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Lee J, Ju S, Hwang S, You J, Jung J, Kang Y, Han S. Disorder-Dependent Li Diffusion in Li 6PS 5Cl Investigated by Machine-Learning Potential. ACS APPLIED MATERIALS & INTERFACES 2024; 16:46442-46453. [PMID: 39185625 DOI: 10.1021/acsami.4c08865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Solid-state electrolytes with argyrodite structures, such as Li6PS5Cl, have attracted considerable attention due to their superior safety compared to liquid electrolytes and higher ionic conductivity than other solid electrolytes. Although experimental efforts have been made to enhance conductivity by controlling the degree of disorder, the underlying diffusion mechanism is not yet fully understood. Moreover, existing theoretical analyses based on ab initio molecular dynamics (MD) simulations have limitations in addressing various types of disorder at room temperature. In this study, we directly investigate Li-ion diffusion in Li6PS5Cl at 300 K using large-scale, long-term MD simulations empowered by machine-learning potentials (MLPs). To ensure the convergence of conductivity values within an error range of 10%, we employ a 25 ns simulation using a 5 × 5 × 5 supercell containing 6500 atoms. The computed Li-ion conductivity, activation energies, and equilibrium site occupancies align well with experimental observations. Notably, Li-ion conductivity peaks when Cl ions occupy 25% of the 4c sites rather than at 50% where the disorder is maximized. In addition, Li-ion diffusion shows non-Arrhenius behavior, leading to different activation energies at high temperatures (>400 K). These phenomena are explained by the interplay between inter- and intracage jumps. By elucidation of the key factors affecting Li-ion diffusion in Li6PS5Cl, this work paves the way for optimizing ionic conductivity in the argyrodite family.
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Affiliation(s)
- Jiho Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Korea
| | - Suyeon Ju
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Korea
| | - Seungwoo Hwang
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Korea
| | - Jinmu You
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Korea
| | - Jisu Jung
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Korea
| | - Youngho Kang
- Department of Materials Science and Engineering, Incheon National University, Incheon 22012, Korea
| | - Seungwu Han
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Korea
- Korea Institute for Advanced Study, Seoul 02455, Korea
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2
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Mitra S, Biswas R. Exploring the capabilities and limitations of the Van Hove function to understand directional correlations in ion movements within Li-ion battery electrolytes. J Chem Phys 2024; 161:064501. [PMID: 39120038 DOI: 10.1063/5.0209481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
Understanding microscopic directional correlations in ion movements within lithium-ion battery (LIB) electrolytes is important because these correlations directly affect the ionic conductivity. Onsager transport coefficients are widely used to understand these correlations. On the other hand, the Van Hove function (VHF) is also capable of determining correlated motions. However, identifying various types of ion correlated motions in LIB electrolytes using VHF is not well explored. Here, we have conducted molecular dynamics simulations of a representative experimental LIB electrolyte system-lithium hexafluorophosphate (LiPF6)-at different concentrations in a (9:1 wt. %) mixture of ethyl methyl carbonate and fluoroethylene carbonate in order to explore the capabilities and limitations of using VHF to understand different types of ion correlations. We conclude that analysis of VHF can qualitatively describe both the positive correlation between cation-anion at different salt concentrations and the negative correlation between cation-cation and anion-anion present in high salt concentration, but it cannot foretell which correlation is dominating at any given electrolyte concentration. This type of quantitative information can be obtained only via Onsager's approach. This could be seen as a limitation of relying solely on VHF to fully understand ion correlation in electrolyte media.
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Affiliation(s)
- Sudipta Mitra
- Department of Chemical and Biological Sciences, S.N. Bose National Centre for Basic Sciences, Block-JD, Sector-3, Salt Lake, Kolkata 700106, India
| | - Ranjit Biswas
- Department of Chemical and Biological Sciences, S.N. Bose National Centre for Basic Sciences, Block-JD, Sector-3, Salt Lake, Kolkata 700106, India
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3
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Prathyusha KR, Saha S, Golestanian R. Anomalous Fluctuations in a Droplet of Chemically Active Colloids or Enzymes. PHYSICAL REVIEW LETTERS 2024; 133:058401. [PMID: 39159108 DOI: 10.1103/physrevlett.133.058401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 06/28/2024] [Indexed: 08/21/2024]
Abstract
Chemically active colloids or enzymes cluster into dense droplets driven by their phoretic response to collectively generated chemical gradients. Employing Brownian dynamics simulation techniques, our study of the dynamics of such a chemically active droplet uncovers a rich variety of structures and dynamical properties, including the full range of fluidlike to solidlike behavior, and non-Gaussian positional fluctuations. Our work sheds light on the complex dynamics of the active constituents of metabolic clusters, which are the main drivers of nonequilibrium activity in living systems.
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Elliott GR, Wanless EJ, Webber GB, Andersson GG, Craig VSJ, Page AJ. Dynamic Ion Correlations and Ion-Pair Lifetimes in Aqueous Alkali Metal Chloride Electrolytes. J Phys Chem B 2024; 128:7438-7444. [PMID: 39037039 DOI: 10.1021/acs.jpcb.4c01992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Electrolytes are central to many technological applications, as well as life itself. The behavior and properties of electrolytes are often described in terms of ion pairs, whereby ions associate as either contact ion pairs (in which ions are "touching") solvent-separated ion pairs (in which ions' solvent shells overlap) or solvent-solvent-separated ion pairs (in which ions' solvent shells are distinct). However, this paradigm is generally restricted to statistically averaged descriptions of solution structure and ignores temporal behavior. Here we elucidate the time-resolved dynamics of these ion-ion interactions in aqueous metal chloride electrolytes using the partial van Hove correlation function, based on polarizable molecular dynamics simulations. Our results show that the existence and persistence of ion pairs in aqueous metal chloride electrolytes should not be assumed a priori, but in fact are ion specific features of the solution with lifetimes on subpicosecond time scales.
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Affiliation(s)
- Gareth R Elliott
- Discipline of Chemistry, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Erica J Wanless
- Discipline of Chemistry, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Grant B Webber
- Discipline of Chemical Engineering, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Gunther G Andersson
- Flinders Institute of Nanoscale Science and Technology, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Vincent S J Craig
- Department of Material Physics, Research School of Physics, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Alister J Page
- Discipline of Chemistry, The University of Newcastle, Callaghan, New South Wales 2308, Australia
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5
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Li A, Zeiger PM, He Z, Xu M, Pennycook SJ, Rusz J, Zhou W. Systematic Absences of Optical Phonon Modes in Phonon Dispersion Measured by Electron Microscopy. PHYSICAL REVIEW LETTERS 2024; 133:046101. [PMID: 39121401 DOI: 10.1103/physrevlett.133.046101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/10/2024] [Indexed: 08/11/2024]
Abstract
Phonon dispersion relations are widely used to elucidate the vibrational properties of materials. As an emerging technique, momentum-resolved vibrational spectroscopy in scanning transmission electron microscopy offers an unparalleled approach to explore q-dependent phonon behavior at local structures. In this study, we systematically investigate the phonon dispersion of monolayer graphene across several Brillouin zones (BZs) using momentum-resolved vibrational spectroscopy and find that the optical phonon signals vanish at the Γ points with indices (hk0) satisfying h+2k=3n (n denoted integers). Theoretical analysis reveals that the observed phenomena arise from the complete destructive interference of the scattered waves from different basis atoms. This observation, corroborated by the study of diamond, should be a general characteristic of materials composed of symmetrically equivalent pairs of the same elements. Moreover, our results emphasize the importance of multiple scattering in interpreting the vibrational signals in bulk materials. We demonstrate that the systematic absences and dynamic effects, which have not been much appreciated before, offer new insights into the experimental assessment of local vibrational properties of materials.
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Karasawa N, Mitsutake A, Takano H. Intermediate scattering function for polymer molecules: An approach based on relaxation mode analysis. J Chem Phys 2024; 161:024902. [PMID: 38973764 DOI: 10.1063/5.0211504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 06/17/2024] [Indexed: 07/09/2024] Open
Abstract
The theory of polymer dynamics describes the intermediate scattering function for a polymer molecule in terms of relaxation modes defined by normal coordinates for the corresponding coarse-grained model. However, due to the difficulty of defining the normal coordinates for arbitrary polymer molecules, it is generally challenging to express the intermediate scattering function for a polymer molecule in terms of relaxation modes. To overcome this challenge, we propose a general method to calculate the intermediate scattering function for a polymer molecule on the basis of a relaxation mode analysis approach [Takano and Miyashita, J. Phys. Soc. Jpn. 64, 3688 (1995)]. In the proposed method, relaxation modes defined by eigenfunctions in a Markov process are evaluated on the basis of the simulation results for a polymer molecule and used to calculate the intermediate scattering function for that molecule. To demonstrate the effectiveness of the present method, we simulate the dynamics of a linear polymer molecule in a dilute solution and apply it to the calculation of the intermediate scattering function for the polymer molecule. The evaluation results regarding the relaxation modes reasonably describe the intermediate scattering function on the length scale of the radius of gyration of the polymer molecule. Accordingly, we examine the contributions of the pure relaxation and oscillatory relaxation processes to the entire intermediate scattering function.
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Affiliation(s)
- Naoyuki Karasawa
- Graduate School of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Ayori Mitsutake
- School of Science and Technology, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Hiroshi Takano
- Faculty of Science and Technology, Keio University, Minato-ku, Tokyo 108-8345, Japan
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Domingues TS, Coifman R, Haji-Akbari A. Estimating Position-Dependent and Anisotropic Diffusivity Tensors from Molecular Dynamics Trajectories: Existing Methods and Future Outlook. J Chem Theory Comput 2024; 20:4427-4455. [PMID: 38815171 DOI: 10.1021/acs.jctc.4c00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Confinement can substantially alter the physicochemical properties of materials by breaking translational isotropy and rendering all physical properties position-dependent. Molecular dynamics (MD) simulations have proven instrumental in characterizing such spatial heterogeneities and probing the impact of confinement on materials' properties. For static properties, this is a straightforward task and can be achieved via simple spatial binning. Such an approach, however, cannot be readily applied to transport coefficients due to lack of natural extensions of autocorrelations used for their calculation in the bulk. The prime example of this challenge is diffusivity, which, in the bulk, can be readily estimated from the particles' mobility statistics, which satisfy the Fokker-Planck equation. Under confinement, however, such statistics will follow the Smoluchowski equation, which lacks a closed-form analytical solution. This brief review explores the rich history of estimating profiles of the diffusivity tensor from MD simulations and discusses various approximate methods and algorithms developed for this purpose. Besides discussing heuristic extensions of bulk methods, we overview more rigorous algorithms, including kernel-based methods, Bayesian approaches, and operator discretization techniques. Additionally, we outline methods based on applying biasing potentials or imposing constraints on tracer particles. Finally, we discuss approaches that estimate diffusivity from mean first passage time or committor probability profiles, a conceptual framework originally developed in the context of collective variable spaces describing rare events in computational chemistry and biology. In summary, this paper offers a concise survey of diverse approaches for estimating diffusivity from MD trajectories, highlighting challenges and opportunities in this area.
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Affiliation(s)
- Tiago S Domingues
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
| | - Ronald Coifman
- Department of Mathematics, Yale University, New Haven, Connecticut 06520, United States
- Department of Computer Science, Yale University, New Haven, Connecticut 06520, United States
| | - Amir Haji-Akbari
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
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8
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Vaibhav V, Dutta S. Entropic timescales of dynamic heterogeneity in supercooled liquid. Phys Rev E 2024; 109:L062102. [PMID: 39020902 DOI: 10.1103/physreve.109.l062102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 05/17/2024] [Indexed: 07/20/2024]
Abstract
Non-Gaussian displacement distributions are universal predictors of dynamic heterogeneity in slowly varying environments. Here, we explore heterogeneous dynamics in supercooled liquid using molecular dynamics simulations and show the efficiency of the relative-entropy based measure, negentropy, in quantifying dynamic heterogeneity over the widely used non-Gaussian parameter. Our analysis shows that the heterogeneity quantified by the negentropy is significantly different from the one obtained using the conventional moment-based definition that considers deviation from Gaussianity up to lower-order moments. We extract the timescales of dynamic heterogeneity using the two methods and show that the differential changes diverge as the system experiences strong intermittency near the glass transition. Further, we interpret the entropic timescales and discuss the general implications of our work.
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9
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Shinohara Y, Iwashita T, Nakanishi M, Dmowski W, Ryu CW, Abernathy DL, Ishikawa D, Baron AQR, Egami T. Real-space local self-motion of protonated and deuterated water. Phys Rev E 2024; 109:064608. [PMID: 39020980 DOI: 10.1103/physreve.109.064608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/17/2024] [Indexed: 07/20/2024]
Abstract
We report on the self-part of the Van Hove correlation function, the correlation function describing the dynamics of a single molecule, of water and deuterated water. The correlation function is determined by transforming inelastic scattering spectra of neutrons or x rays over a wide range of momentum transfer Q and energy transfer E to space R and time t. The short-range diffusivity is estimated from the Van Hove correlation function in the framework of the Gaussian approximation. The diffusivity has been found to be different from the long-range macroscopic diffusivity, providing information about local atomic dynamics.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Takeshi Egami
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Department of Materials Science and Engineering, The University of Tennessee, Knoxville, Tennessee, 37996 USA
- Department of Physics and Astronomy,The University of Tennessee, Knoxville, Tennessee, 37996 USA
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10
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Cameron RP, Alexakis EI, Arnold AS, McArthur D. Theory of Rayleigh-Brillouin optical activity light scattering applicable to chiral liquids. Phys Chem Chem Phys 2024; 26:11641-11648. [PMID: 38546720 DOI: 10.1039/d3cp05109a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
It has long been understood that dilute samples of chiral molecules such as rarefied gases should exhibit Rayleigh optical activity. We extend the existing theory by accounting for molecular dynamics and correlations, thus obtaining a more general theory of Rayleigh-Brillouin optical activity applicable to dense samples such as neat liquids.
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Affiliation(s)
- Robert P Cameron
- SUPA and Department of Physics, University of Strathclyde, Glasgow, G4 0NG, UK.
| | | | - Aidan S Arnold
- SUPA and Department of Physics, University of Strathclyde, Glasgow, G4 0NG, UK.
| | - Duncan McArthur
- SUPA and Department of Physics, University of Strathclyde, Glasgow, G4 0NG, UK.
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11
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Goloviznina K, Serva A, Salanne M. Formation of Polymer-like Nanochains with Short Lithium-Lithium Distances in a Water-in-Salt Electrolyte. J Am Chem Soc 2024; 146:8142-8148. [PMID: 38486506 DOI: 10.1021/jacs.3c12488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Water-in-salts (WiSs) have recently emerged as promising electrolytes for energy storage applications ranging from aqueous batteries to supercapacitors. Here, ab initio molecular dynamics is used to study the structure of a 21 m LiTFSI WiS. The simulation reveals a new feature, in which the lithium ions form polymer-like nanochains that involve up to 10 ions. Despite the strong Coulombic interaction between them, the ions in the chains are found at a distance of 2.5 Å. They show a drastically different solvation shell compared to that of the isolated ions, in which they share on average two water molecules. The nanochains have a highly transient character due to the low free energy barrier for forming/breaking them. Providing new insights into the nanostructure of WiS electrolytes, our work calls for reevaluating our current knowledge of highly concentrated electrolytes and the impact of the modification of the solvation of active species on their electrochemical performances.
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Affiliation(s)
- Kateryna Goloviznina
- Sorbonne Université, CNRS, Physicochimie des Électrolytes et Nanosystèmes Interfaciaux, F-75005 Paris, France
- Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS 3459, 80039 Amiens, Cedex, France
| | - Alessandra Serva
- Sorbonne Université, CNRS, Physicochimie des Électrolytes et Nanosystèmes Interfaciaux, F-75005 Paris, France
- Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS 3459, 80039 Amiens, Cedex, France
| | - Mathieu Salanne
- Sorbonne Université, CNRS, Physicochimie des Électrolytes et Nanosystèmes Interfaciaux, F-75005 Paris, France
- Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS 3459, 80039 Amiens, Cedex, France
- Institut Universitaire de France (IUF), 75231 Paris, France
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12
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Memar ZO, Moosavi M. Assessing OPLS-based force fields for investigating the characteristics of imidazolium-based dicationic ionic liquids: A comparative study with AIMD simulations and experimental findings. J Chem Phys 2023; 159:244504. [PMID: 38149743 DOI: 10.1063/5.0180900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/04/2023] [Indexed: 12/28/2023] Open
Abstract
In this study, we extended the optimized potentials for liquid simulation-ionic-liquid virtual site (OPLS-VSIL) force field (FF) to imidazolium-based dicationic ionic liquids (DILs) and evaluated the ability of different OPLS-based FFs (i.e., OPLS-2009IL, 0.8*OPLS-2009IL, and OPLS-VSIL) in predicting different properties of the studied DIL by comparing their results with ab initio molecular dynamics (AIMD) simulation and experimental results. To achieve this purpose, MD simulations with three different OPLS-based FFs as well as AIMD simulation were performed for [C3(mim)2][NTF2]2 DIL and its structural, dynamical, vibrational, and volumetric properties were analyzed. Structural properties of the studied DIL, i.e., radial distribution functions (RDFs), structure factor, and hydrogen-bond network, showed that compared to 0.8*OPLS-2009IL FF, there is a much better agreement between the results of both OPLS-2009IL and OPLS-VSIL FFs with the AIMD simulation. On the other hand, the results of dynamical properties, such as mean square displacements, van Hove correlation functions as well as hydrogen bond, ion pair, and ion cage dynamics, depicted that in both 0.8*OPLS-2009IL and OPLS-VSIL FFs, the dynamics of the system is almost similar, and compared to OPLS-2009IL FF, they have better agreements with experimental results where they exist. So, it can be seen that although reducing the total charge of studied DIL by 20% leads to an increase in the dynamics of the system, the type distribution of partial charges on each atom does not significantly affect the system's dynamics. The calculated infrared (IR) and power spectra showed that the vibrational features of studied DIL in three OPLS-based FFs are mostly the same and reducing total charge and different type distribution of partial charges have no significant effect on the studied system. Furthermore, in volumetric properties, OPLS-VSIL FF shows somehow better agreement with experimental results. Overall, the evaluation of different structural, dynamical, vibrational, and volumetric properties of [C3(mim)2][NTF2]2 DIL shows that the OPLS-VSIL FF may be the best choice among the different studied OPLS FFs.
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Affiliation(s)
| | - Majid Moosavi
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
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13
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Hu M, Chen H, Wang H, Burov S, Barkai E, Wang D. Triggering Gaussian-to-Exponential Transition of Displacement Distribution in Polymer Nanocomposites via Adsorption-Induced Trapping. ACS NANO 2023; 17:21708-21718. [PMID: 37879044 DOI: 10.1021/acsnano.3c06897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
In many disordered systems, the diffusion of classical particles is described by a displacement distribution P(x, t) that displays exponential tails instead of Gaussian statistics expected for Brownian motion. However, the experimental demonstration of control of this behavior by increasing the disorder strength has remained challenging. In this work, we explore the Gaussian-to-exponential transition by using diffusion of poly(ethylene glycol) (PEG) in attractive nanoparticle-polymer mixtures and controlling the volume fraction of the nanoparticles. In this work, we find "knobs", namely nanoparticle concentration and interaction, which enable the change in the shape of P(x,t) in a well-defined way. The Gaussian-to-exponential transition is consistent with a modified large deviation approach for a continuous time random walk and also with Monte Carlo simulations involving a microscopic model of polymer trapping via reversible adsorption to the nanoparticle surface. Our work bears significance in unraveling the fundamental physics behind the exponential decay of the displacement distribution at the tails, which is commonly observed in soft materials and nanomaterials.
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Affiliation(s)
- Ming Hu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China
- University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Hongbo Chen
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China
| | - Hongru Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China
- University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Stanislav Burov
- Department of Physics, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Eli Barkai
- Department of Physics, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dapeng Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China
- University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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14
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Matam SK, Silverwood IP, Boudjema L, O'Malley AJ, Catlow CRA. Methanol diffusion and dynamics in zeolite H-ZSM-5 probed by quasi-elastic neutron scattering and classical molecular dynamics simulations. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2023; 381:20220335. [PMID: 37691467 PMCID: PMC10493552 DOI: 10.1098/rsta.2022.0335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/31/2023] [Indexed: 09/12/2023]
Abstract
Zeolite ZSM-5 is a key catalyst in commercially relevant processes including the widely studied methanol to hydrocarbon reaction, and molecular diffusion in zeolite pores is known to be a crucial factor in controlling catalytic reactions. Here, we present critical analyses of recent quasi-elastic neutron scattering (QENS) data and complementary molecular dynamics (MD) simulations. The QENS experiments show that the nature of methanol diffusion dynamics in ZSM-5 pores is dependent both on the Si/Al ratio (11, 25, 36, 40 and 140), which determines the Brønsted acid site density of the zeolite, and that the nature of the type of motion observed may vary qualitatively over a relatively small temperature range. At 373 K, on increasing the ratio from 11 to 140, the observed mobile methanol fraction increases and the nature of methanol dynamics changes from rotational (in ZSM-5 with Si/Al of 11) to translational diffusion. The latter is either confined localized diffusion within a pore in zeolites with ratios up to 40 or non-localized, longer-range diffusion in zeolite samples with the ratio of 140. The complementary MD simulations conducted over long time scales (1 ns), which are longer than those measured in the present study by QENS (≈1-440 ps), at 373 K predict the occurrence of long-range translational diffusion of methanol in ZSM-5, independent of the Si/Al ratios (15, 47, 95, 191 and siliceous MFI). The rate of diffusion increases slightly by increasing the ratio from 15 to 95 and thereafter does not depend on zeolite composition. Discrepancies in the observed mobile methanol fraction between the MD simulations (100% methanol mobility in ZSM-5 pores across all Si/Al ratios) and QENS experiments (for example, ≈80% immobile methanol in ZSM-5 with Si/Al of 11) are attributed to the differences in time resolutions of the techniques. This perspective provides comprehensive information on the effect of acid site density on methanol dynamics in ZSM-5 pores and highlights the complementarity of QENS and MD, and their advantages and limitations. This article is part of the theme issue 'Exploring the length scales, timescales and chemistry of challenging materials (Part 2)'.
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Affiliation(s)
- Santhosh K. Matam
- UK Catalysis Hub, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot OX11 0FA, UK
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Ian P. Silverwood
- UK Catalysis Hub, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot OX11 0FA, UK
- ISIS Pulsed Neutron and Muon Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK
| | - Lotfi Boudjema
- UK Catalysis Hub, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot OX11 0FA, UK
- Department of Chemistry, University College London, 20 Gordon Street, London WC1E 6BT, UK
- ICGM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Alexander J. O'Malley
- UK Catalysis Hub, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot OX11 0FA, UK
- Institute for Sustainability, Department of Chemistry, University of Bath, Bath BA2 7AY, UK
| | - C. Richard A. Catlow
- UK Catalysis Hub, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot OX11 0FA, UK
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
- Department of Chemistry, University College London, 20 Gordon Street, London WC1E 6BT, UK
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15
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Lyu L, Lei H. Construction of Coarse-Grained Molecular Dynamics with Many-Body Non-Markovian Memory. PHYSICAL REVIEW LETTERS 2023; 131:177301. [PMID: 37955502 DOI: 10.1103/physrevlett.131.177301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/19/2023] [Indexed: 11/14/2023]
Abstract
We introduce a machine-learning-based coarse-grained molecular dynamics model that faithfully retains the many-body nature of the intermolecular dissipative interactions. Unlike the common empirical coarse-grained models, the present model is constructed based on the Mori-Zwanzig formalism and naturally inherits the heterogeneous state-dependent memory term rather than matching the mean-field metrics such as the velocity autocorrelation function. Numerical results show that preserving the many-body nature of the memory term is crucial for predicting the collective transport and diffusion processes, where empirical forms generally show limitations.
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Affiliation(s)
- Liyao Lyu
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, Michigan 48824, USA
| | - Huan Lei
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Statistics and Probability, Michigan State University, East Lansing, Michigan 48824, USA
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16
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Memar ZO, Moosavi M. Uncovering the Properties of Dicationic Ionic Liquid Nanodroplets through Ab Initio Molecular Dynamics Simulations. J Phys Chem B 2023; 127:9111-9131. [PMID: 37843820 DOI: 10.1021/acs.jpcb.3c03585] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
The behavior of nanodroplets of an imidazolium-based dicationic ionic liquid, i.e., [C1(mim)2][PF6]2, was investigated in this study using ab initio molecular dynamics simulations. The vibrational features as well as the structural, interfacial, and dynamical properties of different sized droplets were analyzed and compared to the bulk phase system. Structural properties of the droplets, such as π-π stacking, radial distribution functions, structure factors, combined distribution functions, and angular distribution functions were analyzed to understand the interactions and orientations of their ions. The vibrational features and hydrogen bonding strength of droplets were studied by calculating their infrared (IR) and power spectra, determining the contribution of different types of hydrogen bonding to each vibrational mode. The calculated spectra showed good overall agreement with the experimental results. The interfacial properties of the droplets and the orientation of their ions were analyzed using density profiles and an exposed surface. The results showed that, in all systems studied, cations and anions were equally likely to exist in both inner and outer layers, and the cations tended to be oriented toward the center of droplets with obtuse angles. Additionally, the droplet densities were extrapolated to predict the bulk phase density with less than 2% deviation. The dynamical properties of hydrogen bonds, mean square displacement, and van Hove correlations of cations and anions were also analyzed. The results indicated that there was no regular trend in the dynamic properties of droplets with an increasing system size.
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Affiliation(s)
| | - Majid Moosavi
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
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17
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Zhang Y, Wang Y, Huang Y, Wang J, Liang Z, Hao L, Gao Z, Li J, Wu Q, Zhang H, Liu Y, Sun J, Lin JF. Collective motion in hcp-Fe at Earth's inner core conditions. Proc Natl Acad Sci U S A 2023; 120:e2309952120. [PMID: 37782810 PMCID: PMC10576103 DOI: 10.1073/pnas.2309952120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/15/2023] [Indexed: 10/04/2023] Open
Abstract
Earth's inner core is predominantly composed of solid iron (Fe) and displays intriguing properties such as strong shear softening and an ultrahigh Poisson's ratio. Insofar, physical mechanisms to explain these features coherently remain highly debated. Here, we have studied longitudinal and shear wave velocities of hcp-Fe (hexagonal close-packed iron) at relevant pressure-temperature conditions of the inner core using in situ shock experiments and machine learning molecular dynamics (MLMD) simulations. Our results demonstrate that the shear wave velocity of hcp-Fe along the Hugoniot in the premelting condition, defined as T/Tm (Tm: melting temperature of iron) above 0.96, is significantly reduced by ~30%, while Poisson's ratio jumps to approximately 0.44. MLMD simulations at 230 to 330 GPa indicate that collective motion with fast diffusive atomic migration occurs in premelting hcp-Fe primarily along [100] or [010] crystallographic direction, contributing to its elastic softening and enhanced Poisson's ratio. Our study reveals that hcp-Fe atoms can diffusively migrate to neighboring positions, forming open-loop and close-loop clusters in the inner core conditions. Hcp-Fe with collective motion at the inner core conditions is thus not an ideal solid previously believed. The premelting hcp-Fe with collective motion behaves like an extremely soft solid with an ultralow shear modulus and an ultrahigh Poisson's ratio that are consistent with seismic observations of the region. Our findings indicate that premelting hcp-Fe with fast diffusive motion represents the underlying physical mechanism to help explain the unique seismic and geodynamic features of the inner core.
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Affiliation(s)
- Youjun Zhang
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu610065, China
- International Center for Planetary Science, College of Earth Sciences, Chengdu University of Technology, Chengdu610059, China
| | - Yong Wang
- National Laboratory of Solid State Microstructures, School of Physics and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing210093, China
| | - Yuqian Huang
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu610065, China
| | - Junjie Wang
- National Laboratory of Solid State Microstructures, School of Physics and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing210093, China
| | - Zhixin Liang
- National Laboratory of Solid State Microstructures, School of Physics and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing210093, China
| | - Long Hao
- National Key Laboratory for Shock Wave and Detonation Physics, Institute of Fluid Physics, China Academy of Engineering Physics, Mianyang621900, China
| | - Zhipeng Gao
- National Key Laboratory for Shock Wave and Detonation Physics, Institute of Fluid Physics, China Academy of Engineering Physics, Mianyang621900, China
| | - Jun Li
- National Key Laboratory for Shock Wave and Detonation Physics, Institute of Fluid Physics, China Academy of Engineering Physics, Mianyang621900, China
| | - Qiang Wu
- National Key Laboratory for Shock Wave and Detonation Physics, Institute of Fluid Physics, China Academy of Engineering Physics, Mianyang621900, China
| | - Hong Zhang
- College of Physics, Sichuan University, Chengdu610065, China
| | - Yun Liu
- International Center for Planetary Science, College of Earth Sciences, Chengdu University of Technology, Chengdu610059, China
| | - Jian Sun
- National Laboratory of Solid State Microstructures, School of Physics and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing210093, China
| | - Jung-Fu Lin
- Department of Earth and Planetary Sciences, Jackson School of Geosciences, The University of Texas at Austin, Austin, TX78712
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18
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Wu JF, Zou Z, Pu B, Ladenstein L, Lin S, Xie W, Li S, He B, Fan Y, Pang WK, Wilkening HMR, Guo X, Xu C, Zhang T, Shi S, Liu J. Liquid-Like Li-Ion Conduction in Oxides Enabling Anomalously Stable Charge Transport across the Li/Electrolyte Interface in All-Solid-State Batteries. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2303730. [PMID: 37358065 DOI: 10.1002/adma.202303730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/21/2023] [Indexed: 06/27/2023]
Abstract
The softness of sulfur sublattice and rotational PS4 tetrahedra in thiophosphates result in liquid-like ionic conduction, leading to enhanced ionic conductivities and stable electrode/thiophosphate interfacial ionic transport. However, the existence of liquid-like ionic conduction in rigid oxides remains unclear, and modifications are deemed necessary to achieve stable Li/oxide solid electrolyte interfacial charge transport. In this study, by combining the neutron diffraction survey, geometrical analysis, bond valence site energy analysis, and ab initio molecular dynamics simulation, 1D liquid-like Li-ion conduction is discovered in LiTa2 PO8 and its derivatives, wherein Li-ion migration channels are connected by four- or five-fold oxygen-coordinated interstitial sites. This conduction features a low activation energy (0.2 eV) and short mean residence time (<1 ps) of Li ions on the interstitial sites, originating from the Li-O polyhedral distortion and Li-ion correlation, which are controlled by doping strategies. The liquid-like conduction enables a high ionic conductivity (1.2 mS cm-1 at 30 °C), and a 700 h anomalously stable cycling under 0.2 mA cm-2 for Li/LiTa2 PO8 /Li cells without interfacial modifications. These findings provide principles for the future discovery and design of improved solid electrolytes that do not require modifications to the Li/solid electrolyte interface to achieve stable ionic transport.
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Affiliation(s)
- Jian-Fang Wu
- College of Materials Science and Engineering, Hunan Joint International Laboratory of Advanced Materials and Technology of Clean Energy, Hunan Province Key Laboratory for Advanced Carbon Materials and Applied Technology, Hunan University, Changsha, 410082, P. R. China
| | - Zheyi Zou
- School of Materials Science and Engineering, Xiangtan University, Xiangtan, 411105, P. R. China
| | - Bowei Pu
- School of Materials Science and Engineering, Materials Genome Institute, Shanghai University, Shanghai, 200444, P. R. China
| | - Lukas Ladenstein
- Institute of Chemistry and Technology of Materials, Christian Doppler Laboratory for Lithium Batteries, Graz University of Technology (NAWI Graz), Graz, 8010, Austria
| | - Shen Lin
- School of Materials Science and Engineering, Materials Genome Institute, Shanghai University, Shanghai, 200444, P. R. China
| | - Wenjing Xie
- School of Materials Science and Engineering, Xiangtan University, Xiangtan, 411105, P. R. China
| | - Shen Li
- School of Materials Science and Engineering, Xiangtan University, Xiangtan, 411105, P. R. China
| | - Bing He
- School of Materials Science and Engineering, Materials Genome Institute, Shanghai University, Shanghai, 200444, P. R. China
| | - Yameng Fan
- Institute for Superconducting & Electronic Materials, University of Wollongong, Wollongong, New South Wales, 2522, Australia
| | - Wei Kong Pang
- Institute for Superconducting & Electronic Materials, University of Wollongong, Wollongong, New South Wales, 2522, Australia
| | - H Martin R Wilkening
- Institute of Chemistry and Technology of Materials, Christian Doppler Laboratory for Lithium Batteries, Graz University of Technology (NAWI Graz), Graz, 8010, Austria
| | - Xin Guo
- State Key Laboratory of Material Processing and Die & Mould Technology, Laboratory of Solid State Ionics, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Chaohe Xu
- College of Aerospace Engineering, Chongqing University, Chongqing, 400044, P. R. China
| | - Tao Zhang
- State Key Lab of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, P. R. China
| | - Siqi Shi
- School of Materials Science and Engineering, Materials Genome Institute, Shanghai University, Shanghai, 200444, P. R. China
| | - Jilei Liu
- College of Materials Science and Engineering, Hunan Joint International Laboratory of Advanced Materials and Technology of Clean Energy, Hunan Province Key Laboratory for Advanced Carbon Materials and Applied Technology, Hunan University, Changsha, 410082, P. R. China
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19
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Shen Z, Carrillo JMY, Sumpter BG, Wang Y. Mesoscopic two-point collective dynamics of glass-forming liquids. J Chem Phys 2023; 159:114501. [PMID: 37712790 DOI: 10.1063/5.0161866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/24/2023] [Indexed: 09/16/2023] Open
Abstract
The collective density-density and hydrostatic pressure-pressure correlations of glass-forming liquids are spatiotemporally mapped out using molecular dynamics simulations. It is shown that the sharp rise of structural relaxation time below the Arrhenius temperature coincides with the emergence of slow, nonhydrodynamic collective dynamics on mesoscopic scales. The observed long-range, nonhydrodynamic mode is independent of wave numbers and closely coupled to the local structural dynamics. Below the Arrhenius temperature, it dominates the slow collective dynamics on length scales immediately beyond the first structural peak in contrast to the well-known behavior at high temperatures. These results highlight a key connection between the qualitative change in mesoscopic two-point collective dynamics and the dynamic crossover phenomenon.
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Affiliation(s)
- Zhiqiang Shen
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Jan-Michael Y Carrillo
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Bobby G Sumpter
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Yangyang Wang
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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20
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Silkin VM, Drechsler SL, Efremov DV. Unusual Low-Energy Collective Charge Excitations in High- Tc Cuprate Superconductors. J Phys Chem Lett 2023; 14:8060-8068. [PMID: 37655950 PMCID: PMC10510710 DOI: 10.1021/acs.jpclett.3c01871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023]
Abstract
Despite decades of intensive experimental and theoretical efforts, the physics of cuprate high-temperature superconductors in general, and, in particular, their normal state, is still under debate. Here, we report our investigation of low-energy charge excitations in the normal state. We find that the peculiarities of the electronic band structure at low energies have a profound impact on the nature of the intraband collective modes. It gives rise to a new kind of mode with huge intensity and non-Lorentzian spectral function in addition to well-known collective excitations like conventional plasmons and spin fluctuation. We predict two such modes with maximal spectral weight in the nodal and antinodal directions. Additionally, we found a long-living quasi-one-dimensional plasmon becoming an intense soft mode over an extended momentum range along the antinodal direction. These modes might explain some of the resonant inelastic X-ray scattering spectroscopy data.
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Affiliation(s)
- Vyacheslav M. Silkin
- Donostia
International Physics Center (DIPC), 20018 San Sebastián/Donostia, Basque Country, Spain
- Departamento
de Polímeros y Materiales Avanzados: Física,
Química y Tecnología, Facultad de Ciencias
Químicas, Universidad del País
Vasco UPV/EHU, 20080 San Sebastián/Donostia, Basque Country, Spain
- IKERBASQUE,
Basque Foundation for Science, 48013 Bilbao, Basque Country, Spain
| | - Stefan-Ludwig Drechsler
- Leibniz
Institute for Solid State and Materials Research IFW Dresden, Helmholtzstrasse 20, 01069 Dresden, Germany
| | - Dmitry V. Efremov
- Leibniz
Institute for Solid State and Materials Research IFW Dresden, Helmholtzstrasse 20, 01069 Dresden, Germany
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21
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Kitamura H, Furukawa T. Multiphonon scattering formula of dynamic structure factors for classical Debye solids. Phys Rev E 2023; 108:034111. [PMID: 37849124 DOI: 10.1103/physreve.108.034111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 08/23/2023] [Indexed: 10/19/2023]
Abstract
A semianalytic formula of the dynamic structure factor S(k,ω) for classical Debye solids over the entire wave-number (k) and frequency (ω) range is constructed by taking into account multiphonon thermal diffuse scattering up to infinite order. The formula adopts Gaussian approximations to the spatial and time decay of the multiphonon part of the displacement correlation function. Numerical illustrations for isotropic polycrystals reveal that, as k increases, sharp peaks due to one-phonon normal scattering in the hydrodynamic regime (k→0) are replaced by diffuse spectra consisting of umklapp scattering and multiphonon continuum; approach toward the ideal-gas spectra in the large-k limit is proven from analytic properties of the multiphonon term. When k coincides with a Bragg reflection point, total thermal diffuse scattering S_{TDS}(k,ω) exhibits a 1/ω divergence as ω→0, which in turn gives rise to a logarithmic enhancement of the corresponding static structure factor S_{TDS}(k). Overall accuracy of the theory is confirmed through the exact zeroth-order frequency-moment sum rule between S_{TDS}(k,ω) and S_{TDS}(k); agreement with the second-order sum rule is shown to be satisfactory except for the vicinity of the Debye cutoff region.
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Affiliation(s)
- Hikaru Kitamura
- Department of Physics, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takaya Furukawa
- Department of Physics, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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22
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Pollak E, Miret-Artés S. Recent Developments in Kramers' Theory of Reaction Rates. Chemphyschem 2023; 24:e202300272. [PMID: 37537153 DOI: 10.1002/cphc.202300272] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/26/2023] [Indexed: 08/05/2023]
Abstract
In this short review, we provide an update of recent developments in Kramers' theory of reaction rates. After a brief introduction stressing the importance of this theory initially developed for chemical reactions, we briefly present the main theoretical formalism starting from the generalized Langevin equation and continue by showing the main points of the modern Pollak, Grabert and Hänggi theory. Kramers' theory is then sketched for quantum and classical surface diffusion. As an illustration the surface diffusion of Na atoms on a Cu(110) surface is discussed showing escape rates, jump distributions and diffusion coefficients as a function of reduced friction. Finally, some very recent applications of turnover theory to different fields such as nanoparticle levitation, microcavity polariton dynamics and simulation of reaction in liquids are presented. We end with several open problems and future challenges faced up by Kramers turnover theory.
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Affiliation(s)
- Eli Pollak
- Chemical and Biological Physics Department, Weizmann Institute of Science, 76100, Rehovoth, Israel
| | - Salvador Miret-Artés
- Instituto de Física Fundamental, Consejo, Superior de Investigaciones Científicas, Serrano 123, 28006, Madrid, Spain
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23
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Lu P, Xia Y, Sun G, Wu D, Wu S, Yan W, Zhu X, Lu J, Niu Q, Shi S, Sha Z, Chen L, Li H, Wu F. Realizing long-cycling all-solid-state Li-In||TiS 2 batteries using Li 6+xM xAs 1-xS 5I (M=Si, Sn) sulfide solid electrolytes. Nat Commun 2023; 14:4077. [PMID: 37429864 DOI: 10.1038/s41467-023-39686-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 06/26/2023] [Indexed: 07/12/2023] Open
Abstract
Inorganic sulfide solid-state electrolytes, especially Li6PS5X (X = Cl, Br, I), are considered viable materials for developing all-solid-state batteries because of their high ionic conductivity and low cost. However, this class of solid-state electrolytes suffers from structural and chemical instability in humid air environments and a lack of compatibility with layered oxide positive electrode active materials. To circumvent these issues, here, we propose Li6+xMxAs1-xS5I (M=Si, Sn) as sulfide solid electrolytes. When the Li6+xSixAs1-xS5I (x = 0.8) is tested in combination with a Li-In negative electrode and Ti2S-based positive electrode at 30 °C and 30 MPa, the Li-ion lab-scale Swagelok cells demonstrate long cycle life of almost 62500 cycles at 2.44 mA cm-2, decent power performance (up to 24.45 mA cm-2) and areal capacity of 9.26 mAh cm-2 at 0.53 mA cm-2.
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Affiliation(s)
- Pushun Lu
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Xia
- Beijing ByteDance Technology Co Ltd, Beijing, 100098, China
| | - Guochen Sun
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dengxu Wu
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Siyuan Wu
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenlin Yan
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiang Zhu
- Nano Science and Technology Institute, University of Science and Technology of China, Suzhou, 215123, China
- Tianmu Lake Institute of Advanced Energy Storage Technologies, Liyang, 213300, Jiangsu, China
| | - Jiaze Lu
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Quanhai Niu
- Tianmu Lake Institute of Advanced Energy Storage Technologies, Liyang, 213300, Jiangsu, China
| | - Shaochen Shi
- Beijing ByteDance Technology Co Ltd, Beijing, 100098, China
| | - Zhengju Sha
- Beijing ByteDance Technology Co Ltd, Beijing, 100098, China
| | - Liquan Chen
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Tianmu Lake Institute of Advanced Energy Storage Technologies, Liyang, 213300, Jiangsu, China
- Yangtze River Delta Physics Research Center, Liyang, 213300, Jiangsu, China
| | - Hong Li
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Nano Science and Technology Institute, University of Science and Technology of China, Suzhou, 215123, China.
- Tianmu Lake Institute of Advanced Energy Storage Technologies, Liyang, 213300, Jiangsu, China.
- Yangtze River Delta Physics Research Center, Liyang, 213300, Jiangsu, China.
| | - Fan Wu
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Nano Science and Technology Institute, University of Science and Technology of China, Suzhou, 215123, China.
- Tianmu Lake Institute of Advanced Energy Storage Technologies, Liyang, 213300, Jiangsu, China.
- Yangtze River Delta Physics Research Center, Liyang, 213300, Jiangsu, China.
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24
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Yu X, Cheng Y, Li Y, Polo-Garzon F, Liu J, Mamontov E, Li M, Lennon D, Parker SF, Ramirez-Cuesta AJ, Wu Z. Neutron Scattering Studies of Heterogeneous Catalysis. Chem Rev 2023. [PMID: 37315192 DOI: 10.1021/acs.chemrev.3c00101] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Understanding the structural dynamics/evolution of catalysts and the related surface chemistry is essential for establishing structure-catalysis relationships, where spectroscopic and scattering tools play a crucial role. Among many such tools, neutron scattering, though less-known, has a unique power for investigating catalytic phenomena. Since neutrons interact with the nuclei of matter, the neutron-nucleon interaction provides unique information on light elements (mainly hydrogen), neighboring elements, and isotopes, which are complementary to X-ray and photon-based techniques. Neutron vibrational spectroscopy has been the most utilized neutron scattering approach for heterogeneous catalysis research by providing chemical information on surface/bulk species (mostly H-containing) and reaction chemistry. Neutron diffraction and quasielastic neutron scattering can also supply important information on catalyst structures and dynamics of surface species. Other neutron approaches, such as small angle neutron scattering and neutron imaging, have been much less used but still give distinctive catalytic information. This review provides a comprehensive overview of recent advances in neutron scattering investigations of heterogeneous catalysis, focusing on surface adsorbates, reaction mechanisms, and catalyst structural changes revealed by neutron spectroscopy, diffraction, quasielastic neutron scattering, and other neutron techniques. Perspectives are also provided on the challenges and future opportunities in neutron scattering studies of heterogeneous catalysis.
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Affiliation(s)
- Xinbin Yu
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37381, United States
| | - Yongqiang Cheng
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Yuanyuan Li
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37381, United States
| | - Felipe Polo-Garzon
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37381, United States
| | - Jue Liu
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Eugene Mamontov
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Meijun Li
- Manufacturing Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - David Lennon
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Stewart F Parker
- ISIS Pulsed Neutron and Muon Facility, STFC Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX, United Kingdom
| | - Anibal J Ramirez-Cuesta
- Neutron Technologies Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Zili Wu
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37381, United States
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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25
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Domingues TS, Coifman RR, Haji-Akbari A. Robust Estimation of Position-Dependent Anisotropic Diffusivity Tensors from Stochastic Trajectories. J Phys Chem B 2023. [PMID: 37261948 DOI: 10.1021/acs.jpcb.3c00670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Materials under confinement can possess properties that deviate considerably from their bulk counterparts. Indeed, confinement makes all physical properties position-dependent and possibly anisotropic, and characterizing such spatial variations and directionality has been an intense area of focus in experimental and computational studies of confined matter. While this task is fairly straightforward for simple mechanical observables, it is far more daunting for transport properties such as diffusivity that can only be estimated from autocorrelations of mechanical observables. For instance, there are well established methods for estimating diffusivity from experimentally observed or computationally generated trajectories in bulk systems. No rigorous generalizations of such methods, however, exist for confined systems. In this work, we present two filtered covariance estimators for computing anisotropic and position-dependent diffusivity tensors and validate them by applying them to stochastic trajectories generated according to known diffusivity profiles. These estimators can accurately capture spatial variations that span over several orders of magnitude and that assume different functional forms. Our kernel-based approach is also very robust to implementation details such as the localization function and time discretization and performs significantly better than estimators that are solely based on local covariance. Moreover, the kernel function does not have to be localized and can instead belong to a dictionary of orthogonal functions. Therefore, the proposed estimator can be readily used to obtain functional estimates of diffusivity rather than a tabulated collection of pointwise estimates. Nonetheless, the susceptibility of the proposed estimators to time discretization is higher at the immediate vicinity of hard boundaries. We demonstrate this heightened susceptibility to be common among all covariance-based estimators.
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Affiliation(s)
- Tiago S Domingues
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
| | - Ronald R Coifman
- Department of Mathematics, Yale University, New Haven, Connecticut 06520, United States
| | - Amir Haji-Akbari
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
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26
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Nagao M, Seto H. Neutron scattering studies on dynamics of lipid membranes. BIOPHYSICS REVIEWS 2023; 4:021306. [PMID: 38504928 PMCID: PMC10903442 DOI: 10.1063/5.0144544] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/01/2023] [Indexed: 03/21/2024]
Abstract
Neutron scattering methods are powerful tools for the study of the structure and dynamics of lipid bilayers in length scales from sub Å to tens to hundreds nm and the time scales from sub ps to μs. These techniques also are nondestructive and, perhaps most importantly, require no additives to label samples. Because the neutron scattering intensities are very different for hydrogen- and deuterium-containing molecules, one can replace the hydrogen atoms in a molecule with deuterium to prepare on demand neutron scattering contrast without significantly altering the physical properties of the samples. Moreover, recent advances in neutron scattering techniques, membrane dynamics theories, analysis tools, and sample preparation technologies allow researchers to study various aspects of lipid bilayer dynamics. In this review, we focus on the dynamics of individual lipids and collective membrane dynamics as well as the dynamics of hydration water.
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Affiliation(s)
| | - Hideki Seto
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0801, Japan
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Yamamoto Y, Lu F, Nakanishi T, Hayashi S. Liquid Structures and Diffusion Dynamics of Alkyl-Pyrene Liquids Studied by Molecular Dynamics Simulations. J Phys Chem B 2023. [PMID: 37093669 DOI: 10.1021/acs.jpcb.2c08385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Functional molecular liquids (FMLs) based on alkylated π-conjugated molecules have attracted attention as solvent-free and nonvolatile liquid materials with prominent optoelectronic features. Recently, novel FML compounds containing pyrene as the functional core were synthesized, and their rheological and photochemical properties were investigated. Although the molecules differ only in the number of alkyl chain substituents and their substitution positions, their viscosity coefficients are largely different beyond the Stokes-Einstein relation on the assumption of identical microscopic friction, indicating that local microscopic molecular interactions are crucial for the macroscopic rheological properties. Here, we report a theoretical study on the rheological properties of the alkyl-pyrene liquids by means of atomistic molecular dynamics (MD) simulations. We performed long-time MD simulations for tens of microseconds to obtain ample statistical samples of the alkyl-pyrene liquids and analyzed their liquid structures and diffusion dynamics based on spatiotemporal correlation functions. We found the formation of characteristic local liquid structures of π-π stacking of the pyrene moieties and locally anisotropic and anomalous diffusion dynamics, which remarkably vary depending on the alkyl substituent patterns. The present results provide an atomistic insight into the macroscopic rheological properties of alkyl-π FMLs and molecular design strategy for them.
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Affiliation(s)
- Yuki Yamamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8052, Japan
| | - Fengniu Lu
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Japan
| | - Takashi Nakanishi
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8052, Japan
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de Las Heras D, Zimmermann T, Sammüller F, Hermann S, Schmidt M. Perspective: How to overcome dynamical density functional theory. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2023; 35:271501. [PMID: 37023762 DOI: 10.1088/1361-648x/accb33] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
We argue in favour of developing a comprehensive dynamical theory for rationalizing, predicting, designing, and machine learning nonequilibrium phenomena that occur in soft matter. To give guidance for navigating the theoretical and practical challenges that lie ahead, we discuss and exemplify the limitations of dynamical density functional theory (DDFT). Instead of the implied adiabatic sequence of equilibrium states that this approach provides as a makeshift for the true time evolution, we posit that the pending theoretical tasks lie in developing a systematic understanding of the dynamical functional relationships that govern the genuine nonequilibrium physics. While static density functional theory gives a comprehensive account of the equilibrium properties of many-body systems, we argue that power functional theory is the only present contender to shed similar insights into nonequilibrium dynamics, including the recognition and implementation of exact sum rules that result from the Noether theorem. As a demonstration of the power functional point of view, we consider an idealized steady sedimentation flow of the three-dimensional Lennard-Jones fluid and machine-learn the kinematic map from the mean motion to the internal force field. The trained model is capable of both predicting and designing the steady state dynamics universally for various target density modulations. This demonstrates the significant potential of using such techniques in nonequilibrium many-body physics and overcomes both the conceptual constraints of DDFT as well as the limited availability of its analytical functional approximations.
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Affiliation(s)
- Daniel de Las Heras
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95447 Bayreuth, Germany
| | - Toni Zimmermann
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95447 Bayreuth, Germany
| | - Florian Sammüller
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95447 Bayreuth, Germany
| | - Sophie Hermann
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95447 Bayreuth, Germany
| | - Matthias Schmidt
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95447 Bayreuth, Germany
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29
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Bolmatov D, Collier CP, Zav’yalov D, Egami T, Katsaras J. Real Space and Time Imaging of Collective Headgroup Dipole Motions in Zwitterionic Lipid Bilayers. MEMBRANES 2023; 13:442. [PMID: 37103869 PMCID: PMC10142431 DOI: 10.3390/membranes13040442] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/05/2023] [Accepted: 04/14/2023] [Indexed: 06/19/2023]
Abstract
Lipid bilayers are supramolecular structures responsible for a range of processes, such as transmembrane transport of ions and solutes, and sorting and replication of genetic materials, to name just a few. Some of these processes are transient and currently, cannot be visualized in real space and time. Here, we developed an approach using 1D, 2D, and 3D Van Hove correlation functions to image collective headgroup dipole motions in zwitterionic phospholipid bilayers. We show that both 2D and 3D spatiotemporal images of headgroup dipoles are consistent with commonly understood dynamic features of fluids. However, analysis of the 1D Van Hove function reveals lateral transient and re-emergent collective dynamics of the headgroup dipoles-occurring at picosecond time scales-that transmit and dissipate heat at longer times, due to relaxation processes. At the same time, the headgroup dipoles also generate membrane surface undulations due a collective tilting of the headgroup dipoles. A continuous intensity band of headgroup dipole spatiotemporal correlations-at nanometer length and nanosecond time scales-indicates that dipoles undergo stretching and squeezing elastic deformations. Importantly, the above mentioned intrinsic headgroup dipole motions can be externally stimulated at GHz-frequency scale, enhancing their flexoelectric and piezoelectric capabilities (i.e., increased conversion efficiency of mechanical energy into electric energy). In conclusion, we discuss how lipid membranes can provide molecular-level insights about biological learning and memory, and as platforms for the development of the next generation of neuromorphic computers.
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Affiliation(s)
- Dima Bolmatov
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA
- Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - C. Patrick Collier
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dmitry Zav’yalov
- Department of Physics, Volgograd State Technical University, Volgograd 400005, Russia
| | - Takeshi Egami
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA
- Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Materials Science and Engineering, The University of Tennessee, Knoxville, TN 37916, USA
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - John Katsaras
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA
- Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Sample Environment Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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30
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de Bruyn E, Dorn AE, Zimmermann O, Rossetti G. SPEADI: Accelerated Analysis of IDP-Ion Interactions from MD-Trajectories. BIOLOGY 2023; 12:biology12040581. [PMID: 37106781 PMCID: PMC10135740 DOI: 10.3390/biology12040581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023]
Abstract
The disordered nature of Intrinsically Disordered Proteins (IDPs) makes their structural ensembles particularly susceptible to changes in chemical environmental conditions, often leading to an alteration of their normal functions. A Radial Distribution Function (RDF) is considered a standard method for characterizing the chemical environment surrounding particles during atomistic simulations, commonly averaged over an entire or part of a trajectory. Given their high structural variability, such averaged information might not be reliable for IDPs. We introduce the Time-Resolved Radial Distribution Function (TRRDF), implemented in our open-source Python package SPEADI, which is able to characterize dynamic environments around IDPs. We use SPEADI to characterize the dynamic distribution of ions around the IDPs Alpha-Synuclein (AS) and Humanin (HN) from Molecular Dynamics (MD) simulations, and some of their selected mutants, showing that local ion-residue interactions play an important role in the structures and behaviors of IDPs.
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Affiliation(s)
- Emile de Bruyn
- Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany
| | - Anton Emil Dorn
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany
| | - Olav Zimmermann
- Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Giulia Rossetti
- Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany
- Department of Neurology, RWTH Aachen University, 52062 Aachen, Germany
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31
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Corci B, Hooiveld O, Dolga AM, Åberg C. Extending the analogy between intracellular motion in mammalian cells and glassy dynamics. SOFT MATTER 2023; 19:2529-2538. [PMID: 36939775 DOI: 10.1039/d2sm01672a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
How molecules, organelles, and foreign objects move within living cells has been studied in organisms ranging from bacteria to human cells. In mammalian cells, in particular, cellular vesicles move across the cell using motor proteins that carry the vesicle down the cytoskeleton to their destination. We have recently noted several similarities between the motion of such vesicles and that in disordered, "glassy", systems, but the generality of this observation remains unclear. Here we follow the motion of mitochondria, the organelles responsible for cell energy production, in mammalian cells over timescales from 50 ms to 70 s. Qualitative observations show that single mitochondria remain within a spatially limited region for extended periods of time, before moving longer distances relatively quickly. The displacement distribution is roughly Gaussian for shorter distances (≲0.05 μm) but exhibits exponentially decaying tails at longer distances (up to 0.40 μm). This behaviour is well-described by a model developed to describe the motion in glassy systems. These observations are extended to in total 3 different objects (mitochondria, lysosomes and nano-sized beads enclosed in vesicles), 3 different mammalian cell types (HEK 293, HeLa, and HT22), from 2 different organisms (human and mouse). Further evidence that supports glass-like characteristics of the motion is a difference between the time it takes to move a longer distance for the first time and subsequent times, as well as a weak ergodicity breaking of the motion. Overall, we demonstrate the ubiquity of glass-like motion in mammalian cells, providing a different perspective on intracellular motion.
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Affiliation(s)
- Beatrice Corci
- Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Oscar Hooiveld
- Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
| | - Amalia M Dolga
- Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
| | - Christoffer Åberg
- Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
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32
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Torres-Miyares EE, Ward DJ, Rojas-Lorenzo G, Rubayo-Soneira J, Allison W, Miret-Artés S. The stochastic wave function method for diffusion of alkali atoms on metallic surfaces. Phys Chem Chem Phys 2023; 25:6225-6231. [PMID: 36756814 DOI: 10.1039/d2cp05511b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The stochastic wave function method is proposed to study the diffusion regimes of alkali atoms on metallic surfaces. The Lindblad approach, based on the microscopic Hamiltonian information in the Caldeira-Leggett model, is presented and numerical calculations of the dynamics are carried out to characterize surface diffusion for two different systems: Na-Cu(111) and Li-Cu(111). Calculations of the intermediate scattering function for an isolated adsorbate are compared, in the Brownian limit, with results deduced from helium spin-echo (HeSE) experiments after reducing them to single adsorbate dynamics. To illustrate the method we present the dependence on momentum transfer and the temperature dependency. Results show that the experiment can be described at a quantitative level by the 1-D quantum model (reduced dimensionality).
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Affiliation(s)
- E E Torres-Miyares
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas, Serrano 123, 28006, Madrid, Spain.
| | - D J Ward
- SMF Cavendish Laboratory, JJ Thomson Avenue, Cambridge, UK.
| | - G Rojas-Lorenzo
- Instituto Superior de Tecnologías y Ciencias Aplicadas (InSTEC),Universidad de La Habana, Avenida Allende No. 1110, Plaza, La Habana, 10400, Cuba.
| | - J Rubayo-Soneira
- Instituto Superior de Tecnologías y Ciencias Aplicadas (InSTEC),Universidad de La Habana, Avenida Allende No. 1110, Plaza, La Habana, 10400, Cuba. .,Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal, 4, 20018, Donostia-San Sebastian, Spain
| | - W Allison
- SMF Cavendish Laboratory, JJ Thomson Avenue, Cambridge, UK.
| | - S Miret-Artés
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas, Serrano 123, 28006, Madrid, Spain. .,Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal, 4, 20018, Donostia-San Sebastian, Spain
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33
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Shi Y, Jiang P, Wang S, Chen W, Wei B, Lu X, Qian G, Kan WH, Chen H, Yin W, Sun Y, Lu X. Slight compositional variation-induced structural disorder-to-order transition enables fast Na + storage in layered transition metal oxides. Nat Commun 2022; 13:7888. [PMID: 36550128 PMCID: PMC9780345 DOI: 10.1038/s41467-022-35597-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
The omnipresent Na+/vacancy orderings change substantially with the composition that inevitably actuate the ionic diffusion in rechargeable batteries. Therefore, it may hold the key to the electrode design with high rate capability. Herein, the influence of Na+/vacancy ordering on Na+ mobility is demonstrated firstly through a comparative investigation in P2-Na2/3Ni1/3Mn2/3O2 and P2-Na2/3Ni0.3Mn0.7O2. The large zigzag Na+/vacancy intralayer ordering is found to accelerate Na+ migration in P2-type Na2/3Ni1/3Mn2/3O2. By theoretical simulations, it is revealed that the Na+ ordering enables the P2-type Na2/3Ni1/3Mn2/3O2 with higher diffusivities and lower activation energies of 200 meV with respect to the P3 one. The quantifying diffusional analysis further prove that the higher probability of the concerted Na+ ionic diffusion occurs in P2-type Na2/3Ni1/3Mn2/3O2 due to the appropriate ratio of high energy ordered Na ions (Naf) occupation. As a result, the interplay between the Na+/vacancy ordering and Na+ kinetic is well understood in P2-type layered cathodes.
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Affiliation(s)
- Yuansheng Shi
- grid.12981.330000 0001 2360 039XSchool of Materials, Sun Yat-sen University, Shenzhen, 518107 People’s Republic of China
| | - Pengfeng Jiang
- grid.12981.330000 0001 2360 039XSchool of Materials, Sun Yat-sen University, Shenzhen, 518107 People’s Republic of China
| | - Shicheng Wang
- grid.12981.330000 0001 2360 039XSchool of Materials, Sun Yat-sen University, Shenzhen, 518107 People’s Republic of China
| | - Weixin Chen
- grid.12981.330000 0001 2360 039XSchool of Materials, Sun Yat-sen University, Shenzhen, 518107 People’s Republic of China
| | - Bin Wei
- grid.12981.330000 0001 2360 039XSchool of Materials, Sun Yat-sen University, Shenzhen, 518107 People’s Republic of China
| | - Xueyi Lu
- grid.12981.330000 0001 2360 039XSchool of Materials, Sun Yat-sen University, Shenzhen, 518107 People’s Republic of China
| | - Guoyu Qian
- grid.12981.330000 0001 2360 039XSchool of Materials, Sun Yat-sen University, Shenzhen, 518107 People’s Republic of China
| | - Wang Hay Kan
- grid.495581.4Spallation Neutron Source Science Center, Dongguan, 523803 People’s Republic of China ,grid.9227.e0000000119573309Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Huaican Chen
- grid.495581.4Spallation Neutron Source Science Center, Dongguan, 523803 People’s Republic of China ,grid.9227.e0000000119573309Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Wen Yin
- grid.495581.4Spallation Neutron Source Science Center, Dongguan, 523803 People’s Republic of China ,grid.9227.e0000000119573309Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Yang Sun
- grid.12981.330000 0001 2360 039XSchool of Materials, Sun Yat-sen University, Shenzhen, 518107 People’s Republic of China
| | - Xia Lu
- grid.12981.330000 0001 2360 039XSchool of Materials, Sun Yat-sen University, Shenzhen, 518107 People’s Republic of China
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Lingerfelt DB, Yoshimura A, Jakowski J, Ganesh P, Sumpter BG. Extracting Inelastic Scattering Cross Sections for Finite and Aperiodic Materials from Electronic Dynamics Simulations. J Chem Theory Comput 2022; 18:7093-7107. [PMID: 36375179 DOI: 10.1021/acs.jctc.2c00882] [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]
Abstract
Explicit time-dependent electronic structure theory methods are increasingly prevalent in the areas of condensed matter physics and quantum chemistry, with the broad-band optical absorptivity of molecular and small condensed-phase systems nowadays routinely studied with such approaches. In this paper, it is demonstrated that electronic dynamics simulations can similarly be employed to study cross sections for the scattering-induced electronic excitations probed in nonresonant inelastic X-ray scattering and momentum-resolved electron energy loss spectroscopies. A method is put forth for evaluating the electronic dynamic structure factor, which involves the application of a momentum boost-type perturbation and transformation of the resulting reciprocal space density fluctuations into the frequency domain. Good agreement is first demonstrated between the dynamic structure factor extracted from these electronic dynamics simulations and the corresponding transition matrix elements from linear response theory. The method is then applied to some extended (quasi)one-dimensional systems, for which the wave vector becomes a good quantum number in the thermodynamic limit. Finally, the dispersion of many-body excitations in a series of hydrogen-terminated graphene flakes (and twisted bilayers thereof) is investigated to highlight the utility of the presented approach for capturing morphology-dependent effects in the inelastic scattering cross sections of nanostructured and/or noncrystalline materials.
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Affiliation(s)
- David B Lingerfelt
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States
| | - Anthony Yoshimura
- Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Jacek Jakowski
- Computing and Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States
| | - Panchapakesan Ganesh
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States
| | - Bobby G Sumpter
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States
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35
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Savici AT, Gigg MA, Arnold O, Tolchenov R, Whitfield RE, Hahn SE, Zhou W, Zaliznyak IA. Efficient data reduction for time-of-flight neutron scattering experiments on single crystals. J Appl Crystallogr 2022; 55:1514-1527. [PMID: 36570664 PMCID: PMC9721335 DOI: 10.1107/s1600576722009645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
Event-mode data collection presents remarkable new opportunities for time-of-flight neutron scattering studies of collective excitations, diffuse scattering from short-range atomic and magnetic structures, and neutron crystallography. In these experiments, large volumes of the reciprocal space are surveyed, often using different wavelengths and counting times. These data then have to be added together, with accurate propagation of the counting errors. This paper presents a statistically correct way of adding and histogramming the data for single-crystal time-of-flight neutron scattering measurements. In order to gain a broader community acceptance, particular attention is given to improving the efficiency of calculations.
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Affiliation(s)
- Andrei T. Savici
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA,Correspondence e-mail:
| | - Martyn A. Gigg
- ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, UK,Tessella Ltd, Abingdon, UK
| | - Owen Arnold
- ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, UK,Tessella Ltd, Abingdon, UK
| | - Roman Tolchenov
- ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, UK,Tessella Ltd, Abingdon, UK
| | - Ross E. Whitfield
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA,Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Steven E. Hahn
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA,Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Wenduo Zhou
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA,Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Igor A. Zaliznyak
- Condensed Matter Physics and Materials Science Division, Brookhaven National Laboratory, Upton, NY, 11973, USA
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36
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Ostadsharif Memar Z, Moosavi M. A combined QTAIM, DFT and molecular dynamics study on the nanoscale dynamical and structural organization of imidazolium-based dicationic ionic liquids. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Scheie A, Laurell P, Lake B, Nagler SE, Stone MB, Caux JS, Tennant DA. Quantum wake dynamics in Heisenberg antiferromagnetic chains. Nat Commun 2022; 13:5796. [PMID: 36184666 PMCID: PMC9527252 DOI: 10.1038/s41467-022-33571-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022] Open
Abstract
Traditional spectroscopy, by its very nature, characterizes physical system properties in the momentum and frequency domains. However, the most interesting and potentially practically useful quantum many-body effects emerge from local, short-time correlations. Here, using inelastic neutron scattering and methods of integrability, we experimentally observe and theoretically describe a local, coherent, long-lived, quasiperiodically oscillating magnetic state emerging out of the distillation of propagating excitations following a local quantum quench in a Heisenberg antiferromagnetic chain. This “quantum wake” displays similarities to Floquet states, discrete time crystals and nonlinear Luttinger liquids. We also show how this technique reveals the non-commutativity of spin operators, and is thus a model-agnostic measure of a magnetic system’s “quantumness.” It has long been suggested that the inverse Fourier transform of neutron scattering data gives access to space- and time-resolved spin-spin correlations. Scheie et al. perform this procedure on high-precision experimental data from a 1D quantum antiferromagnet and uncover new features in short-term quench dynamics.
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Affiliation(s)
- A Scheie
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - P Laurell
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, 37996, USA
| | - B Lake
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Hahn-Meitner Platz 1, D-14109, Berlin, Germany.,Institut für Festkörperphysik, Technische Universität Berlin, Hardenbergstraße 36, D-10623, Berlin, Germany
| | - S E Nagler
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Quantum Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - M B Stone
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - J-S Caux
- Institute of Physics and Institute for Theoretical Physics, University of Amsterdam, PO Box 94485, 1090 GL, Amsterdam, The Netherlands
| | - D A Tennant
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Quantum Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Shull Wollan Center - A Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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38
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Khanal R, Irle S. Quantum chemical investigation of the effect of alkali metal ions on the dynamic structure of water in aqueous solutions. RSC Adv 2022; 12:25500-25510. [PMID: 36275866 PMCID: PMC9480497 DOI: 10.1039/d2ra04563j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/26/2022] [Indexed: 11/21/2022] Open
Abstract
We report quantum chemical molecular dynamics (MD) simulations based on the density-functional tight-binding (DFTB) method to investigate the effect of K+, Na+, and Mg2+ ions in aqueous solutions on the static and dynamic structure of bulk water at room temperature and with various concentrations. The DFTB/MD simulations were validated for the description of ion solvation in aqueous ionic solutions by comparing static pair distribution functions (PDFs) as well as the cation solvation shell between experimental and available ab initio DFT data. The effect of the cations on the water structure, as well as relative differences between K+, Na+, and Mg2+ cations, were analyzed in terms of atomically resolved PDFs as well as time-dependent Van Hove correlation functions (VHFs). The investigation of the VHFs reveals that salt ions generally slow down the dynamic decay of the pair correlations in the water solvation sphere, irrespective of the cation size or charge. The analysis of partial metal-oxygen VHFs indicates that there are long-lived correlations between water and Na+ over long distances, in contrast to K+ and Mg2+.
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Affiliation(s)
- Rabi Khanal
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory Oak Ridge Tennessee 37831 USA
| | - Stephan Irle
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory Oak Ridge Tennessee 37831 USA
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39
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Unravelling the Adaptation Mechanisms to High Pressure in Proteins. Int J Mol Sci 2022; 23:ijms23158469. [PMID: 35955607 PMCID: PMC9369236 DOI: 10.3390/ijms23158469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 02/06/2023] Open
Abstract
Life is thought to have appeared in the depth of the sea under high hydrostatic pressure. Nowadays, it is known that the deep biosphere hosts a myriad of life forms thriving under high-pressure conditions. However, the evolutionary mechanisms leading to their adaptation are still not known. Here, we show the molecular bases of these mechanisms through a joint structural and dynamical study of two orthologous proteins. We observed that pressure adaptation involves the decoupling of protein–water dynamics and the elimination of cavities in the protein core. This is achieved by rearranging the charged residues on the protein surface and using bulkier hydrophobic residues in the core. These findings will be the starting point in the search for a complete genomic model explaining high-pressure adaptation.
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40
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Khatua P, Gupta M, Bandyopadhyay S. Exploring Heterogeneous Dynamical Environment around an Ensemble of Aβ 42 Peptide Monomer Conformations. J Chem Inf Model 2022; 62:3453-3462. [PMID: 35816665 DOI: 10.1021/acs.jcim.2c00593] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Exploring the conformational properties of amyloid β (Aβ) peptides and the role of solvent (water) in guiding the dynamical environment at their interfaces is crucial for microscopic understanding of Aβ misfolding, which is involved in causing the most common neurodegenerative disorder, i.e., Alzheimer's disease. While numerous studies in the past have emphasized examining the conformational states of Aβ peptides, the role of water has not received much attention. Here, we have performed all-atom molecular dynamics simulations of several full-length Aβ42 peptide monomers with different initial configurations. Our efforts are directed toward probing the origin of the heterogeneous dynamics of water around various segments of the Aβ peptide, identified as the two terminal segments (N-term and C-term) and the two hydrophobic segments (hp1 and hp2), along with the central turn region interconnecting hp1 and hp2. Our results revealed that water hydrating hp1, hp2, and turn (nonterminal segments) and C-term segments exhibit nonuniformly restricted translational as well as rotational motions. The degree of such restriction has been found to be correlated with the hydrogen bond relaxation time scales at the interface. Importantly, it is revealed that the water molecules around hp1 and, to some extent, around hp2, form relatively rigid hydration layers, compared to that around the other segments. Such rigid hydration layers arise due to relatively more solid-like caging motions resulting in relatively lesser hydration entropy. As hp1 and hp2 have been demonstrated to play a central role in Aβ aggregation, we believe that distinct water dynamics in the vicinity of these two segments, as outlined in this study, can provide vital information in understanding the early stages of the onset of the aggregation process of such peptides at higher concentration that can further aid toward advances in AD therapeutics.
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Affiliation(s)
- Prabir Khatua
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
| | - Madhulika Gupta
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand - 826004, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
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41
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Onitsuka Y, Tachibana Y, Takahashi M. Asymptotic behavior of the electron-atom Compton profile due to the intramolecular H-atom motion in H 2. Phys Chem Chem Phys 2022; 24:19716-19721. [PMID: 35792708 DOI: 10.1039/d2cp02461f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the asymptotic behavior of the electron-atom Compton profile due to the intramolecular H-atom motion in H2. The experiment has been performed at a scattering angle of 135° and at incident electron energies from 1.0 to 2.2 keV, thus covering a momentum transfer (K) range from 15.8 to 23.5 a.u. It is shown that with the increase in K, the Compton profile changes in shape and becomes more symmetric. Furthermore, it is found that the experiment reaches the limit of sufficiently large K at an incident electron energy of 2.0 keV, where the plane-wave impulse approximation is applicable to directly relate the Compton profile to the momentum distribution of the H atom.
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Affiliation(s)
- Yuuki Onitsuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, 980-8577, Japan.
| | - Yuichi Tachibana
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, 980-8577, Japan.
| | - Masahiko Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, 980-8577, Japan.
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42
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Shen Z, Carrillo JMY, Sumpter BG, Wang Y. Decoding polymer self-dynamics using a two-step approach. Phys Rev E 2022; 106:014502. [PMID: 35974619 DOI: 10.1103/physreve.106.014502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
The self-correlation function and corresponding self-intermediate scattering function in Fourier space are important quantities for describing the molecular motions of liquids. This work draws attention to a largely overlooked issue concerning the analysis of these space-time density-density correlation functions of polymers. We show that the interpretation of non-Gaussian behavior of polymers is generally complicated by intrachain averaging of distinct self-dynamics of different segments. By the very nature of the mathematics involved, the averaging process not only conceals critical dynamical information, but also contributes to the observed non-Gaussian dynamics. To fully expose this issue and provide a thorough benchmark of polymer self-dynamics, we perform analyses of coarse-grained molecular dynamics simulations of linear and ring polymer melts as well as several theoretical models using a "two-step" approach, where interchain and intrachain averagings of segmental self-dynamics are separated. While past investigations primarily focused on the average behavior, our results indicate that a more nuanced approach to polymer self-dynamics is clearly required.
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Affiliation(s)
- Zhiqiang Shen
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Jan-Michael Y Carrillo
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Bobby G Sumpter
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Yangyang Wang
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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43
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Shinohara Y, Ivanov AS, Maltsev D, Granroth GE, Abernathy DL, Dai S, Egami T. Real-Space Local Dynamics of Molten Inorganic Salts Using Van Hove Correlation Function. J Phys Chem Lett 2022; 13:5956-5962. [PMID: 35735362 DOI: 10.1021/acs.jpclett.2c01230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Molten inorganic salts are attracting resurgent attention because of their unique physicochemical properties, making them promising media for next-generation concentrating solar power systems and molten salt reactors. The dynamics of these highly disordered ionic media is largely studied by theoretical simulations, while the robust experimental techniques capable of observing local dynamics are not well-developed. To provide fundamental insights into the atomic-scale transport properties of molten salts, we report the real-space dynamics of molten magnesium chloride at high temperatures employing the Van Hove correlation function obtained by inelastic neutron scattering. Our results directly depict the distance-dependent dynamics of a molten salt on the picosecond time scale. This study demonstrates the capability of the developed approach to describe the locally correlated- and self-dynamics in molten salts, significantly improving our understanding of the interplay between microscopic structural parameters and their dynamics that ultimately control physical properties of condensed matter in extreme environments.
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Affiliation(s)
- Yuya Shinohara
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Alexander S Ivanov
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Dmitry Maltsev
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Garrett E Granroth
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Douglas L Abernathy
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Sheng Dai
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Takeshi Egami
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Materials Science and Engineering and Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, United States
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44
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Torres-Miyares EE, Rojas-Lorenzo G, Rubayo-Soneira J, Miret-Artés S. Surface diffusion within the Caldeira-Leggett formalism. Phys Chem Chem Phys 2022; 24:15871-15890. [PMID: 35762560 DOI: 10.1039/d2cp01579j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Surface diffusion is described in terms of the intermediate scattering function in the time domain and reciprocal space. Two extreme time regimes are analyzed, ballistic (very short times) and Brownian or diffusive (very long times). This open dynamics is studied from the master equation for the reduced density matrix within the Caldeira-Leggett formalism. Several characteristic magnitudes in this decoherence process such as the coherence length, ensemble width and purity of the density matrix are analyzed. Furthermore, for flat surfaces, the surface diffusion is considered for the Schrödinger cat states and identical adsorbates or adparticles, bosons and fermions. The analytical results are compared with those issued from solving the Lindblad master equation through the stochastic wave function method. This numerical analysis is extended to be applied to corrugated surfaces.
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Affiliation(s)
- E E Torres-Miyares
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas, Serrano 123, 28006 Madrid, Spain.
| | - G Rojas-Lorenzo
- Instituto Superior de Tecnologías y Ciencias Aplicadas (InSTEC), Universidad de La Habana, Avenida Allende No. 1110, Plaza, La Habana 10400, Cuba.
| | - J Rubayo-Soneira
- Instituto Superior de Tecnologías y Ciencias Aplicadas (InSTEC), Universidad de La Habana, Avenida Allende No. 1110, Plaza, La Habana 10400, Cuba.
| | - S Miret-Artés
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas, Serrano 123, 28006 Madrid, Spain.
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Xu S, Noguere G. Generation of thermal scattering files with the CINEL code. EPJ NUCLEAR SCIENCES & TECHNOLOGIES 2022. [DOI: 10.1051/epjn/2022004] [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
The CINEL code dedicated to generate the thermal neutron scattering files in ENDF-6 format for solid crystalline, free gas materials and liquid water is presented. Compared to the LEAPR module of the NJOY code, CINEL is able to calculate the coherent and incoherent elastic scattering cross sections for any solid crystalline materials. Specific material properties such as anharmonicity and texture can be taken into account in CINEL. The calculation of the thermal scattering laws can be accelerated by using graphics processing unit (GPU), which enables to remove the short collision time approximation for large values of momentum transfer. CINEL is able to generate automatically the grids of dimensionless momentum and energy transfers. The Sampling the Velocity of the Target nucleus (SVT) algorithm capable of determining the scattered neutron distributions is implemented in CINEL. The obtained distributions for free target nuclei such as hydrogen and oxygen are in good agreement with analytical results and Monte-Carlo simulations when incident neutron energies are above a few eV. The introduction of the effective temperature and the rejection step to the SVT algorithm shows improvements to the neutron up-scattering treatment of hydrogen bound in liquid water.
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46
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Medvedev N, Akhmetov F, Rymzhanov RA, Voronkov R, Volkov AE. Modeling Time‐Resolved Kinetics in Solids Induced by Extreme Electronic Excitation. ADVANCED THEORY AND SIMULATIONS 2022. [DOI: 10.1002/adts.202200091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nikita Medvedev
- Institute of Physics Czech Academy of Sciences Na Slovance 1999/2 Prague 8 182 21 Czech Republic
- Institute of Plasma Physics Czech Academy of Sciences Za Slovankou 3 Prague 8 182 00 Czech Republic
| | - Fedor Akhmetov
- Industrial Focus Group XUV Optics MESA+ Institute for Nanotechnology University of Twente Drienerlolaan 5 NB Enschede 7522 The Netherlands
| | - Ruslan A. Rymzhanov
- Joint Institute for Nuclear Research Joliot‐Curie 6 Dubna Moscow Region 141980 Russia
- The Institute of Nuclear Physics Ibragimov St. 1 Almaty 050032 Kazakhstan
| | - Roman Voronkov
- P.N. Lebedev Physical Institute of the Russian Academy of Sciences Leninskij pr., 53 Moscow 119991 Russia
| | - Alexander E. Volkov
- P.N. Lebedev Physical Institute of the Russian Academy of Sciences Leninskij pr., 53 Moscow 119991 Russia
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47
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Brownell M, Frischknecht AL, Wilson MA. Subdiffusive High-Pressure Hydrogen Gas Dynamics in Elastomers. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew Brownell
- Computational Materials and Data Science, Sandia National Laboratories, P.O. Box 5800, Albuquerque, New Mexico 87185-0889, United States
| | - Amalie L. Frischknecht
- Center for Integrated Nanotechnologies, Sandia National Laboratories, P.O. Box 5800, Albuquerque, New Mexico 87185-1303, United States
| | - Mark A. Wilson
- Computational Materials and Data Science, Sandia National Laboratories, P.O. Box 5800, Albuquerque, New Mexico 87185-0889, United States
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48
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Mondal S, Ghanta KP, Bandyopadhyay S. Dynamic Heterogeneity at the Interface of an Intrinsically Disordered Peptide. J Chem Inf Model 2022; 62:1942-1955. [PMID: 35384652 DOI: 10.1021/acs.jcim.2c00019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
It is believed that water around an intrinsically disordered protein or peptide (IDP) in an aqueous environment plays an important role in guiding its conformational properties and aggregation behavior. However, despite its importance, only a handful of studies exploring the correlation between the conformational motions of an IDP and the microscopic properties of water at its surface are reported. Attempts have been made in this work to study the dynamic properties of water present in the vicinity of α-synuclein, an IDP associated with Parkinson's disease (PD). Room temperature molecular dynamics (MD) simulations of eight α-synuclein1-95 peptides with a wide range of initial conformations have been carried out in aqueous media. The calculations revealed that due to solid-like caging motions, the translational and rotational mobility of water molecules near the surfaces of the peptide repeat unit segments R1 to R7 are significantly restricted. A small degree of dynamic heterogeneity in the hydration environment around the repeat units has been observed with water near the hydrophobic R6 unit exhibiting relatively more restricted diffusivity. The time scales involving the overall structural relaxations of peptide-water and water-water hydrogen bonds near the peptide have been found to be correlated with the time scale of diffusion of the interfacial water molecules. We believe that the relatively more hindered dynamic environment near R6 can help create water-mediated contacts centered around R6 between peptide monomers at a higher concentration, thereby enhancing the early stages of peptide aggregation.
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Affiliation(s)
- Souvik Mondal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Krishna Prasad Ghanta
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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49
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A Time-Dependent Hierarchical Model for Elastic and Inelastic Scattering Data Analysis of Aerogels and Similar Soft Materials. Gels 2022; 8:gels8040236. [PMID: 35448137 PMCID: PMC9025713 DOI: 10.3390/gels8040236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 12/10/2022] Open
Abstract
Soft nanomaterials like aerogels are subject to thermal fluctuations, so that their structure randomly fluctuates with time. Neutron elastic and inelastic scattering experiments provide unique structural and dynamic information on such systems with nanometer and nanosecond resolution. The data, however, come in the form of space- and time-correlation functions, and models are required to convert them into time-dependent structures. We present here a general time-dependent stochastic model of hierarchical structures, with scale-invariant fractals as a particular case, which enables one to jointly analyze elastic and inelastic scattering data. In order to describe thermal fluctuations, the model builds on time-dependent generalisations of the Boolean model of penetrable spheres, whereby each sphere is allowed to move either ballistically or diffusively. Analytical expressions are obtained for the correlation functions, which can be used for data fitting. The model is then used to jointly analyze previously published small-angle neutron scattering (SANS) and neutron spin-echo (NSE) data measured on silica aerogels. In addition to structural differences, the approach provides insight into the different scale-dependent mobility of the aggregates that make up the aerogels, in relation with their different connectivities.
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50
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Hartling K, Li G, Bentoumi G, Yamani Z. Molecular Dynamics of Supercritical Water for Nuclear Data Development. JOURNAL OF NUCLEAR ENGINEERING AND RADIATION SCIENCE 2022. [DOI: 10.1115/1.4051790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Abstract
The Canadian supercritical water-cooled reactor was selected as one of the Generation IV International Forum initiatives for reactor design. It uses supercritical light water as a coolant under operating conditions of 25 MPa (250 bar) and 623–898 K. However, the simulation codes used to assess the performance and safety of such a design depend upon the accuracy of available nuclear data parametrizations, which currently do not include models of light water in the supercritical regime. In this paper, we present a study of supercritical water (SCW) through molecular dynamics simulations. Flexible variants of the TIP4P/2005 and simple point charge models for H2O are assessed to determine their ability to reproduce experimental measurements of SCW properties, and their suitability for the future development of nuclear data parametrizations for thermal neutron scattering from SCW. Planned experiments measuring thermal neutron scattering from SCW to inform nuclear data development are also summarized.
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Affiliation(s)
- Katy Hartling
- Canadian Nuclear Laboratories, Chalk River, ON K0J 1J0, Canada
| | - Gang Li
- Canadian Nuclear Laboratories, Chalk River, ON K0J 1J0, Canada
| | | | - Zahra Yamani
- Canadian Nuclear Laboratories, Chalk River, ON K0J 1J0, Canada
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