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Mileo PGM, Krauter CM, Sanders JM, Coscia BJ, Browning AR, Halls MD. Nanoscale Simulation of Plastic Contaminants Migration in Packaging Materials and Potential Leaching into Model Food Fluids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:12475-12487. [PMID: 38847174 DOI: 10.1021/acs.langmuir.4c00859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2024]
Abstract
Polymers are the most commonly used packaging materials for nutrition and consumer products. The ever-growing concern over pollution and potential environmental contamination generated from single-use packaging materials has raised safety questions. Polymers used in these materials often contain impurities, including unreacted monomers and small oligomers. The characterization of transport properties, including diffusion and leaching of these molecules, is largely hampered by the long timescales involved in shelf life experiments. In this work, we employ atomistic molecular simulation techniques to explore the main mechanisms involved in the bulk and interfacial transport of monomer molecules from three polymers commonly employed as packaging materials: polyamide-6, polycarbonate, and poly(methyl methacrylate). Our simulations showed that both hopping and continuous diffusion play important roles in inbound monomer diffusion and that solvent-polymer compatibility significantly affects monomer leaching. These results provide rationalization for monomer leaching in model food formulations as well as bulky industry-relevant molecules. Through this molecular-scale characterization, we offer insights to aid in the design of polymer/consumer product interfaces with reduced risk of contamination and longer shelf life.
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Affiliation(s)
- Paulo G M Mileo
- Schrödinger, GmbH, Glücksteinallee 25, Mannheim 68159, Germany
| | | | - Jeffrey M Sanders
- Schrödinger, Inc., 1540 Broadway, New York, New York 10036, United States
| | - Benjamin J Coscia
- Schrödinger, Inc., 01 SW Main St. #1300, Portland, Oregon 97204, United States
| | - Andrea R Browning
- Schrödinger, Inc., 01 SW Main St. #1300, Portland, Oregon 97204, United States
| | - Mathew D Halls
- Schrödinger, Inc., 5820 Oberlin Dr., San Diego, California 92121, United States
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2
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Bottoms CM, Stein GE, Doxastakis M. Accelerated Diffusion Following Deprotection in Chemically Amplified Resists. J Phys Chem B 2022; 126:6562-6574. [PMID: 35984912 DOI: 10.1021/acs.jpcb.2c03775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polymeric chemically amplified resists (CARs) are critical materials for high-throughput lithographic processes. A photoactivated acid-anion catalyst changes the polymer's solubility via a deprotection reaction, which enables pattern development through selective dissolution. To capture observed reaction kinetics, reaction-diffusion models employ a catalyst diffusivity that is accelerated by reaction. However, the microscopic origin and factors contributing to this phenomena remain unclear. Herein, we employ detailed atomistic molecular dynamics simulations to examine the impact of protecting group removal and material relaxation on catalyst mobility. We report data on polymer density, catalyst dispersion, excess free volume, and segmental dynamics with increasing time/extent of deprotection. We then propose simple kinetic Monte Carlo algorithms that can describe both molecular dynamics simulations of deprotection reactions and experimental data.
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Affiliation(s)
- Christopher M Bottoms
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Gila E Stein
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Manolis Doxastakis
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
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3
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Kikutsuji T, Mori Y, Okazaki KI, Mori T, Kim K, Matubayasi N. Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI). J Chem Phys 2022; 156:154108. [DOI: 10.1063/5.0087310] [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
A method for obtaining appropriate reaction coordinates is required to identify transition states distinguishing product and reactant in complex molecular systems. Recently, abundant research has been devoted to obtaining reaction coordinates using artificial neural networks from deep learning literature, where many collective variables are typically utilized in the input layer. However, it is difficult to explain the details of which collective variables contribute to the predicted reaction coordinates owing to the complexity of the nonlinear functions in deep neural networks. To overcome this limitation, we used Explainable Artificial Intelligence (XAI) methods of the Local Interpretable Model-agnostic Explanation (LIME) and the game theory-based framework known as Shapley Additive exPlanations (SHAP). We demonstrated that XAI enables us to obtain the degree of contribution of each collective variable to reaction coordinates that is determined by nonlinear regressions with deep learning for the committor of the alanine dipeptide isomerization in vacuum. In particular, both LIME and SHAP provide important features to the predicted reaction coordinates, which are characterized by appropriate dihedral angles consistent with those previously reported from the committor test analysis. The present study offers an AI-aided framework to explain the appropriate reaction coordinates, which acquires considerable significance when the number of degrees of freedom increases.
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Affiliation(s)
| | | | - Kei-ichi Okazaki
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Japan
| | - Toshifumi Mori
- Kyushu University Institute for Materials Chemistry and Engineering, Japan
| | - Kang Kim
- Graduate School of Engineering Science, Osaka University - Toyonaka Campus, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Japan
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4
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Effects of molecular design parameters on plasticizer performance in poly(vinyl chloride): A comprehensive molecular simulation study. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2021.117334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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5
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Mei B, Schweizer KS. Theory of the effect of external stress on the activated dynamics and transport of dilute penetrants in supercooled liquids and glasses. J Chem Phys 2021; 155:054505. [PMID: 34364324 DOI: 10.1063/5.0056920] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We generalize the self-consistent cooperative hopping theory for a dilute spherical penetrant or tracer activated dynamics in dense metastable hard sphere fluids and glasses to address the effect of external stress, the consequences of which are systematically established as a function of matrix packing fraction and penetrant-to-matrix size ratio. All relaxation processes speed up under stress, but the difference between the penetrant and matrix hopping (alpha relaxation) times decreases significantly with stress corresponding to less time scale decoupling. A dynamic crossover occurs at a critical "slaving onset" stress beyond which the matrix activated hopping relaxation time controls the penetrant hopping time. This characteristic stress increases (decreases) exponentially with packing fraction (size ratio) and can be well below the absolute yield stress of the matrix. Below the slaving onset, the penetrant hopping time is predicted to vary exponentially with stress, differing from the power law dependence of the pure matrix alpha time due to system-specificity of the stress-induced changes in the penetrant local cage and elastic barriers. An exponential growth of the penetrant alpha relaxation time with size ratio under stress is predicted, and at a fixed matrix packing fraction, the exponential relation between penetrant hopping time and stress for different size ratios can be collapsed onto a master curve. Direct connections between the short- and long-time activated penetrant dynamics and between the penetrant (or matrix) alpha relaxation time and matrix thermodynamic dimensionless compressibility are also predicted. The presented results should be testable in future experiments and simulations.
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Affiliation(s)
- Baicheng Mei
- Department of Materials Science, University of Illinois, Urbana, Illinois 61801, USA
| | - Kenneth S Schweizer
- Department of Materials Science, University of Illinois, Urbana, Illinois 61801, USA
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6
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Mei B, Schweizer KS. Activated penetrant dynamics in glass forming liquids: size effects, decoupling, slaving, collective elasticity and correlation with matrix compressibility. SOFT MATTER 2021; 17:2624-2639. [PMID: 33528485 DOI: 10.1039/d0sm02215b] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We employ the microscopic self-consistent cooperative hopping theory of penetrant activated dynamics in glass forming viscous liquids and colloidal suspensions to address new questions over a wide range of high matrix packing fractions and penetrant-to-matrix particle size ratios. The focus is on the mean activated relaxation time of smaller tracers in a hard sphere fluid of larger particle matrices. This quantity also determines the penetrant diffusion constant and connects directly with the structural relaxation time probed in an incoherent dynamic structure factor measurement. The timescale of the non-activated fast dissipative process is also studied and is predicted to follow power laws with the contact value of the penetrant-matrix pair correlation function and the penetrant-matrix size ratio. For long time penetrant relaxation, in the relatively lower packing fraction metastable regime the local cage barriers are dominant and matrix collective elasticity effects unimportant. As packing fraction and/or penetrant size grows, much higher barriers emerge and the collective elasticity associated with the correlated matrix dynamic displacement that facilitates penetrant hopping becomes important. This results in a non-monotonic variation with packing fraction of the degree of decoupling between the matrix and penetrant alpha relaxation times. The conditions required for penetrant hopping to become slaved to the matrix alpha process are determined, which depend mainly on the penetrant to matrix particle size ratio. By analyzing the absolute and relative importance of the cage and elastic barriers we establish a mechanistic understanding of the origin of the predicted exponential growth of the penetrant hopping time with size ratio predicted at very high packing fractions. A dynamics-thermodynamics power law connection between the penetrant activation barrier and the matrix dimensionless compressibility is established as a prediction of theory, with different scaling exponents depending on whether matrix collective elasticity effects are important. Quantitative comparisons with simulations of the penetrant relaxation time, diffusion constant, and transient localization length of tracers in dense colloidal suspensions and cold viscous liquids reveal good agreements. Multiple new predictions are made that are testable via future experiments and simulations. Extension of the theoretical approach to more complex systems of high experimental interest (nonspherical molecules, semiflexible polymers, crosslinked networks) interacting via variable hard or soft repulsions and/or short range attractions is possible, including under external deformation.
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Affiliation(s)
- Baicheng Mei
- Department of Materials Science, University of Illinois, Urbana, IL 61801, USA. and Materials Research Laboratory, University of Illinois, Urbana, IL 61801, USA
| | - Kenneth S Schweizer
- Department of Materials Science, University of Illinois, Urbana, IL 61801, USA. and Materials Research Laboratory, University of Illinois, Urbana, IL 61801, USA and Department of Chemistry, University of Illinois, Urbana, IL 61801, USA and Department of Chemical & Biomolecular Engineering, University of Illinois, Urbana, IL 61801, USA
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7
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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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8
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Levintov L, Paul S, Vashisth H. Reaction Coordinate and Thermodynamics of Base Flipping in RNA. J Chem Theory Comput 2021; 17:1914-1921. [PMID: 33594886 DOI: 10.1021/acs.jctc.0c01199] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Base flipping is a key biophysical event involved in recognition of various ligands by ribonucleic acid (RNA) molecules. However, the mechanism of base flipping in RNA remains poorly understood, in part due to the lack of atomistic details on complex rearrangements in neighboring bases. In this work, we applied transition path sampling (TPS) methods to study base flipping in a double-stranded RNA (dsRNA) molecule that is known to interact with RNA-editing enzymes through this mechanism. We obtained an ensemble of 1000 transition trajectories to describe the base-flipping process. We used the likelihood maximization method to determine the refined reaction coordinate (RC) consisting of two collective variables (CVs), a distance and a dihedral angle between nucleotides that form stacking interactions with the flipping base. The free energy profile projected along the refined RC revealed three minima, two corresponding to the initial and final states and one for a metastable state. We suggest that the metastable state likely represents a wobbled conformation of nucleobases observed in NMR studies that is often characterized as the flipped state. The analyses of reactive trajectories further revealed that the base flipping is coupled to a global conformational change in a stem-loop of dsRNA.
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Affiliation(s)
- Lev Levintov
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, United States
| | - Sanjib Paul
- Department of Chemistry, New York University, New York 10003, New York, United States
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, United States
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9
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Bottoms CM, Terlier T, Stein GE, Doxastakis M. Ion Diffusion in Chemically Amplified Resists. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher M. Bottoms
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Tanguy Terlier
- Shared Equipment Authority, Rice University, Houston, Texas 77005, United States
| | - Gila E. Stein
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Manolis Doxastakis
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
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10
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Mori Y, Okazaki KI, Mori T, Kim K, Matubayasi N. Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide. J Chem Phys 2020; 153:054115. [DOI: 10.1063/5.0009066] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Yusuke Mori
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | | | - Toshifumi Mori
- Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
- The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
| | - Kang Kim
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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11
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Kim M, Moon J, Park S, Cho M. Selective Dissolution Resistance Control of EUV Photoresist Using Multiscale Simulation: Rational Design of Hybrid System. Macromolecules 2020. [DOI: 10.1021/acs.macromol.9b02378] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Muyoung Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul, Republic of Korea
- Division of Multiscale Mechanical Design, School of Mechanical and Aerospace Engineering, Seoul National University, Seoul, Republic of Korea
| | - Junghwan Moon
- Institute of Advanced Machines and Design, Seoul National University, Seoul, Republic of Korea
- Division of Multiscale Mechanical Design, School of Mechanical and Aerospace Engineering, Seoul National University, Seoul, Republic of Korea
| | - Sungwoo Park
- Division of Multiscale Mechanical Design, School of Mechanical and Aerospace Engineering, Seoul National University, Seoul, Republic of Korea
| | - Maenghyo Cho
- Institute of Advanced Machines and Design, Seoul National University, Seoul, Republic of Korea
- Division of Multiscale Mechanical Design, School of Mechanical and Aerospace Engineering, Seoul National University, Seoul, Republic of Korea
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12
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Greenfield ML. Representing polymer molecular structure using molecular simulations for the study of liquid sorption and diffusion. Curr Opin Chem Eng 2020. [DOI: 10.1016/j.coche.2020.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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13
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Vergadou N, Theodorou DN. Molecular Modeling Investigations of Sorption and Diffusion of Small Molecules in Glassy Polymers. MEMBRANES 2019; 9:E98. [PMID: 31398889 PMCID: PMC6723301 DOI: 10.3390/membranes9080098] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 11/16/2022]
Abstract
With a wide range of applications, from energy and environmental engineering, such as in gas separations and water purification, to biomedical engineering and packaging, glassy polymeric materials remain in the core of novel membrane and state-of the art barrier technologies. This review focuses on molecular simulation methodologies implemented for the study of sorption and diffusion of small molecules in dense glassy polymeric systems. Basic concepts are introduced and systematic methods for the generation of realistic polymer configurations are briefly presented. Challenges related to the long length and time scale phenomena that govern the permeation process in the glassy polymer matrix are described and molecular simulation approaches developed to address the multiscale problem at hand are discussed.
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Affiliation(s)
- Niki Vergadou
- Molecular Thermodynamics and Modelling of Materials Laboratory, Institute of Nanoscience and Nanotechnology, National Center for Scientific Research Demokritos, Aghia Paraskevi Attikis, GR-15310 Athens, Greece.
| | - Doros N Theodorou
- School of Chemical Engineering, National Technical University of Athens, GR 15780 Athens, Greece
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14
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Paul S, Nair NN, Vashisth H. Phase space and collective variable based simulation methods for studies of rare events. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1634268] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Sanjib Paul
- Department of Chemical Engineering, University of New Hampshire, Durham, NH, USA
| | - Nisanth N. Nair
- Department of Chemistry, Indian Institute of Technology, Kanpur, India
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham, NH, USA
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15
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Xi L. Molecular simulation for predicting the rheological properties of polymer melts. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1605600] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Li Xi
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario, Canada
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16
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Li D, Panchal K, Mafi R, Xi L. An Atomistic Evaluation of the Compatibility and Plasticization Efficacy of Phthalates in Poly(vinyl chloride). Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b00756] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Dongyang Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Department of Chemical Engineering, McMaster Universtiy, Hamilton, Ontario L8S 4L7, Canada
| | - Kushal Panchal
- Department of Chemical Engineering, McMaster Universtiy, Hamilton, Ontario L8S 4L7, Canada
| | - Roozbeh Mafi
- Canadian General
Tower, Ltd., Cambridge, Ontario N1R 5T6, Canada
| | - Li Xi
- Department of Chemical Engineering, McMaster Universtiy, Hamilton, Ontario L8S 4L7, Canada
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17
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Kanduč M, Kim WK, Roa R, Dzubiella J. Selective Molecular Transport in Thermoresponsive Polymer Membranes: Role of Nanoscale Hydration and Fluctuations. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b00735] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Matej Kanduč
- Research Group for Simulations of Energy Materials, Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany
| | - Won Kyu Kim
- Research Group for Simulations of Energy Materials, Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany
| | - Rafael Roa
- Research Group for Simulations of Energy Materials, Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany
- Departamento de Física Aplicada I, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071 Málaga, Spain
| | - Joachim Dzubiella
- Research Group for Simulations of Energy Materials, Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Strasse 3, D-79104 Freiburg, Germany
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18
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Meng D, Zhang K, Kumar SK. Size-dependent penetrant diffusion in polymer glasses. SOFT MATTER 2018; 14:4226-4230. [PMID: 29774356 DOI: 10.1039/c8sm00701b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Molecular Dynamics simulations are used to understand the underpinning basis of the transport of gas-like solutes in deeply quenched polymeric glasses. As found in previous work, small solutes, with sizes smaller than 0.15 times the chain monomer size, move as might be expected in a medium with large pores. In contrast, the motion of larger solutes is activated and is strongly facilitated by matrix motion. In particular, solute motion is coupled to the local elastic fluctuations of the matrix as characterized by the Debye-Waller factor. While similar ideas have been previously proposed for the viscosity of supercooled liquids above their glass transition, to our knowledge, this is the first illustration of this concept in the context of solute mass transport in deeply quenched polymer glasses.
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Affiliation(s)
- Dong Meng
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA.
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19
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Zhang R, Schweizer KS. Correlated matrix-fluctuation-mediated activated transport of dilute penetrants in glass-forming liquids and suspensions. J Chem Phys 2017; 146:194906. [PMID: 28527449 DOI: 10.1063/1.4983224] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We formulate a microscopic, force-level statistical mechanical theory for the activated diffusion of dilute penetrants in dense liquids, colloidal suspensions, and glasses. The approach explicitly and self-consistently accounts for coupling between penetrant hopping and matrix dynamic displacements that actively facilitate the hopping event. The key new ideas involve two mechanistically (at a stochastic trajectory level) coupled dynamic free energy functions for the matrix and spherical penetrant particles. A single dynamic coupling parameter quantifies how much the matrix displaces relative to the penetrant when the latter reaches its transition state which is determined via the enforcement of a temporal causality or coincidence condition. The theory is implemented for dilute penetrants smaller than the matrix particles, with or without penetrant-matrix attractive forces. Model calculations reveal a rich dependence of the penetrant diffusion constant and degree of dynamic coupling on size ratio, volume fraction, and attraction strength. In the absence of attractions, a near exponential decrease of penetrant diffusivity with size ratio over an intermediate range is predicted, in contrast to the much steeper, non-exponential variation if one assumes local matrix dynamical fluctuations are not correlated with penetrant motion. For sticky penetrants, the relative and absolute influence of caging versus physical bond formation is studied. The conditions for a dynamic crossover from the case where a time scale separation between penetrant and matrix activated hopping exists to a "slaved" or "constraint release" fully coupled regime are determined. The particle mixture model is mapped to treat experimental thermal systems and applied to make predictions for the diffusivity of water, toluene, methanol, and oxygen in polyvinylacetate liquids and glasses. The theory agrees well with experiment with values of the penetrant-matrix size ratio close to their chemically intuitive values.
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Affiliation(s)
- Rui Zhang
- Department of Materials Science, University of Illinois, Urbana, Illinois 61801, USA
| | - Kenneth S Schweizer
- Department of Materials Science, University of Illinois, Urbana, Illinois 61801, USA
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20
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Domenek S, Fernandes-Nassar S, Ducruet V. Rheology, Mechanical Properties, and Barrier Properties of Poly(lactic acid). SYNTHESIS, STRUCTURE AND PROPERTIES OF POLY(LACTIC ACID) 2017. [DOI: 10.1007/12_2016_17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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21
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Zhang R, Schweizer KS. Statistical Mechanical Theory of Penetrant Diffusion in Polymer Melts and Glasses. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b00725] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rui Zhang
- Department of Materials Science
and Frederick Seitz Materials Research Laboratory, University of Illinois, 1304 West Green Street, Urbana, Illinois 61801, United States
| | - Kenneth S. Schweizer
- Department of Materials Science
and Frederick Seitz Materials Research Laboratory, University of Illinois, 1304 West Green Street, Urbana, Illinois 61801, United States
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22
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Zhang R, Schweizer KS. Theory of activated penetrant diffusion in viscous fluids and colloidal suspensions. J Chem Phys 2015; 143:144906. [PMID: 26472397 DOI: 10.1063/1.4932679] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We heuristically formulate a microscopic, force level, self-consistent nonlinear Langevin equation theory for activated barrier hopping and non-hydrodynamic diffusion of a hard sphere penetrant in very dense hard sphere fluid matrices. Penetrant dynamics is controlled by a rich competition between force relaxation due to penetrant self-motion and collective matrix structural (alpha) relaxation. In the absence of penetrant-matrix attraction, three activated dynamical regimes are predicted as a function of penetrant-matrix size ratio which are physically distinguished by penetrant jump distance and the nature of matrix motion required to facilitate its hopping. The penetrant diffusion constant decreases the fastest with size ratio for relatively small penetrants where the matrix effectively acts as a vibrating amorphous solid. Increasing penetrant-matrix attraction strength reduces penetrant diffusivity due to physical bonding. For size ratios approaching unity, a distinct dynamical regime emerges associated with strong slaving of penetrant hopping to matrix structural relaxation. A crossover regime at intermediate penetrant-matrix size ratio connects the two limiting behaviors for hard penetrants, but essentially disappears if there are strong attractions with the matrix. Activated penetrant diffusivity decreases strongly with matrix volume fraction in a manner that intensifies as the size ratio increases. We propose and implement a quasi-universal approach for activated diffusion of a rigid atomic/molecular penetrant in a supercooled liquid based on a mapping between the hard sphere system and thermal liquids. Calculations for specific systems agree reasonably well with experiments over a wide range of temperature, covering more than 10 orders of magnitude of variation of the penetrant diffusion constant.
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Affiliation(s)
- Rui Zhang
- Department of Materials Science and Frederick Seitz Materials Research Laboratory, University of Illinois, 1304 West Green Street, Urbana, Illinois 61801, USA
| | - Kenneth S Schweizer
- Department of Materials Science and Frederick Seitz Materials Research Laboratory, University of Illinois, 1304 West Green Street, Urbana, Illinois 61801, USA
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Paul S, Taraphder S. Determination of the Reaction Coordinate for a Key Conformational Fluctuation in Human Carbonic Anhydrase II. J Phys Chem B 2015; 119:11403-15. [DOI: 10.1021/acs.jpcb.5b03655] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sanjib Paul
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Srabani Taraphder
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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Mullen RG, Shea JE, Peters B. Easy Transition Path Sampling Methods: Flexible-Length Aimless Shooting and Permutation Shooting. J Chem Theory Comput 2015; 11:2421-8. [DOI: 10.1021/acs.jctc.5b00032] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ryan Gotchy Mullen
- Department of Chemical Engineering, ‡Department of Chemistry & Biochemistry, §Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemical Engineering, ‡Department of Chemistry & Biochemistry, §Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Baron Peters
- Department of Chemical Engineering, ‡Department of Chemistry & Biochemistry, §Department of Physics, University of California, Santa Barbara, California 93106, United States
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Li W, Ma A. Recent developments in methods for identifying reaction coordinates. MOLECULAR SIMULATION 2014; 40:784-793. [PMID: 25197161 PMCID: PMC4152980 DOI: 10.1080/08927022.2014.907898] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In the study of rare events in complex systems with many degrees of freedom, a key element is to identify the reaction coordinates of a given process. Over recent years, a number of methods and protocols have been developed to extract the reaction coordinates based on limited information from molecular dynamics simulations. In this review, we provide a brief survey over a number of major methods developed in the past decade, some of which are discussed in greater detail, to provide an overview of the problems that are partially solved and challenges that still remain. A particular emphasis has been placed on methods for identifying reaction coordinates that are related to the committor.
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Affiliation(s)
- Wenjin Li
- Department of Bioengineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607, USA
| | - Ao Ma
- Department of Bioengineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607, USA
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