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Sheydaafar Z, Dyre JC, Schrøder TB. Scaling Properties of Liquid Dynamics Predicted from a Single Configuration: Small Rigid Molecules. J Phys Chem B 2023; 127:3478-3487. [PMID: 37040433 DOI: 10.1021/acs.jpcb.3c01574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Isomorphs are curves in the thermodynamic phase diagram along which structure and dynamics are invariant to a good approximation. There are two main ways to trace out isomorphs, the configurational-adiabat method and the direct-isomorph-check method. Recently a new method based on the scaling properties of forces was introduced and shown to work very well for atomic systems [T. B. Schrøder, Phys. Rev. Lett. 2022, 129, 245501]. A unique feature of this method is that it only requires a single equilibrium configuration for tracing out an isomorph. We here test generalizations of this method to molecular systems and compare to simulations of three simple molecular models: the asymmetric dumbbell model of two Lennard-Jones spheres, the symmetric inverse-power-law dumbbell model, and the Lewis-Wahnström o-terphenyl model. We introduce and test two force-based and one torque-based methods, all of which require just a single configuration for tracing out an isomorph. Overall, the method based on requiring invariant center-of-mass reduced forces works best.
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Affiliation(s)
- Zahraa Sheydaafar
- Glass and Time, IMFUFA, Department of Science and Environment, Roskilde University, P.O. Box 260, DK-4000 Roskilde, Denmark
| | - Jeppe C Dyre
- Glass and Time, IMFUFA, Department of Science and Environment, Roskilde University, P.O. Box 260, DK-4000 Roskilde, Denmark
| | - Thomas B Schrøder
- Glass and Time, IMFUFA, Department of Science and Environment, Roskilde University, P.O. Box 260, DK-4000 Roskilde, Denmark
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Mausbach P, Fingerhut R, Vrabec J. Thermodynamic metric geometry and the Fisher-Widom line of simple fluids. Phys Rev E 2022; 106:034136. [PMID: 36266912 DOI: 10.1103/physreve.106.034136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/12/2022] [Indexed: 06/16/2023]
Abstract
Two boundary lines are frequently discussed in the literature, separating state regions dominated by repulsion or attraction. The Fisher-Widom line indicates where the longest-range decay of the total pair correlation function crosses from monotonic to exponentially damped oscillatory. In the context of thermodynamic metric geometry, such a transition exists where the Ricci curvature scalar vanishes, R=0. To establish a possible relation between these two lines, R is worked out for four simple fluids. The truncated and shifted Lennard-Jones, a colloid-like and the square-well potential are analyzed to investigate the influence of the repulsive nature on the location of the R=0 line. For the longer-ranged Lennard-Jones potential, the influence of the cutoff radius on the R=0 line is studied. The results are compared with literature data on the Fisher-Widom line. Since such data are rare for the longer-ranged Lennard-Jones potential, dedicated simulations are carried out to determine the number of zeros of the total correlation function, which may provide approximate information about the position of the Fisher-Widom line. An increase of the repulsive strength toward hard sphere interaction leads to the disappearance of the R=0 line in the fluid phase. A rising attraction range results in the nonexistence of the Fisher-Widom line, while it has little effect on the R=0 line as long as it is present in the fluid state.
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Affiliation(s)
- Peter Mausbach
- Plant and Process Engineering, Technical University of Cologne, 50678 Cologne, Germany
| | - Robin Fingerhut
- Thermodynamics and Process Engineering, Technical University of Berlin, 10587 Berlin, Germany
| | - Jadran Vrabec
- Thermodynamics and Process Engineering, Technical University of Berlin, 10587 Berlin, Germany
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Bolmatov D. The Phonon Theory of Liquids and Biological Fluids: Developments and Applications. J Phys Chem Lett 2022; 13:7121-7129. [PMID: 35950307 DOI: 10.1021/acs.jpclett.2c01779] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Among the three basic states of matter (solid, liquid, and gas), the liquid state has always eluded general theoretical approaches for describing liquid energy and heat capacity. In this Viewpoint, we derive the phonon theory of liquids and biological fluids stemming from Frenkel's microscopic picture of the liquid state. Specifically, the theory predicts the existence of phonon gaps in vibrational spectra of liquids and a thermodynamic boundary in the supercritical state. Direct experimental evidence reaffirming these theoretical predictions was achieved through a combination of techniques using static compression X-ray diffraction and inelastic X-ray scattering on deeply supercritical argon in a diamond anvil cell. Furthermore, these findings inspired and then led to the discovery of phonon gaps in liquid crystals (mesogens), block copolymers, and biological membranes. Importantly, phonon gaps define viscoelastic crossovers in cellular membranes responsible for lipid self-diffusion, lateral molecular-level stress propagation, and passive transmembrane transport of small molecules and solutes. Finally, molecular interactions mediated by external stimuli result in synaptic activity controlling biological membranes' plasticity resulting in learning and memory. Therefore, we also discuss learning and memory effects─equally important for neuroscience as well as for the development of neuromorphic devices─facilitated in biological membranes by external stimuli.
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Affiliation(s)
- Dima Bolmatov
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, United States
- Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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Bell I, Fingerhut R, Vrabec J, Costigliola L. Connecting Entropy Scaling and Density Scaling. J Chem Phys 2022; 157:074501. [DOI: 10.1063/5.0097088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
It is shown that the residual entropy (entropy minus that of the ideal gas at the same temperature and density) is mostly synonymous with the independent variable of density scaling, identifying a direct link between these two approaches. The residual entropy and the effective hardness of interaction (itself a derivative at constant residual entropy) are studied for the Lennard-Jones monomer and dimer as well as a range of rigid molecular models for carbon dioxide. It is observed that the density scaling exponent appears to be related to the two-body interactions in the dilute-gas limit.
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Affiliation(s)
- Ian Bell
- National Institute of Standards and Technology Applied Chemicals and Materials Division, United States of America
| | | | - Jadran Vrabec
- Process Engineering, Technical University of Berlin, Germany
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Singh AN, Dyre JC, Pedersen UR. Solid–liquid coexistence of neon, argon, krypton, and xenon studied by simulations. J Chem Phys 2021; 154:134501. [DOI: 10.1063/5.0045398] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Aditya N. Singh
- Department of Chemistry, University of California, Berkeley, California 94720, USA and Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53703, USA
| | - Jeppe C. Dyre
- Glass and Time, IMFUFA, Department of Science and Environment, Roskilde University, P. O. Box 260, DK-4000 Roskilde, Denmark
| | - Ulf R. Pedersen
- Glass and Time, IMFUFA, Department of Science and Environment, Roskilde University, P. O. Box 260, DK-4000 Roskilde, Denmark
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Simar C, Cebolla AM, Chartier G, Petieau M, Bontempi G, Berthoz A, Cheron G. Hyperscanning EEG and Classification Based on Riemannian Geometry for Festive and Violent Mental State Discrimination. Front Neurosci 2020; 14:588357. [PMID: 33424535 PMCID: PMC7793677 DOI: 10.3389/fnins.2020.588357] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/04/2020] [Indexed: 12/14/2022] Open
Abstract
Interactions between two brains constitute the essence of social communication. Daily movements are commonly executed during social interactions and are determined by different mental states that may express different positive or negative behavioral intent. In this context, the effective recognition of festive or violent intent before the action execution remains crucial for survival. Here, we hypothesize that the EEG signals contain the distinctive features characterizing movement intent already expressed before movement execution and that such distinctive information can be identified by state-of-the-art classification algorithms based on Riemannian geometry. We demonstrated for the first time that a classifier based on covariance matrices and Riemannian geometry can effectively discriminate between neutral, festive, and violent mental states only on the basis of non-invasive EEG signals in both the actor and observer participants. These results pave the way for new electrophysiological discrimination of mental states based on non-invasive EEG recordings and cutting-edge machine learning techniques.
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Affiliation(s)
- Cédric Simar
- Machine Learning Group (MLG), Computer Science Department, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Ana-Maria Cebolla
- Laboratory of Neurophysiology and Movement Biomechanics, ULB Neuroscience Institute, Université libre de Bruxelles, Brussels, Belgium
| | - Gaëlle Chartier
- Centre Interdisciplinaire de Biologie, Collège de France-CNRS, Paris, France.,Department of Health, Medicine and Human Biology, Université Paris 13, Bobigny, France
| | - Mathieu Petieau
- Laboratory of Neurophysiology and Movement Biomechanics, ULB Neuroscience Institute, Université libre de Bruxelles, Brussels, Belgium
| | - Gianluca Bontempi
- Machine Learning Group (MLG), Computer Science Department, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Alain Berthoz
- Centre Interdisciplinaire de Biologie, Collège de France-CNRS, Paris, France
| | - Guy Cheron
- Laboratory of Neurophysiology and Movement Biomechanics, ULB Neuroscience Institute, Université libre de Bruxelles, Brussels, Belgium.,Laboratory of Electrophysiology, Université de Mons-Hainaut, Mons, Belgium
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Bell IH, Dyre JC, Ingebrigtsen TS. Excess-entropy scaling in supercooled binary mixtures. Nat Commun 2020; 11:4300. [PMID: 32855393 PMCID: PMC7453028 DOI: 10.1038/s41467-020-17948-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/22/2020] [Indexed: 11/09/2022] Open
Abstract
Transport coefficients, such as viscosity or diffusion coefficient, show significant dependence on density or temperature near the glass transition. Although several theories have been proposed for explaining this dynamical slowdown, the origin remains to date elusive. We apply here an excess-entropy scaling strategy using molecular dynamics computer simulations and find a quasiuniversal, almost composition-independent, relation for binary mixtures, extending eight orders of magnitude in viscosity or diffusion coefficient. Metallic alloys are also well captured by this relation. The excess-entropy scaling predicts a quasiuniversal breakdown of the Stokes-Einstein relation between viscosity and diffusion coefficient in the supercooled regime. Additionally, we find evidence that quasiuniversality extends beyond binary mixtures, and that the origin is difficult to explain using existing arguments for single-component quasiuniversality.
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Affiliation(s)
- Ian H Bell
- Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, CO, 80305, USA
| | - Jeppe C Dyre
- Glass and Time, IMFUFA, Department of Science and Environment, Roskilde University, Postbox 260, Roskilde, DK-4000, Denmark
| | - Trond S Ingebrigtsen
- Glass and Time, IMFUFA, Department of Science and Environment, Roskilde University, Postbox 260, Roskilde, DK-4000, Denmark.
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Bell IH. Effective hardness of interaction from thermodynamics and viscosity in dilute gases. J Chem Phys 2020; 152:164508. [PMID: 32357769 DOI: 10.1063/5.0007583] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The hardness of the effective inverse power law (IPL) potential, which can be obtained from thermodynamics or collision integrals, can be used to demonstrate similarities between thermodynamic and transport properties. This link is investigated for systems of increasing complexity (i.e., the EXP, square-well, Lennard-Jones, and Stockmayer potentials; ab initio results for small molecules; and rigid linear chains of Lennard-Jones sites). These results show that while the two approaches do not yield precisely the same values of effective IPL exponent, their qualitative behavior is intriguingly similar, offering a new way of understanding the effective interactions between molecules, especially at high temperatures. In both approaches, the effective hardness is obtained from a double-logarithmic temperature derivative of an effective area.
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Affiliation(s)
- Ian H Bell
- Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, Colorado 80305, USA
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Mausbach P, May HO, Ruppeiner G. Thermodynamic metric geometry of the two-state ST2 model for supercooled water. J Chem Phys 2019. [DOI: 10.1063/1.5101075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bell IH, Messerly R, Thol M, Costigliola L, Dyre JC. Modified Entropy Scaling of the Transport Properties of the Lennard-Jones Fluid. J Phys Chem B 2019; 123:6345-6363. [PMID: 31241958 DOI: 10.1021/acs.jpcb.9b05808] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rosenfeld proposed two different scaling approaches to model the transport properties of fluids, separated by 22 years, one valid in the dilute gas, and another in the liquid phase. In this work, we demonstrate that these two limiting cases can be connected through the use of a novel approach to scaling transport properties and a bridging function. This approach, which is empirical and not derived from theory, is used to generate reference correlations for the transport properties of the Lennard-Jones 12-6 fluid of viscosity, thermal conductivity, and self-diffusion. This approach, with a very simple functional form, allows for the reproduction of the most accurate simulation data to within nearly their statistical uncertainty. The correlations are used to confirm that for the Lennard-Jones fluid the appropriately scaled transport properties are nearly monovariate functions of the excess entropy from low-density gases into the supercooled phase and up to extreme temperatures. This study represents the most comprehensive metastudy of the transport properties of the Lennard-Jones fluid to date.
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Affiliation(s)
- Ian H Bell
- Applied Chemicals and Materials Division , National Institute of Standards and Technology , Boulder , Colorado 80305 , United States
| | - Richard Messerly
- Applied Chemicals and Materials Division , National Institute of Standards and Technology , Boulder , Colorado 80305 , United States
| | - Monika Thol
- Thermodynamics , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany
| | - Lorenzo Costigliola
- DNRF Centre "Glass and Time," IMFUFA, Department of Science and Environment , Roskilde University , Postbox 260, DK-4000 Roskilde , Denmark
| | - Jeppe C Dyre
- DNRF Centre "Glass and Time," IMFUFA, Department of Science and Environment , Roskilde University , Postbox 260, DK-4000 Roskilde , Denmark
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Probing the link between residual entropy and viscosity of molecular fluids and model potentials. Proc Natl Acad Sci U S A 2019; 116:4070-4079. [PMID: 30770449 DOI: 10.1073/pnas.1815943116] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This work investigates the link between residual entropy and viscosity based on wide-ranging, highly accurate experimental and simulation data. This link was originally postulated by Rosenfeld in 1977 [Rosenfeld Y (1977) Phys Rev A 15:2545-2549], and it is shown that this scaling results in an approximately monovariate relationship between residual entropy and reduced viscosity for a wide range of molecular fluids [argon, methane, [Formula: see text], [Formula: see text], refrigerant R-134a (1,1,1,2-tetrafluoroethane), refrigerant R-125 (pentafluoroethane), methanol, and water] and a range of model potentials (hard sphere, inverse power, Lennard-Jones, and Weeks-Chandler-Andersen). While the proposed "universal" correlation of Rosenfeld is shown to be far from universal, when used with the appropriate density scaling for molecular fluids, the viscosity of nonassociating molecular fluids can be mapped onto the model potentials. This mapping results in a length scale that is proportional to the cube root of experimentally measurable liquid volume values.
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