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Drisko CR, Gezelter JD. A Reverse Nonequilibrium Molecular Dynamics Algorithm for Coupled Mass and Heat Transport in Mixtures. J Chem Theory Comput 2024; 20:4986-4997. [PMID: 38833377 DOI: 10.1021/acs.jctc.4c00182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
We present a new method for introducing stable nonequilibrium concentration gradients in molecular dynamics simulations of mixtures. This method extends earlier reverse nonequilibrium molecular dynamics (RNEMD) methods, which use kinetic energy scaling moves to create temperature or velocity gradients. In the new scaled particle flux (SPF-RNEMD) algorithm, energies and forces are computed simultaneously for a molecule existing in two nonadjacent regions of a simulation box, and the system evolves under a linear combination of these interactions. A continuously increasing particle scaling variable is responsible for the migration of the molecule between the regions as the simulation progresses, allowing for simulations under an applied particle flux. To test the method, we investigate diffusivity in mixtures of identical but distinguishable particles and in a simple mixture of multiple Lennard-Jones particles. The resulting concentration gradients provide Fick diffusion constants for mixtures. We also discuss using the new method to obtain coupled transport properties using simultaneous particle and thermal fluxes to compute the temperature dependence of the diffusion coefficient and activation energies for diffusion from a single simulation. Lastly, we demonstrate the use of this new method in interfacial systems by computing the diffusive permeability of a molecular fluid moving through a nanoporous graphene membrane.
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Affiliation(s)
- Cody R Drisko
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - J Daniel Gezelter
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
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Transport Properties of Binary Lennard-Jones Mixtures: Insights from Entropy Scaling and Conformal Solution Theory. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Fakhardji W, Szabó P, El-Kader MSA, Haskopoulos A, Maroulis G, Gustafsson M. Collision-induced absorption in Ar-Kr gas mixtures: A molecular dynamics study with new potential and dipole data. J Chem Phys 2019; 151:144303. [PMID: 31615255 DOI: 10.1063/1.5099700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have implemented a scheme for classical molecular dynamics simulations of collision-induced absorption. The program has been applied to a gas mixture of argon (Ar) and krypton (Kr). The simulations are compared with accurate quantum dynamical calculations. The comparisons of the absorption coefficients show that classical molecular dynamics is correct within 10% for photon wave numbers up to 220 cm-1 at a temperature of 200 K for this system. At higher temperatures, the agreement is even better. Molecular dynamics accounts for many-body interactions, which, for example, give rise to continuous dimer formation and destruction in the gas. In this way, the method has an advantage compared with bimolecular classical (trajectory) treatments. The calculations are carried out with a new empirical Ar-Kr pair potential. This has been obtained through extensive analysis of experimental thermophysical and transport properties. We also present a new high level ab initio Ar-Kr potential curve for comparison, as well as ab initio interaction-induced dipole curves computed with different methods. In addition, the Ar-Kr polarizability and hyperpolarizability are reported. A comparison of the computed absorption spectra with an experiment taken at 300 K shows satisfactory agreement although a difference in absolute magnitude of 10%-15% persists. This discrepancy we attribute mainly to experimental uncertainty.
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Affiliation(s)
- Wissam Fakhardji
- Applied Physics, Division of Materials Science, Department of Engineering Science and Mathematics, Luleå University of Technology, 97187 Luleå, Sweden
| | - Péter Szabó
- Applied Physics, Division of Materials Science, Department of Engineering Science and Mathematics, Luleå University of Technology, 97187 Luleå, Sweden
| | - M S A El-Kader
- Department of Engineering Mathematics and Physics, Faculty of Engineering, Cairo University, Giza 12211, Egypt
| | | | - George Maroulis
- Department of Chemistry, University of Patras, Patras GR-26500, Greece
| | - Magnus Gustafsson
- Applied Physics, Division of Materials Science, Department of Engineering Science and Mathematics, Luleå University of Technology, 97187 Luleå, Sweden
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Hirose R, Nakaya T, Naito Y, Daidoji T, Bandou R, Inoue K, Dohi O, Yoshida N, Konishi H, Itoh Y. Situations Leading to Reduced Effectiveness of Current Hand Hygiene against Infectious Mucus from Influenza Virus-Infected Patients. mSphere 2019; 4:e00474-19. [PMID: 31533996 PMCID: PMC6751490 DOI: 10.1128/msphere.00474-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/21/2019] [Indexed: 01/05/2023] Open
Abstract
Both antiseptic hand rubbing (AHR) using ethanol-based disinfectants (EBDs) and antiseptic hand washing (AHW) are important means of infection control to prevent seasonal influenza A virus (IAV) outbreaks. However, previous reports suggest a reduced efficacy of ethanol disinfection against pathogens in mucus. We aimed to elucidate the situations and mechanisms underlying the reduced efficacy of EBDs against IAV in infectious mucus. We evaluated IAV inactivation and ethanol concentration change using IAV-infected patients' mucus (sputum). Additionally, AHR and AHW effectiveness against infectious mucus adhering to the hands and fingers was evaluated in 10 volunteers. Our clinical study showed that EBD effectiveness against IAV in mucus was extremely reduced compared to IAV in saline. IAV in mucus remained active despite 120 s of AHR; however, IAV in saline was completely inactivated within 30 s. Due to the low rate of diffusion/convection because of the physical properties of mucus as a hydrogel, the time required for the ethanol concentration to reach an IAV inactivation level and thus for EBDs to completely inactivate IAV was approximately eight times longer in mucus than in saline. On the other hand, AHR inactivated IAV in mucus within 30 s when the mucus dried completely because the hydrogel characteristics were lost. Additionally, AHW rapidly inactivated IAV. Until infectious mucus has completely dried, infectious IAV can remain on the hands and fingers, even after appropriate AHR using EBD, thereby increasing the risk of IAV transmission. We clarified the ineffectiveness of EBD use against IAV in infectious mucus.IMPORTANCE Antiseptic hand rubbing (AHR) and antiseptic hand washing (AHW) are important to prevent the spread of influenza A virus (IAV). This study elucidated the situations/mechanisms underlying the reduced efficacy of AHR against infectious mucus derived from IAV-infected individuals and indicated the weaknesses of the current hand hygiene regimens. Due to the low rate of diffusion/convection because of the physical properties of mucus as a hydrogel, the efficacy of AHR using ethanol-based disinfectant against mucus is greatly reduced until infectious mucus adhering to the hands/fingers has completely dried. If there is insufficient time before treating the next patient (i.e., if the infectious mucus is not completely dry), medical staff should be aware that effectiveness of AHR is reduced. Since AHW is effective against both dry and nondry infectious mucus, AHW should be adopted to compensate for these weaknesses of AHR.
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Affiliation(s)
- Ryohei Hirose
- Department of Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takaaki Nakaya
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuji Naito
- Department of Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tomo Daidoji
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Risa Bandou
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Forensics Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ken Inoue
- Department of Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Osamu Dohi
- Department of Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Naohisa Yoshida
- Department of Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hideyuki Konishi
- Department of Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshito Itoh
- Department of Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
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