcello S. Rigutto, Sofia Calero, Thijs J. H. Vlugt & David Dubbeldam. (2023) RUPTURA: simulation code for breakthrough, ideal adsorption solution theory computations, and fitting of isotherm models. Molecular Simulation 49:9, pages 893-953.
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Mohsen Farshad, Mark J. DelloStritto, Antonio Suma & Vincenzo Carnevale. (2023) Detecting Liquid–Liquid Phase Separations Using Molecular Dynamics Simulations and Spectral Clustering. The Journal of Physical Chemistry B 127:16, pages 3682-3689.
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Øystein Gullbrekken, Ingeborg Treu Røe, Sverre Magnus Selbach & Sondre Kvalvåg Schnell. (2023) Charge Transport in Water–NaCl Electrolytes with Molecular Dynamics Simulations. The Journal of Physical Chemistry B 127:12, pages 2729-2738.
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Yunguo Li & Huaiwei Ni. (2023) MD2D: A python module for accurate determination of diffusion coefficient from molecular dynamics. Computer Physics Communications 284, pages 108599.
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Luis F. Salas-Guerrero, Cristian Buendia-Atencio & Gustavo A. Orozco. (2023) Thermodynamics and transport properties of CBD and -THC: A first attempt using molecular dynamics . Journal of Molecular Liquids 371, pages 121048.
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W. A. van Rooijen, P. Habibi, K. Xu, P. Dey, T. J. H. Vlugt, H. Hajibeygi & O. A. Moultos. (2023) Interfacial Tensions, Solubilities, and Transport Properties of the H 2 /H 2 O/NaCl System: A Molecular Simulation Study . Journal of Chemical & Engineering Data.
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H. Mert Polat, Frédérick de Meyer, Céline Houriez, Christophe Coquelet, Othonas A. Moultos & Thijs J.H. Vlugt. (2023) Transport properties of mixtures of acid gases with aqueous monoethanolamine solutions: A molecular dynamics study. Fluid Phase Equilibria 564, pages 113587.
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Ioannis N. Tsimpanogiannis & Othonas A. Moultos. (2023) Is Stokes-Einstein relation valid for the description of intra-diffusivity of hydrogen and oxygen in liquid water?. Fluid Phase Equilibria 563, pages 113568.
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Subin Sahu, Nathanael S. Schwindt, Benjamin J. Coscia & Michael R. Shirts. (2022) Obtaining and Characterizing Stable Bicontinuous Cubic Morphologies and Their Nanochannels in Lyotropic Liquid Crystal Membranes. The Journal of Physical Chemistry B 126:48, pages 10098-10110.
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Fazhan Zeng, Ren Wan, Yongjun Xiao, Fan Song, Changjun Peng & Honglai Liu. (2022) Predicting the Self-Diffusion Coefficient of Liquids Based on Backpropagation Artificial Neural Network: A Quantitative Structure–Property Relationship Study. Industrial & Engineering Chemistry Research 61:48, pages 17697-17706.
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Yuanhang Zhang, Maozhong An, Peixia Yang & Jinqiu Zhang. (2022) Electrochemical behavior of through-hole electrodeposition inhibitor EO-PO under periodic pulse reverse. Colloids and Surfaces A: Physicochemical and Engineering Aspects 655, pages 130238.
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Parsa Habibi, Ahmadreza Rahbari, Samuel Blazquez, Carlos Vega, Poulumi Dey, Thijs J. H. Vlugt & Othonas A. Moultos. (2022) A New Force Field for OH – for Computing Thermodynamic and Transport Properties of H 2 and O 2 in Aqueous NaOH and KOH Solutions . The Journal of Physical Chemistry B 126:45, pages 9376-9387.
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Qian Wang, Nan Gui, Xiaoxi Zhang, Xingtuan Yang, Jiyuan Tu & Shengyao Jiang. (2022) Diffusion and thermo-driven migration of silver, palladium, and ruthenium nanoparticles in cubic SiC matrix using molecular dynamics. International Journal of Heat and Mass Transfer 197, pages 123359.
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J.-M. Simon, P. Krüger, S. K. Schnell, T. J. H. Vlugt, S. Kjelstrup & D. Bedeaux. (2022) Kirkwood–Buff integrals: From fluctuations in finite volumes to the thermodynamic limit. The Journal of Chemical Physics 157:13.
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Marianna Yiannourakou, Xavier Rozanska, Benoit Minisini & Frédérick de Meyer. (2022) Molecular simulations for improved process modeling of an acid gas removal unit. Fluid Phase Equilibria 560, pages 113478.
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Yuanyuan Huang, Heng Chen, Dongdong Li, Rulong Zhou & Bo Zhang. (2022) The relationship between inter-diffusion and self-diffusion of different liquid metals studied by molecular dynamics simulations. Physica B: Condensed Matter 638, pages 413844.
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Yunguo Li, Xuan Guo, Lidunka Vočadlo, John P. Brodholt & Huaiwei Ni. (2022) The effect of water on the outer core transport properties. Physics of the Earth and Planetary Interiors 329-330, pages 106907.
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Todd M. Alam, Joshua P. Allers, Calen J. Leverant & Jacob A. Harvey. (2022) Symbolic regression development of empirical equations for diffusion in Lennard-Jones fluids. The Journal of Chemical Physics 157:1.
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Bin Fang, Tao Lü, Liwei Cheng, Dongdong Wang, Yang Ni, Bowen Fan, Jiuling Meng, Thijs J. H. Vlugt & Fulong Ning. (2022) Negative Effects of Inorganic Salt Invasion on the Dissociation Kinetics of Silica-Confined Gas Hydrate via Thermal Stimulation. Energy & Fuels 36:12, pages 6216-6228.
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Michelle A. Hunter, Baris Demir, Charlotte F. Petersen & Debra J. Searles. (2022) New Framework for Computing a General Local Self-Diffusion Coefficient Using Statistical Mechanics. Journal of Chemical Theory and Computation 18:6, pages 3357-3363.
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Qizhang Jia, B. Jill Venton & Kateri H. DuBay. (2022) Structure and Dynamics of Adsorbed Dopamine on Solvated Carbon Nanotubes and in a CNT Groove. Molecules 27:12, pages 3768.
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Cheng Chen, Daniel Mira & Xi Jiang. (2022) A molecular simulation study on transport properties of FAMEs in high-pressure conditions. Fuel 316, pages 123356.
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Federico Grasselli. (2022) Investigating finite-size effects in molecular dynamics simulations of ion diffusion, heat transport, and thermal motion in superionic materials. The Journal of Chemical Physics 156:13.
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Ioannis N. Tsimpanogiannis, Samadarshi Maity, Alper T. Celebi & Othonas A. Moultos. (2021) Engineering Model for Predicting the Intradiffusion Coefficients of Hydrogen and Oxygen in Vapor, Liquid, and Supercritical Water based on Molecular Dynamics Simulations. Journal of Chemical & Engineering Data 66:8, pages 3226-3244.
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Gabriela Guevara-Carrion, Robin Fingerhut & Jadran Vrabec. (2021) Diffusion in multicomponent aqueous alcoholic mixtures. Scientific Reports 11:1.
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Alper T. Celebi, Noura Dawass, Othonas A. Moultos & Thijs J. H. Vlugt. (2021) How sensitive are physical properties of choline chloride–urea mixtures to composition changes: Molecular dynamics simulations and Kirkwood–Buff theory. The Journal of Chemical Physics 154:18.
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Hirad S. Salehi, Alper T. Celebi, Thijs J. H. Vlugt & Othonas A. Moultos. (2021) Thermodynamic, transport, and structural properties of hydrophobic deep eutectic solvents composed of tetraalkylammonium chloride and decanoic acid. The Journal of Chemical Physics 154:14.
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Máté Erdős, Michalis Frangou, Thijs J.H. Vlugt & Othonas A. Moultos. (2021) Diffusivity of α-, β-, γ-cyclodextrin and the inclusion complex of β-cyclodextrin: Ibuprofen in aqueous solutions; A molecular dynamics simulation study. Fluid Phase Equilibria 528, pages 112842.
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Calen J. Leverant, Jacob A. Harvey & Todd M. Alam. (2020) Machine Learning-Based Upscaling of Finite-Size Molecular Dynamics Diffusion Simulations for Binary Fluids. The Journal of Physical Chemistry Letters 11:24, pages 10375-10381.
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Ioannis Tsimpanogiannis & Othonas A. Moultos. (2022) Is Stokes−Einstein Relation Valid for the Description Of Intra-Diffusivity of Hydrogen and Oxygen in Liquid Water?. SSRN Electronic Journal.
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