1
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Daware SV, Mondal R, Kothari M, Chowdhury A, Liu ACY, Prabhakar R, Kumaraswamy G. Synthesis and Characterization of Monolayer Colloidal Sheets. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024. [PMID: 39288076 DOI: 10.1021/acs.langmuir.4c02262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
Sheet-like colloidal assemblies represent model systems to investigate the structure and properties of two-dimensional materials. Here, we report a simple yet versatile method for the preparation of colloidal monolayer sheet-like assemblies that affords control over the size, crystalline order, flexibility, and defect density. The protocol that we report relies on self-assembly of colloids as a sessile drop of dispersion is evaporated on an oil-covered substrate. In this case, the contact line continually moves as the drop shrinks. Polyethyleneimine polymer-covered micrometer-sized colloidal particles are transported to the air-water interface and assemble to form a monolayer sheet as the drop dries. Cross-linking the polymer renders the colloidal assembly permanent. Interestingly, monodisperse colloidal particles form disordered assemblies when dried from low concentration dispersions, while polycrystalline ordered assemblies form at higher concentrations. We demonstrate that increasing the cross-linker to polymer ratio decreases the flexibility of the assembly. Introduction of different-sized colloidal particles in a sheet leads to increased disorder. Removal of sacrificial particles from the sheet allowed the introduction of "holes" in the sheets. Thus, these colloidal sheets are models for probing the effects of disorder, doping, and vacancies in two-dimensional systems.
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Affiliation(s)
- Santosh Vasant Daware
- Department of Chemical Engineering, Indian Institute of Bombay, Mumbai 400076, India
- IITB Monash Research Academy, IIT Bombay, Powai 400076, India
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton 3800, Australia
| | - Ranajit Mondal
- Department of Chemical Engineering, IIT Hyderabad, Kandi, Telangana 502284, India
| | - Mansi Kothari
- Department of Chemistry, Indian Institute of Bombay, Mumbai 400076, India
| | - Arindam Chowdhury
- Department of Chemistry, Indian Institute of Bombay, Mumbai 400076, India
| | - Amelia C Y Liu
- School of Physics and Astronomy, Monash University, Clayton 3800, Australia
| | - Ranganathan Prabhakar
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton 3800, Australia
| | - Guruswamy Kumaraswamy
- Department of Chemical Engineering, Indian Institute of Bombay, Mumbai 400076, India
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2
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Gupta S, Moini R. Tough Cortical Bone-Inspired Tubular Architected Cement-Based Material with Disorder. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2313904. [PMID: 39252668 DOI: 10.1002/adma.202313904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 07/05/2024] [Indexed: 09/11/2024]
Abstract
Cortical bone is a tough biological material composed of tube-like osteons embedded in the organic matrix surrounded by weak interfaces known as cement lines. The cement lines provide a microstructurally preferable crack path, hence triggering in-plane crack deflection around osteons due to cement line-crack interaction. Inspired by this toughening mechanism and facilitated by a hybrid (3D-printing/casting) process, the study engineers architected tubular cement-based materials with the stepwise cracking toughening mechanism, that enables a non-brittle fracture. Using experimental and theoretical approaches, the study demonstrates the competition between tube size and shape on stress intensity factor from which engineering stepwise cracking can emerge. Two competing mechanisms, both positively and negatively affected by the growing tube size, arise to significantly enhance the overall fracture toughness by up to 5.6-fold compared to the monolithic brittle counterpart without sacrificing the specific strength. This is enabled by crack-tube interaction and engineering the tube size, shape, and orientation, which promotes rising resistance-curves (R-curve). "Disorder" curves and statistical mechanics parameters are proposed for the first time to quantitatively characterize the degree of disorder for describing the representation of the architected arrangement of materials in lieu of otherwise inadequate "periodicity" classification and misperceived disorder parameters (perturbation and Voronoi tessellation methods).
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Affiliation(s)
- Shashank Gupta
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Reza Moini
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ, 08544, USA
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3
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Meer DJ, Galoustian I, Manuel JGDF, Weeks ER. Estimating random close packing density from circle radius distributions. Phys Rev E 2024; 109:064905. [PMID: 39021009 DOI: 10.1103/physreve.109.064905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 05/24/2024] [Indexed: 07/20/2024]
Abstract
Circles of a single size can pack together densely in a hexagonal lattice, but adding in size variety disrupts the order of those packings. We conduct simulations which generate dense random packings of circles with specified size distributions and measure the area fraction in each case. While the size distributions can be arbitrary, we find that for a wide range of size distributions the random close-packing area fraction ϕ_{rcp} under this general protocol is determined to high accuracy by the polydispersity and skewness of the size distribution. At low skewness, all packings tend to a minimum packing fraction ϕ_{0}≈0.840 independent of polydispersity. In the limit of high skewness, ϕ_{rcp} becomes independent of skewness, asymptoting to a polydispersity-dependent limit. We show how these results can be predicted from the behavior of bidisperse or bi-Gaussian circle size distributions.
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4
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Palmer JC, Sarupria S, Truskett TM. Tribute to Pablo G. Debenedetti. J Phys Chem B 2023; 127:8075-8078. [PMID: 37766640 DOI: 10.1021/acs.jpcb.3c06020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Affiliation(s)
- Jeremy C Palmer
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, United States
| | - Sapna Sarupria
- Department of Chemistry, Chemical Theory Center, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Thomas M Truskett
- McKetta Department of Chemical Engineering and Department of Physics, The University of Texas at Austin, Austin, Texas 78712, United States
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5
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Zielkiewicz J. Mechanism of antifreeze protein functioning and the "anchored clathrate water" concept. J Chem Phys 2023; 159:085101. [PMID: 37622597 DOI: 10.1063/5.0158590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
In liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case, the interactions of water molecules with the protein surface shift the equilibrium of the process. In this paper, we analyze the structural properties of the solvation water in antifreeze proteins (AFPs). The results of molecular dynamics analysis with the use of various parameters related to the structure of solvation water on the protein surface are presented. We found that in the vicinity of the active region responsible for the binding of AFPs to ice, the equilibrium is clearly shifted toward the formation of "ice-like aggregates," and the solvation water has a more ordered ice-like structure. We have demonstrated that a reduction in the tendency to create "ice-like aggregates" results in a significant reduction in the antifreeze activity of the protein. We conclude that shifting the equilibrium in favor of the formation of "ice-like aggregates" in the solvation water in the active region is a prerequisite for the biological functionality of AFPs, at least for AFPs having a well-defined ice binding area. In addition, our results fully confirm the validity of the "anchored clathrate water" concept, formulated by Garnham et al. [Proc. Natl. Acad. Sci. U. S. A. 108, 7363 (2011)].
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Affiliation(s)
- Jan Zielkiewicz
- Faculty of Chemistry, Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
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6
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Anzivino C, Casiulis M, Zhang T, Moussa AS, Martiniani S, Zaccone A. Estimating random close packing in polydisperse and bidisperse hard spheres via an equilibrium model of crowding. J Chem Phys 2023; 158:044901. [PMID: 36725501 DOI: 10.1063/5.0137111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We show that an analogy between crowding in fluid and jammed phases of hard spheres captures the density dependence of the kissing number for a family of numerically generated jammed states. We extend this analogy to jams of mixtures of hard spheres in d = 3 dimensions and, thus, obtain an estimate of the random close packing volume fraction, ϕRCP, as a function of size polydispersity. We first consider mixtures of particle sizes with discrete distributions. For binary systems, we show agreement between our predictions and simulations using both our own results and results reported in previous studies, as well as agreement with recent experiments from the literature. We then apply our approach to systems with continuous polydispersity using three different particle size distributions, namely, the log-normal, Gamma, and truncated power-law distributions. In all cases, we observe agreement between our theoretical findings and numerical results up to rather large polydispersities for all particle size distributions when using as reference our own simulations and results from the literature. In particular, we find ϕRCP to increase monotonically with the relative standard deviation, sσ, of the distribution and to saturate at a value that always remains below 1. A perturbative expansion yields a closed-form expression for ϕRCP that quantitatively captures a distribution-independent regime for sσ < 0.5. Beyond that regime, we show that the gradual loss in agreement is tied to the growth of the skewness of size distributions.
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Affiliation(s)
- Carmine Anzivino
- Department of Physics "A. Pontremoli," University of Milan, Via Celoria 16, 20133 Milan, Italy
| | - Mathias Casiulis
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York 10003, USA
| | - Tom Zhang
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York 10003, USA
| | | | - Stefano Martiniani
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York 10003, USA
| | - Alessio Zaccone
- Department of Physics "A. Pontremoli," University of Milan, Via Celoria 16, 20133 Milan, Italy
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7
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Sorkin B, Ricouvier J, Diamant H, Ariel G. Resolving entropy contributions in nonequilibrium transitions. Phys Rev E 2023; 107:014138. [PMID: 36797967 DOI: 10.1103/physreve.107.014138] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 12/13/2022] [Indexed: 02/03/2023]
Abstract
We derive a functional for the entropy contributed by any microscopic degrees of freedom as arising from their measurable pair correlations. Applicable both in and out of equilibrium, this functional yields the maximum entropy which a system can have given a certain correlation function. When applied to different correlations, the method allows us to identify the degrees of freedom governing a certain physical regime, thus capturing and characterizing dynamic transitions. The formalism applies also to systems whose translational invariance is broken by external forces and whose number of particles may vary. We apply it to experimental results for jammed bidisperse emulsions, capturing the crossover of this nonequilibrium system from crystalline to disordered hyperuniform structures as a function of mixture composition. We discover that the cross-correlations between the positions and sizes of droplets in the emulsion play the central role in the formation of the disordered hyperuniform states. We discuss implications of the approach for entropy estimation out of equilibrium and for characterizing transitions in disordered systems.
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Affiliation(s)
- Benjamin Sorkin
- School of Chemistry and Center for Physics and Chemistry of Living Systems, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Joshua Ricouvier
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Haim Diamant
- School of Chemistry and Center for Physics and Chemistry of Living Systems, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Gil Ariel
- Department of Mathematics, Bar-Ilan University, 52000 Ramat Gan, Israel
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8
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Gartner TE, Piaggi PM, Car R, Panagiotopoulos AZ, Debenedetti PG. Liquid-Liquid Transition in Water from First Principles. PHYSICAL REVIEW LETTERS 2022; 129:255702. [PMID: 36608224 DOI: 10.1103/physrevlett.129.255702] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
A long-standing question in water research is the possibility that supercooled liquid water can undergo a liquid-liquid phase transition (LLT) into high- and low-density liquids. We used several complementary molecular simulation techniques to evaluate the possibility of an LLT in an ab initio neural network model of water trained on density functional theory calculations with the SCAN exchange correlation functional. We conclusively show the existence of a first-order LLT and an associated critical point in the SCAN description of water, representing the first definitive computational evidence for an LLT in water from first principles.
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Affiliation(s)
- Thomas E Gartner
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Pablo M Piaggi
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Roberto Car
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
- Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, USA
- Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, New Jersey 08544, USA
| | | | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
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9
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Amigo N, Cortés P, Valencia FJ. Research on metallic glasses at the atomic scale: a systematic review. SN APPLIED SCIENCES 2022; 4:281. [PMID: 36196063 PMCID: PMC9523636 DOI: 10.1007/s42452-022-05170-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 09/21/2022] [Indexed: 11/28/2022] Open
Abstract
Metallic glasses (MGs) have been long investigated in material science to understand the origin of their remarkable properties. With the help of computational simulations, researchers have delved into structure-property relationships, leading to a large number of reports. To quantify the available literature, we employed systematic review and bibliometric analysis on studies related to MGs and classical molecular dynamics simulations from 2000 to 2021. It was found that the total number of articles has increased remarkably, with China and the USA producing more than half of the reports. However, high-impact articles were mainly conducted in the latter. Collaboration networks revealed that top contributor authors are strongly connected with other researchers, which emphasizes the relevance of scientific cooperation. In regard to the evolution of research topics, according to article keywords, plastic behavior has been a recurrent subject since the early 2000s. Nevertheless, the traditional approach of studying monolithic MGs at the short-range order evolved to complex composites with characterizations at the medium-range order, including topics such as nanoglasses, amorphous/crystalline nanolaminates, rejuvenation, among others. As a whole, these findings provide researchers with an overview of past and current trends of research areas, as well as some of the leading authors, productivity statistics, and collaboration networks.
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Affiliation(s)
- Nicolás Amigo
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Bellavista 7, Santiago, 8420524 Chile
| | - Pablo Cortés
- Independent Researcher, Tegualda 2000, 7770547 Ñuñoa, Chile
| | - Felipe J. Valencia
- Departamento de Computación e Industrias, Facultad de Ciencias de la Ingeniería, Universidad Católica del Maule, Talca, Chile
- Centro para el Desarrollo de la Nanociencia y la Nanotecnologa, CEDENNA, Avda. Ecuador 3493, Santiago, Chile
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10
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Shi J, Fulford M, Li H, Marzook M, Reisjalali M, Salvalaglio M, Molteni C. Investigating the quasi-liquid layer on ice surfaces: a comparison of order parameters. Phys Chem Chem Phys 2022; 24:12476-12487. [PMID: 35576067 DOI: 10.1039/d2cp00752e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ice surfaces are characterized by pre-melted quasi-liquid layers (QLLs), which mediate both crystal growth processes and interactions with external agents. Understanding QLLs at the molecular level is necessary to unravel the mechanisms of ice crystal formation. Computational studies of the QLLs heavily rely on the accuracy of the methods employed for identifying the local molecular environment and arrangements, discriminating between solid-like and liquid-like water molecules. Here we compare the results obtained using different order parameters to characterize the QLLs on hexagonal ice (Ih) and cubic ice (Ic) model surfaces investigated with molecular dynamics (MD) simulations in a range of temperatures. For the classification task, in addition to the traditional Steinhardt order parameters in different flavours, we select an entropy fingerprint and a deep learning neural network approach (DeepIce), which are conceptually different methodologies. We find that all the analysis methods give qualitatively similar trends for the behaviours of the QLLs on ice surfaces with temperature, with some subtle differences in the classification sensitivity limited to the solid-liquid interface. The thickness of QLLs on the ice surface increases gradually as the temperature increases. The trends of the QLL size and of the values of the order parameters as a function of temperature for the different facets may be linked to surface growth rates which, in turn, affect crystal morphologies at lower vapour pressure. The choice of the order parameter can be therefore informed by computational convenience except in cases where a very accurate determination of the liquid-solid interface is important.
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Affiliation(s)
- Jihong Shi
- Department of Physics, King's College London, Strand, London WC2R 2LS, UK.
| | - Maxwell Fulford
- Department of Physics, King's College London, Strand, London WC2R 2LS, UK.
| | - Hui Li
- Department of Physics, King's College London, Strand, London WC2R 2LS, UK.
| | - Mariam Marzook
- Department of Physics, King's College London, Strand, London WC2R 2LS, UK.
| | - Maryam Reisjalali
- Department of Physics, King's College London, Strand, London WC2R 2LS, UK.
| | - Matteo Salvalaglio
- Department of Chemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
| | - Carla Molteni
- Department of Physics, King's College London, Strand, London WC2R 2LS, UK.
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11
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Algaba J, Acuña E, Míguez JM, Mendiboure B, Zerón IM, Blas FJ. Simulation of the carbon dioxide hydrate-water interfacial energy. J Colloid Interface Sci 2022; 623:354-367. [PMID: 35594594 DOI: 10.1016/j.jcis.2022.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 10/18/2022]
Abstract
HYPOTHESIS Carbon dioxide hydrates are ice-like nonstoichiometric inclusion solid compounds with importance to global climate change, and gas transportation and storage. The thermodynamic and kinetic mechanisms that control carbon dioxide nucleation critically depend on hydrate-water interfacial free energy. Only two independent indirect experiments are available in the literature. Interfacial energies show large uncertainties due to the conditions at which experiments are performed. Under these circumstances, we hypothesize that accurate molecular models for water and carbon dioxide combined with computer simulation tools can offer an alternative but complementary way to estimate interfacial energies at coexistence conditions from a molecular perspective. CALCULATIONS We have evaluated the interfacial free energy of carbon dioxide hydrates at coexistence conditions (three-phase equilibrium or dissociation line) implementing advanced computational methodologies, including the novel Mold Integration methodology. Our calculations are based on the definition of the interfacial free energy, standard statistical thermodynamic techniques, and the use of the most reliable and used molecular models for water (TIP4P/Ice) and carbon dioxide (TraPPE) available in the literature. FINDINGS We find that simulations provide an interfacial energy value, at coexistence conditions, consistent with the experiments from its thermodynamic definition. Our calculations are reliable since are based on the use of two molecular models that accurately predict: (1) The ice-water interfacial free energy; and (2) the dissociation line of carbon dioxide hydrates. Computer simulation predictions provide alternative but reliable estimates of the carbon dioxide interfacial energy. Our pioneering work demonstrates that is possible to predict interfacial energies of hydrates from a truly computational molecular perspective and opens a new door to the determination of free energies of hydrates.
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Affiliation(s)
- Jesús Algaba
- Department of Chemical Engineering, South Kensington Campus, Imperial College London, SW7 2AZ London, United Kingdom
| | - Esteban Acuña
- Laboratorio de Simulacion Molecular y Quimica Computacional, CIQSO-Centro de Investigacion en Quimica Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21007 Huelva, Spain
| | - José Manuel Míguez
- Laboratorio de Simulacion Molecular y Quimica Computacional, CIQSO-Centro de Investigacion en Quimica Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21007 Huelva, Spain
| | - Bruno Mendiboure
- Laboratoire des Fluides Complexes et Leurs Reservoirs, UMR5150, Universite de Pau et des Pays de l'Adour, B. P. 1155, Pau Cedex 64014, France
| | - Iván M Zerón
- Laboratorio de Simulacion Molecular y Quimica Computacional, CIQSO-Centro de Investigacion en Quimica Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21007 Huelva, Spain
| | - Felipe J Blas
- Laboratorio de Simulacion Molecular y Quimica Computacional, CIQSO-Centro de Investigacion en Quimica Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21007 Huelva, Spain.
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12
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Martelli F, Palmer JC. Signatures of sluggish dynamics and local structural ordering during ice nucleation. J Chem Phys 2022; 156:114502. [DOI: 10.1063/5.0083638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate the microscopic pathway of spontaneous crystallization in the ST2 model of water under deeply supercooled conditions via unbiased classical molecular dynamics simulations. After quenching below the liquid–liquid critical point, the ST2 model spontaneously separates into low-density liquid (LDL) and high-density liquid phases, respectively. The LDL phase, which is characterized by lower molecular mobility and enhanced structural order, fosters the formation of a sub-critical ice nucleus that, after a stabilization time, develops into the critical nucleus and grows. Polymorphic selection coincides with the development of the sub-critical nucleus and favors the formation of cubic (Ic) over hexagonal (Ih) ice. We rationalize polymorphic selection in terms of geometric arguments based on differences in the symmetry of second neighbor shells of ice Ic and Ih, which are posited to favor formation of the former. The rapidly growing critical nucleus absorbs both Ic and Ih crystallites dispersed in the liquid phase, a crystal with stacking faults. Our results are consistent with, and expand upon, recent observations of non-classical nucleation pathways in several systems.
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Affiliation(s)
- Fausto Martelli
- IBM Research Europe, Hartree Centre, Daresbury WA4 4AD, United Kingdom
| | - Jeremy C. Palmer
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA
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13
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Mitra S, Marín-Aguilar S, Sastry S, Smallenburg F, Foffi G. Correlation between plastic rearrangements and local structure in a cyclically driven glass. J Chem Phys 2022; 156:074503. [DOI: 10.1063/5.0077851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | - Srikanth Sastry
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, India
| | | | - Giuseppe Foffi
- Laboratoire de Physique des Solides, Laboratoire de Physique des Solides, France
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14
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Leoni F, Calero C, Franzese G. Nanoconfined Fluids: Uniqueness of Water Compared to Other Liquids. ACS NANO 2021; 15:19864-19876. [PMID: 34807577 PMCID: PMC8717635 DOI: 10.1021/acsnano.1c07381] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/18/2021] [Indexed: 05/27/2023]
Abstract
Nanoconfinement can drastically change the behavior of liquids, puzzling us with counterintuitive properties. It is relevant in applications, including decontamination and crystallization control. However, it still lacks a systematic analysis for fluids with different bulk properties. Here we address this gap. We compare, by molecular dynamics simulations, three different liquids in a graphene slit pore: (1) A simple fluid, such as argon, described by a Lennard-Jones potential; (2) an anomalous fluid, such as a liquid metal, modeled with an isotropic core-softened potential; and (3) water, the prototypical anomalous liquid, with directional HBs. We study how the slit-pore width affects the structure, thermodynamics, and dynamics of the fluids. All the fluids show similar oscillating properties by changing the pore size. However, their free-energy minima are quite different in nature: (i) are energy-driven for the simple liquid; (ii) are entropy-driven for the isotropic core-softened potential; and (iii) have a changing nature for water. Indeed, for water, the monolayer minimum is entropy driven, at variance with the simple liquid, while the bilayer minimum is energy driven, at variance with the other anomalous liquid. Also, water has a large increase in diffusion for subnm slit pores, becoming faster than bulk. Instead, the other two fluids have diffusion oscillations much smaller than water, slowing down for decreasing slit-pore width. Our results, clarifying that water confined at the subnm scale behaves differently from other (simple or anomalous) fluids under similar confinement, are possibly relevant in nanopores applications, for example, in water purification from contaminants.
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Affiliation(s)
- Fabio Leoni
- Department
of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Carles Calero
- Secció
de Física Estadística i Interdisciplinària-Departament
de Física de la Matèria Condensada, Institut de Nanociència i Nanotecnologia (IN2UB), Universitat
de Barcelona, Carrer Martí i Franquès 1, 08028 Barcelona, Spain
| | - Giancarlo Franzese
- Secció
de Física Estadística i Interdisciplinària-Departament
de Física de la Matèria Condensada, Institut de Nanociència i Nanotecnologia (IN2UB), Universitat
de Barcelona, Carrer Martí i Franquès 1, 08028 Barcelona, Spain
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15
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Zou Z, Tsai ST, Tiwary P. Toward Automated Sampling of Polymorph Nucleation and Free Energies with the SGOOP and Metadynamics. J Phys Chem B 2021; 125:13049-13056. [PMID: 34788047 DOI: 10.1021/acs.jpcb.1c07595] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding the driving forces behind the nucleation of different polymorphs is of great importance for material sciences and the pharmaceutical industry. This includes understanding the reaction coordinate that governs the nucleation process and correctly calculating the relative free energies of different polymorphs. Here, we demonstrate, for the prototypical case of urea nucleation from the melt, how one can learn such a one-dimensional reaction coordinate as a function of prespecified order parameters and use it to perform efficient biased all-atom molecular dynamics simulations. The reaction coordinate is learnt as a function of the generic thermodynamic and structural order parameters using the "spectral gap optimization of order parameters (SGOOP)" approach [Tiwary, P. and Berne, B. J. Proc. Natl. Acad. Sci. U.S.A. (2016)] and is biased using well-tempered metadynamics simulations. The reaction coordinate gives insights into the role played by different structural and thermodynamics order parameters, and the biased simulations obtain accurate relative free energies for different polymorphs. This includes an accurate prediction of the approximate pressure at which urea undergoes a phase transition and one of the metastable polymorphs becomes the most stable conformation. We believe the ideas demonstrated in this work will facilitate efficient sampling of nucleation in complex, generic systems.
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Affiliation(s)
- Ziyue Zou
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Sun-Ting Tsai
- Department of Physics, University of Maryland, College Park, Maryland 20742, United States.,Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
| | - Pratyush Tiwary
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States.,Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
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16
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Xu J, Wang Y, Ma X. Phase distribution including a bubblelike region in supercritical fluid. Phys Rev E 2021; 104:014142. [PMID: 34412334 DOI: 10.1103/physreve.104.014142] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 07/02/2021] [Indexed: 11/07/2022]
Abstract
Pseudoboiling in supercritical fluid (SF) has been paid great attention in recent years. Available works mainly focus on thermodynamics analysis. Fewer studies were reported on the spatial time phase distribution. Here, SF is investigated in a multiphase fluid framework using molecular dynamics (MD) simulations. A simulation box contains 10 976 argon atoms, with periodic boundary conditions applied on all the box surfaces. Pressure and temperature are well controlled. Based on MD simulation results, an onset pseudoboiling temperature T^{-} and a termination pseudoboiling temperature T^{+} are defined using the neighboring molecules method, the radial distribution function method, and the two-body excess entropy method. The two transition temperatures divide the whole phase diagram into three regimes of liquidlike, two-phase-like (TPL), and gaslike, and the MD determined T^{-} and T^{+} well matched the thermodynamics-determined values. In the TPL regime, nanovoids are observed to have two distinct characteristics: (1) Particles are sparsely distributed to have gas density inside the void, but are densely populated to have liquid density outside the void. (2) Voids have a curved interface. These characteristics are very similar to bubble characteristics in subcritical pressure. Hence, voids in the supercritical state are called "bubblelike" in this paper. Nonlinear dynamics demonstrates chaotic behavior in the TPL regime, similar to the two-phase regime in the subcritical domain. The above findings give strong evidence that SF in the TPL regime consists of a mixture of bubblelike voids and surrounding liquids. Our work highlights the multiphase feature of a SF, hence, the well-established multiphase theory in subcritical pressures can be introduced to handle the complex SF.
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Affiliation(s)
- Jinliang Xu
- Beijing Key Laboratory of Multiphase Flow and Heat Transfer for Low Grade Energy Utilization, North China Electric Power University, Beijing, 102206, China.,Key Laboratory of Power Station Energy Transfer Conversion and System, North China Electric Power University, Ministry of Education, Beijing, 102206, China
| | - Yan Wang
- Beijing Key Laboratory of Multiphase Flow and Heat Transfer for Low Grade Energy Utilization, North China Electric Power University, Beijing, 102206, China
| | - Xiaojing Ma
- Beijing Key Laboratory of Multiphase Flow and Heat Transfer for Low Grade Energy Utilization, North China Electric Power University, Beijing, 102206, China
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17
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Ravnik V, Hribar-Lee B, Pizio O, Lukšič M. Tetrahedrality, hydrogen bonding and the density anomaly of the central force water model. A Monte Carlo study. CONDENSED MATTER PHYSICS 2021; 24:33503. [PMID: 35095377 PMCID: PMC8794338 DOI: 10.5488/cmp.24.33503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Monte Carlo computer simulations in the canonical and grand canonical statistical ensemble were used to explore the properties of the central force (CF1) water model. The intramolecular structure of the H2O molecule is well reproduced by the model. Emphasis was made on hydrogen bonding, and on the tehrahedral, q, and translational, τ, order parameters. An energetic definition of the hydrogen bond gives more consistent results for the average number of hydrogen bonds compared to the one-parameter distance criterion. At 300 K, an average value of 3.8 was obtained. The q and τ metrics were used to elucidate the water-like anomalous behaviour of the CF1 model. The structural anomalies lead to the density anomaly, with a good agreement of the model's density with the experimental ρ(T) trends. The chemical potential-density projection of the model's equation of state was explored. Vapour-liquid coexistence was observed at sufficiently low temperatures.
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Affiliation(s)
- V. Ravnik
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - B. Hribar-Lee
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - O. Pizio
- Instituto de Química, Universidad Nacional Autonoma de México, Circuito Exterior, Ciudad Universitaria, 04510, Cd. de México, México
| | - M. Lukšič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
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18
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Moradzadeh A, Aluru NR. Understanding simple liquids through statistical and deep learning approaches. J Chem Phys 2021; 154:204503. [PMID: 34241171 DOI: 10.1063/5.0046226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Statistical and deep learning-based methods are employed to obtain insights into the quasi-universal properties of simple liquids. In the first part, a statistical model is employed to provide a probabilistic explanation for the similarity in the structure of simple liquids interacting with different pair potential forms, collectively known as simple liquids. The methodology works by sampling the radial distribution function and the number of interacting particles within the cutoff distance, and it produces the probability density function of the net force. We show that matching the probability distribution of the net force can be a direct route to parameterize simple liquid pair potentials with a similar structure, as the net force is the main component of the Newtonian equations of motion. The statistical model is assessed and validated against various cases. In the second part, we exploit DeepILST [A. Moradzadeh and N. R. Aluru, J. Phys. Chem. Lett. 10, 1242-1250 (2019)], a data-driven and deep-learning assisted framework to parameterize the standard 12-6 Lennard-Jones (LJ) pair potential, to find structurally equivalent/isomorphic LJ liquids that identify constant order parameter [τ=∫0 ξcf gξ-1ξ2dξ, where gξ and ξ(=rρ13) are the reduced radial distribution function and radial distance, respectively] systems in the space of non-dimensional temperature and density of the LJ liquids. We also investigate the consistency of DeepILST in reproducibility of radial distribution functions of various quasi-universal potentials, e.g., exponential, inverse-power-law, and Yukawa pair potentials, quantified based on the radial distribution functions and Kullback-Leibler errors. Our results provide insights into the quasi-universality of simple liquids using the statistical and deep learning methods.
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Affiliation(s)
- A Moradzadeh
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - N R Aluru
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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19
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Goswami A, Singh JK. A hybrid topological and shape-matching approach for structure analysis. J Chem Phys 2021; 154:154502. [DOI: 10.1063/5.0046419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Amrita Goswami
- Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Jayant K. Singh
- Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
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20
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Abstract
The molecular structure of bound layers at attractive polymer-nanoparticle interfaces strongly influences the properties of nanocomposites. Thus, a unifying theoretical framework that can provide insights into the correlations between the molecular structure of the bound layers, their thermodynamics, and macroscopic properties is highly desirable. In this work, molecular dynamics simulations were used in combination with local fingerprint analysis of configurational entropy and interaction energy at the segmental scale, with the goal to establish such physical grounds. The thickness of bound polymer layers is found to be independent of the polymer chain length, as deduced from density oscillations at the surface of a nanotube. The local configurational entropy of layers is estimated from pair correlations in equilibrium structures. By plotting mean layer entropy vs internal energy on a phase diagram, a one-to-one equivalence is established between the local structures of layers and their thermodynamic properties. Moreover, a gradient in local dynamics of segments in bound layers under equilibrium is observed normal to the nanoparticle surface. The relaxation times of individual layers show correspondence to their phase diagram fingerprints, thus suggesting that a unified perspective can be envisioned for such materials built on the grounds of locally heterogeneous interfaces.
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Affiliation(s)
- Ali Gooneie
- Laboratory of Advanced Fibers, Empa, Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, CH-9014 St. Gallen, Switzerland
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21
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Grebe V, Liu M, Weck M. Quantifying patterns in optical micrographs of one- and two-dimensional ellipsoidal particle assemblies. SOFT MATTER 2020; 16:10900-10909. [PMID: 33118580 DOI: 10.1039/d0sm01692f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Current developments in colloidal science include the assembly of anisotropic colloids with broad geometric diversity. As the complexity of particle assemblies increases, the need for ubiquitous algorithms that quantitatively analyze images of the assemblies to deliver key information such as quantification of crystal structures becomes more urgent. This contribution describes algorithms capable of image analysis for classifying colloidal structures based on abstracted interparticle relationship information and quantitatively analyzing the abundance of each structure in mixed pattern assemblies. The algorithm parameters can be adjusted, allowing for the algorithms to be adapted for different image analyses. Three different ellipsoidal particle assembly images are presented to demonstrate the effectiveness of the algorithms: a one-dimensional (1D) particle chain assembly and two two-dimensional (2D) polymorphic crystals each consisting of assemblies of two distinct plane symmetry groups. Angle relationships between neighbouring particles are calculated and neighbour counts of each particle are determined. Combining these two parameters as rules for classification criteria allows for the labeling and quantification of each particle into a defined symmetry class within an assembly. The algorithms provide a labelled image comprising classification results and particle counts of each defined class. For multiple images or individual frames from a video, the script can be looped to achieve automatic processing. The yielded classification data allow for more in-depth image analysis of mixed pattern particle assemblies. We envision that these algorithms will have utility in quantitative analysis of images comprising ellipsoidal colloidal materials, nanoparticles, or biological matter.
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Affiliation(s)
- Veronica Grebe
- Molecular Design Institute and Department of Chemistry, New York University, New York, NY 10003, USA.
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22
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Desgranges C, Delhommelle J. Entropy in Molecular Fluids: Interplay between Interaction Complexity and Criticality. J Phys Chem B 2020; 124:11463-11471. [PMID: 33267580 DOI: 10.1021/acs.jpcb.0c08014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using flat-histogram simulations, we calculate the entropy of molecular fluids along the vapor-liquid phase boundary. Our simulation approach is based on the evaluation of the canonical and grand-canonical partition functions, which, in turn, provide access to entropy through the statistical mechanics formalism. The results allow us to determine the critical entropy of molecular fluids and to uncover that the transition occurs symmetrically from an entropic standpoint. This can best be seen through the patterns exhibited by the thermodynamic variables temperature and pressure when plotted against the entropy of the coexisting phases. This behavior is found to hold for apolar, quadrupolar, and dipolar fluids. Finally, we identify functional forms that characterize the relation between thermodynamic variables and entropy along the coexistence curve up to the critical point.
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Affiliation(s)
- Caroline Desgranges
- Department of Chemistry, New York University, New York, New York 10003, United States.,Department of Chemistry & Molecular Simulation of NonEquilibrium Processes (MSNEP), University of North Dakota, Suite 2300, Tech Accelerator, Grand Forks, North Dakota 58202, United States
| | - Jerome Delhommelle
- Department of Chemistry, New York University, New York, New York 10003, United States.,Department of Chemistry & Molecular Simulation of NonEquilibrium Processes (MSNEP), University of North Dakota, Suite 2300, Tech Accelerator, Grand Forks, North Dakota 58202, United States
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23
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An isolated water droplet in the aqueous solution of a supramolecular tetrahedral cage. Proc Natl Acad Sci U S A 2020; 117:32954-32961. [PMID: 33318176 PMCID: PMC7777103 DOI: 10.1073/pnas.2012545117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Water under nanoconfinement at ambient conditions has exhibited low-dimensional ice formation and liquid-solid phase transitions, but with structural and dynamical signatures that map onto known regions of water's phase diagram. Using terahertz (THz) absorption spectroscopy and ab initio molecular dynamics, we have investigated the ambient water confined in a supramolecular tetrahedral assembly, and determined that a dynamically distinct network of 9 ± 1 water molecules is present within the nanocavity of the host. The low-frequency absorption spectrum and theoretical analysis of the water in the Ga4L6 12- host demonstrate that the structure and dynamics of the encapsulated droplet is distinct from any known phase of water. A further inference is that the release of the highly unusual encapsulated water droplet creates a strong thermodynamic driver for the high-affinity binding of guests in aqueous solution for the Ga4L6 12- supramolecular construct.
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24
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Nada H. Melt crystallization mechanism analyzed with dimensional reduction of high-dimensional data representing distribution function geometries. Sci Rep 2020; 10:15465. [PMID: 32963268 PMCID: PMC7508891 DOI: 10.1038/s41598-020-72455-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/02/2020] [Indexed: 11/21/2022] Open
Abstract
Melt crystallization is essential to many industrial processes, including semiconductor, ice, and food manufacturing. Nevertheless, our understanding of the melt crystallization mechanism remains poor. This is because the molecular-scale structures of melts are difficult to clarify experimentally. Computer simulations, such as molecular dynamics (MD), are often used to investigate melt structures. However, the time evolution of the structural order in a melt during crystallization must be analyzed properly. In this study, dimensional reduction (DR), which is an unsupervised machine learning technique, is used to evaluate the time evolution of structural order. The DR is performed for high-dimensional data representing an atom–atom pair distribution function and the distribution function of the angle formed by three nearest neighboring atoms at each period during crystallization, which are obtained by an MD simulation of a supercooled Lennard–Jones melt. The results indicate that crystallization occurs via the following activation processes: nucleation of a crystal with a distorted structure and reconstruction of the crystal to a more stable structure. The time evolution of the local structures during crystallization is also evaluated with this method. The present method can be applied to studies of the mechanism of crystallization from a disordered system for real materials, even for complicated multicomponent materials.
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25
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Grabowska J, Kuffel A, Zielkiewicz J. Interfacial water controls the process of adsorption of hyperactive antifreeze proteins onto the ice surface. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Munaò G, Saija F. Evidence of Structural Inhomogeneities in Hard-Soft Dimeric Particles without Attractive Interactions. MATERIALS 2019; 13:ma13010084. [PMID: 31877947 PMCID: PMC6981562 DOI: 10.3390/ma13010084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 11/16/2022]
Abstract
We perform Monte Carlo simulations of a simple hard-soft dimeric model constituted by two tangent spheres experiencing different interactions. Specifically, two hard spheres belonging to different dimers interact via a bare hard-core repulsion, whereas two soft spheres experience a softly repulsive Hertzian interaction. The cross correlations are soft as well. By exploring a wide range of temperatures and densities we investigate the capability of this model to document the existence of structural inhomogeneities indicating the possible onset of aggregates, even if no attraction is set. The fluid phase behavior is studied by analyzing structural and thermodynamical properties of the observed structures, in particular by computing radial distribution functions, structure factors and cluster size distributions. The numerical results are supported by integral equation theories of molecular liquids which allow for a finer and faster spanning of the temperature-density diagram. Our results may serve as a framework for a more systematic investigation of self-assembled structures of functionalized hard-soft dimers able to aggregate in a variety of structures widely oberved in colloidal dispersion.
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Affiliation(s)
- Gianmarco Munaò
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università degli Studi di Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
- Correspondence: (G.M.); (F.S.)
| | - Franz Saija
- CNR-IPCF, Viale F. Stagno d’Alcontres 37, 98158 Messina, Italy
- Correspondence: (G.M.); (F.S.)
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27
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Kubala P, Cieśla M, Ziff RM. Random sequential adsorption of particles with tetrahedral symmetry. Phys Rev E 2019; 100:052903. [PMID: 31870013 DOI: 10.1103/physreve.100.052903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Indexed: 06/10/2023]
Abstract
We study random sequential adsorption (RSA) of a class of solids that can be obtained from a cube by specific cutting of its vertices, in order to find out how the transition from tetrahedral to octahedral symmetry affects the densities of the resulting jammed packings. We find that in general solids of octahedral symmetry form less dense packing; however, the lowest density was obtained for the packing built of tetrahedra. The densest packing is formed by a solid close to a tetrahedron but with vertices and edges slightly cut. Its density is θ_{max}=0.41278±0.00059 and is higher than the mean packing fraction of spheres or cuboids but is lower than that for the densest RSA packings built of ellipsoids or spherocylinders. The density autocorrelation function of the studied packings is typical for random media and vanishes very quickly with distance.
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Affiliation(s)
- Piotr Kubala
- M. Smoluchowski Institute of Physics, Department of Statistical Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Michał Cieśla
- M. Smoluchowski Institute of Physics, Department of Statistical Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Robert M Ziff
- Center for the Study of Complex Systems and Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109-2136, USA
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28
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29
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Giovambattista N, Starr FW, Poole PH. State variables for glasses: The case of amorphous ice. J Chem Phys 2019; 150:224502. [DOI: 10.1063/1.5092586] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nicolas Giovambattista
- Department of Physics, Brooklyn College of the City University of New York, Brooklyn, New York 11210, USA
- Ph.D. Programs in Chemistry and Physics, The Graduate Center of the City University of New York, New York, New York 10016, USA
| | - Francis W. Starr
- Department of Physics, Wesleyan University, Middletown, Connecticut 06459, USA
| | - Peter H. Poole
- Department of Physics, St. Francis Xavier University, Antigonish, Nova Scotia B2G 2W5, Canada
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30
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Ghosh K, Krishnamurthy CV. Soft-wall induced structure and dynamics of partially confined supercritical fluids. J Chem Phys 2019; 150:111102. [PMID: 30901989 DOI: 10.1063/1.5092121] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The interplay between the structure and dynamics of partially confined Lennard Jones (LJ) fluids, deep into the supercritical phase, is studied over a wide range of densities in the context of the Frenkel line (FL), which separates rigid liquidlike and non-rigid gaslike regimes in the phase diagram of the supercritical fluids. Extensive molecular dynamics simulations carried out at the two ends of the FL (P = 5000 bars, T = 300 K, and T = 1500 K) reveal intriguing features in supercritical fluids as a function of stiffness of the partially confining atomistic walls. The liquidlike regime of a LJ fluid (P = 5000 bars, T = 300 K), mimicking argon, partially confined between walls separated by 10 Å along the z-axis, and otherwise unconstrained, reveals amorphous and liquidlike structural signatures in the radial distribution function parallel to the walls and enhanced self-diffusion as the wall stiffness is decreased. In sharp contrast, in the gas-like regime (P = 5000 bars, T = 1500 K), soft walls lead to increasing structural order hindering self-diffusion. Furthermore, the correlations between the structure and self-diffusion are found to be well captured by excess entropy. The rich behaviour shown by supercritical fluids under partial confinement, even with simple interatomic potentials, is found to be fairly independent of hydrophilicity and hydrophobicity. The study identifies persisting sub-diffusive features over intermediate time scales, emerging from the strong interplay between density and confinement, to dictate the evolution and stabilization of structures. It is anticipated that these results may help gain a better understanding of the behaviour of partially confined complex fluids found in nature.
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Affiliation(s)
- Kanka Ghosh
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
| | - C V Krishnamurthy
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
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31
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Abstract
During development of biological organisms, multiple complex structures are formed. In many instances, these structures need to exhibit a high degree of order to be functional, although many of their constituents are intrinsically stochastic. Hence, it has been suggested that biological robustness ultimately must rely on complex gene regulatory networks and clean-up mechanisms. Here we explore developmental processes that have evolved inherent robustness against stochasticity. In the context of the Drosophila eye disc, multiple optical units, ommatidia, develop into crystal-like patterns. During the larva-to-pupa stage of metamorphosis, the centers of the ommatidia are specified initially through the diffusion of morphogens, followed by the specification of R8 cells. Establishing the R8 cell is crucial in setting up the geometric, and functional, relationships of cells within an ommatidium and among neighboring ommatidia. Here we study an PDE mathematical model of these spatio-temporal processes in the presence of parametric stochasticity, defining and applying measures that quantify order within the resulting spatial patterns. We observe a universal sigmoidal response to increasing transcriptional noise. Ordered patterns persist up to a threshold noise level in the model parameters. In accordance with prior qualitative observations, as the noise is further increased past a threshold point of no return, these ordered patterns rapidly become disordered. Such robustness in development allows for the accumulation of genetic variation without any observable changes in phenotype. We argue that the observed sigmoidal dependence introduces robustness allowing for sizable amounts of genetic variation and transcriptional noise to be tolerated in natural populations without resulting in phenotype variation.
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32
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33
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Protonotarios ED, Griffin LD, Johnston A, Landy MS. A spatial frequency spectral peakedness model predicts discrimination performance of regularity in dot patterns. Vision Res 2018; 149:102-114. [PMID: 29958873 PMCID: PMC6089074 DOI: 10.1016/j.visres.2018.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 01/21/2023]
Abstract
Subjective assessments of spatial regularity are common in everyday life and also in science, for example in developmental biology. It has recently been shown that regularity is an adaptable visual dimension. It was proposed that regularity is coded via the peakedness of the distribution of neural responses across receptive field size. Here, we test this proposal for jittered square lattices of dots. We examine whether discriminability correlates with a simple peakedness measure across different presentation conditions (dot number, size, and average spacing). Using a filter-rectify-filter model, we determined responses across scale. Consistently, two peaks are present: a lower frequency peak corresponding to the dot spacing of the regular pattern and a higher frequency peak corresponding to the pattern element (dot). We define the "peakedness" of a particular presentation condition as the relative heights of these two peaks for a perfectly regular pattern constructed using the corresponding dot size, number and spacing. We conducted two psychophysical experiments in which observers judged relative regularity in a 2-alternative forced-choice task. In the first experiment we used a single reference pattern of intermediate regularity and, in the second, Thurstonian scaling of patterns covering the entire range of regularity. In both experiments discriminability was highly correlated with peakedness for a wide range of presentation conditions. This supports the hypothesis that regularity is coded via peakedness of the distribution of responses across scale.
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Affiliation(s)
- Emmanouil D Protonotarios
- Department of Psychology, New York University, New York, USA; CoMPLEX, University College London, London, UK.
| | - Lewis D Griffin
- Department of Computer Science, University College London, London, UK; CoMPLEX, University College London, London, UK
| | - Alan Johnston
- School of Psychology, University of Nottingham, Nottingham, UK; Experimental Psychology, Psychology and Language Sciences, University College London, London, UK; CoMPLEX, University College London, London, UK
| | - Michael S Landy
- Department of Psychology, New York University, New York, USA; Center for Neural Science, New York University, New York, USA
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34
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Torquato S. Perspective: Basic understanding of condensed phases of matter via packing models. J Chem Phys 2018; 149:020901. [DOI: 10.1063/1.5036657] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- S. Torquato
- Department of Chemistry, Department of Physics, Princeton Center for Theoretical Science, Princeton Institute for the Science and Technology of Materials, and Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, USA
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35
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Elola MD, Rodriguez J. Influence of Cholesterol on the Dynamics of Hydration in Phospholipid Bilayers. J Phys Chem B 2018; 122:5897-5907. [PMID: 29742895 DOI: 10.1021/acs.jpcb.8b00360] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate the dynamics of interfacial waters in dipalmitoylphosphatidylcholine (DPPC) bilayers upon the addition of cholesterol, by molecular dynamics simulations. Our data reveal that the inclusion of cholesterol modifies the membrane aqueous interfacial dynamics: waters diffuse faster, their rotational decay time is shorter, and the DPPC/water hydrogen bond dynamics relaxes faster than in the pure DPPC membrane. The observed acceleration of the translational water dynamics agrees with recent experimental results, in which, by means of NMR techniques, an increment of the surface water diffusivity is measured upon the addition of cholesterol. A microscopic analysis of the lipid/water hydrogen bond network at the interfacial region suggests that the mechanism underlying the observed water mobility enhancement is given by the rupture of a fraction of interlipid water bridge hydrogen bonds connecting two different DPPC molecules, concomitant to the formation of new lipid/solvent bonds, whose dynamics is faster than that of the former. The consideration of a simple two-state model for the decay of the hydrogen bond correlation function yielded excellent results, obtaining two well-separated characteristic time scales: a slow one (∼250 ps) associated with bonds linking two DPPC molecules, and a fast one (∼15 ps), related to DPPC/solvent bonds.
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Affiliation(s)
- M Dolores Elola
- Departamento de Física , Comisión Nacional de Energía Atómica , Av Libertador 8250, 1429 Buenos Aires , Argentina
| | - Javier Rodriguez
- Departamento de Física , Comisión Nacional de Energía Atómica , Av Libertador 8250, 1429 Buenos Aires , Argentina.,ECyT , UNSAM , Martín de Irigoyen 3100, 1650 San Martín, Provincia de Buenos Aires , Argentina
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36
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Ghosh K, Krishnamurthy CV. Structural behavior of supercritical fluids under confinement. Phys Rev E 2018; 97:012131. [PMID: 29448330 DOI: 10.1103/physreve.97.012131] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Indexed: 11/07/2022]
Abstract
The existence of the Frenkel line in the supercritical regime of a Lennard-Jones (LJ) fluid shown through molecular dynamics (MD) simulations initially and later corroborated by experiments on argon opens up possibilities of understanding the structure and dynamics of supercritical fluids in general and of the Frenkel line in particular. The location of the Frenkel line, which demarcates two distinct physical states, liquidlike and gaslike within the supercritical regime, has been established through MD simulations of the velocity autocorrelation (VACF) and radial distribution function (RDF). We, in this article, explore the changes in the structural features of supercritical LJ fluid under partial confinement using atomistic walls. The study is carried out across the Frenkel line through a series of MD simulations considering a set of thermodynamics states in the supercritical regime (P=5000 bar, 240K≤T≤1500K) of argon well above the critical point. Confinement is partial, with atomistic walls located normal to z and extending to "infinity" along the x and y directions. In the "liquidlike" regime of the supercritical phase, particles are found to be distributed in distinct layers along the z axis with layer spacing less than one atomic diameter and the lateral RDF showing amorphous-like structure for specific spacings (packing frustration) and non-amorphous-like structure for other spacings. Increasing the rigidity of the atomistic walls is found to lead to stronger layering and increased structural order. For confinement with reflective walls, layers are found to form with one atomic diameter spacing and the lateral RDF showing close-packed structure for the smaller confinements. Translational order parameter and excess entropy assessment confirms the ordering taking place for atomistic wall and reflective wall confinements. In the "gaslike" regime of the supercritical phase, particle distribution along the spacing and the lateral RDF exhibit features not significantly different from that due to normal gas regime. The heterogeneity across the Frenkel line, found to be present both in bulk and confined systems, might cause the breakdown of the universal scaling between structure and dynamics of fluids necessitating the determination of a unique relationship between them.
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Affiliation(s)
- Kanka Ghosh
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
| | - C V Krishnamurthy
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
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DiStasio RA, Zhang G, Stillinger FH, Torquato S. Rational design of stealthy hyperuniform two-phase media with tunable order. Phys Rev E 2018; 97:023311. [PMID: 29548140 DOI: 10.1103/physreve.97.023311] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Indexed: 06/08/2023]
Abstract
Disordered stealthy hyperuniform materials are exotic amorphous states of matter that have attracted recent attention because of their novel structural characteristics (hidden order at large length scales) and physical properties, including desirable photonic and transport properties. It is therefore useful to devise algorithms that enable one to design a wide class of such amorphous configurations at will. In this paper, we present several algorithms enabling the systematic identification and generation of discrete (digitized) stealthy hyperuniform patterns with a tunable degree of order, paving the way towards the rational design of disordered materials endowed with novel thermodynamic and physical properties. To quantify the degree of order or disorder of the stealthy systems, we utilize the discrete version of the τ order metric, which accounts for the underlying spatial correlations that exist across all relevant length scales in a given digitized two-phase (or, equivalently, a two-spin state) system of interest. Our results impinge on a myriad of fields, ranging from physics, materials science and engineering, visual perception, and information theory to modern data science.
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Affiliation(s)
- Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Ge Zhang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Frank H Stillinger
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Salvatore Torquato
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
- Department of Physics, Princeton Institute for the Science and Technology of Materials, and Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, USA
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38
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Lomba E, Weis JJ, Torquato S. Disordered hyperuniformity in two-component nonadditive hard-disk plasmas. Phys Rev E 2017; 96:062126. [PMID: 29347400 DOI: 10.1103/physreve.96.062126] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Indexed: 06/07/2023]
Abstract
We study the behavior of a classical two-component ionic plasma made up of nonadditive hard disks with additional logarithmic Coulomb interactions between them. Due to the Coulomb repulsion, long-wavelength total density fluctuations are suppressed and the system is globally hyperuniform. Short-range volume effects lead to phase separation or to heterocoordination for positive or negative nonadditivities, respectively. These effects compete with the hidden long-range order imposed by hyperuniformity. As a result, the critical behavior of the mixture is modified, with long-wavelength concentration fluctuations partially damped when the system is charged. It is also shown that the decrease of configurational entropy due to hyperuniformity originates from contributions beyond the two-particle level. Finally, despite global hyperuniformity, we show that in our system the spatial configuration associated with each component separately is not hyperuniform, i.e., the system is not "multihyperuniform."
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Affiliation(s)
- Enrique Lomba
- Instituto de Química Física Rocasolano, CSIC, Calle Serrano 119, E-28006 Madrid, Spain
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Jean-Jacques Weis
- Université de Paris-Sud, Laboratoire de Physique Théorique, UMR8627, Bâtiment 210, 91405 Orsay Cedex, France
| | - Salvatore Torquato
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
- Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, New Jersey 08544, USA
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39
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Gaines JC, Clark AH, Regan L, O'Hern CS. Packing in protein cores. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:293001. [PMID: 28557791 DOI: 10.1088/1361-648x/aa75c2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and predicting protein structure and stability. It is well-established that a large contribution to protein stability originates from the sequestration from solvent of hydrophobic residues in the protein core. How are such hydrophobic residues arranged in the core; how can one best model the packing of these residues, and are residues loosely packed with multiple allowed side chain conformations or densely packed with a single allowed side chain conformation? Here we show that to properly model the packing of residues in protein cores it is essential that amino acids are represented by appropriately calibrated atom sizes, and that hydrogen atoms are explicitly included. We show that protein cores possess a packing fraction of [Formula: see text], which is significantly less than the typically quoted value of 0.74 obtained using the extended atom representation. We also compare the results for the packing of amino acids in protein cores to results obtained for jammed packings from discrete element simulations of spheres, elongated particles, and composite particles with bumpy surfaces. We show that amino acids in protein cores pack as densely as disordered jammed packings of particles with similar values for the aspect ratio and bumpiness as found for amino acids. Knowing the structural properties of protein cores is of both fundamental and practical importance. Practically, it enables the assessment of changes in the structure and stability of proteins arising from amino acid mutations (such as those identified as a result of the massive human genome sequencing efforts) and the design of new folded, stable proteins and protein-protein interactions with tunable specificity and affinity.
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Affiliation(s)
- J C Gaines
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, United States of America. Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, CT 06520, United States of America
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40
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Piaggi PM, Valsson O, Parrinello M. Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations. PHYSICAL REVIEW LETTERS 2017; 119:015701. [PMID: 28731736 DOI: 10.1103/physrevlett.119.015701] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Indexed: 06/07/2023]
Abstract
Crystallization is a process of great practical relevance in which rare but crucial fluctuations lead to the formation of a solid phase starting from the liquid. As in all first order first transitions, there is an interplay between enthalpy and entropy. Based on this idea, in order to drive crystallization in molecular simulations, we introduce two collective variables, one enthalpic and the other entropic. Defined in this way, these collective variables do not prejudge the structure into which the system is going to crystallize. We show the usefulness of this approach by studying the cases of sodium and aluminum that crystallize in the bcc and fcc crystalline structures, respectively. Using these two generic collective variables, we perform variationally enhanced sampling and well tempered metadynamics simulations and find that the systems transform spontaneously and reversibly between the liquid and the solid phases.
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Affiliation(s)
- Pablo M Piaggi
- Theory and Simulation of Materials (THEOS), École Polytechnique Fédérale de Lausanne, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
- Facoltà di Informatica, Istituto di Scienze Computazionali, and National Center for Computational Design and Discovery of Novel Materials MARVEL, Università della Svizzera italiana (USI), Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Omar Valsson
- Facoltà di Informatica, Istituto di Scienze Computazionali, and National Center for Computational Design and Discovery of Novel Materials MARVEL, Università della Svizzera italiana (USI), Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
- Department of Chemistry and Applied Biosciences, ETH Zurich, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Michele Parrinello
- Facoltà di Informatica, Istituto di Scienze Computazionali, and National Center for Computational Design and Discovery of Novel Materials MARVEL, Università della Svizzera italiana (USI), Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
- Department of Chemistry and Applied Biosciences, ETH Zurich, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
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41
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Ricci F, Debenedetti PG. A free energy study of the liquid-liquid phase transition of the Jagla two-scale potential. J CHEM SCI 2017. [DOI: 10.1007/s12039-017-1315-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Xu L, Wang G, Jiang L, Chen J, Huang G, Zhang Z. Distinguishing Liquid from Solid by Atom Transport Coefficient Distribution: Predicting Melting Point of Ionic Liquids as an Example. ChemistrySelect 2017. [DOI: 10.1002/slct.201700309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Liancai Xu
- Department of Material and Chemical engineering; Zhengzhou University of Light Industry, Zhengzhou; Henan 450002 China PRC
| | - Guoqing Wang
- Department of Material and Chemical engineering; Zhengzhou University of Light Industry, Zhengzhou; Henan 450002 China PRC
| | - Ling Jiang
- Department of Material and Chemical engineering; Zhengzhou University of Light Industry, Zhengzhou; Henan 450002 China PRC
| | - Junli Chen
- Department of Material and Chemical engineering; Zhengzhou University of Light Industry, Zhengzhou; Henan 450002 China PRC
| | - Gailing Huang
- Department of Material and Chemical engineering; Zhengzhou University of Light Industry, Zhengzhou; Henan 450002 China PRC
| | - Zhiqiang Zhang
- Department of Material and Chemical engineering; Zhengzhou University of Light Industry, Zhengzhou; Henan 450002 China PRC
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Munaò G, Saija F. Integral equation study of soft-repulsive dimeric fluids. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:115101. [PMID: 28155850 DOI: 10.1088/1361-648x/aa5306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We study fluid structure and water-like anomalies of a system constituted by dimeric particles interacting via a purely repulsive core-softened potential by means of integral equation theories. In our model, dimers interact through a repulsive pair potential of inverse-power form with a softened repulsion strength. By employing the Ornstein-Zernike approach and the reference interaction site model (RISM) theory, we study the behavior of water-like anomalies upon progressively increasing the elongation λ of the dimers from the monomeric case ([Formula: see text]) to the tangent configuration ([Formula: see text]). For each value of the elongation we consider two different values of the interaction potential, corresponding to one and two length scales, with the aim to provide a comprehensive description of the possible fluid scenarios of this model. Our theoretical results are systematically compared with already existing or newly generated Monte Carlo data: we find that theories and simulations agree in providing the picture of a fluid exhibiting density and structural anomalies for low values of λ and for both the two values of the interaction potential. Integral equation theories give accurate predictions for pressure and radial distribution functions, whereas the temperatures where anomalies occur are underestimated. Upon increasing the elongation, the RISM theory still predicts the existence of anomalies; the latter are no longer observed in simulations, since their development is likely precluded by the onset of crystallization. We discuss our results in terms of the reliability of integral equation theories in predicting the existence of water-like anomalies in core-softened fluids.
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Affiliation(s)
- Gianmarco Munaò
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università degli Studi di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
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Grabowska J, Kuffel A, Zielkiewicz J. Structure of solvation water around the active and inactive regions of a type III antifreeze protein and its mutants of lowered activity. J Chem Phys 2017; 145:075101. [PMID: 27544127 DOI: 10.1063/1.4961094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Water molecules from the solvation shell of the ice-binding surface are considered important for the antifreeze proteins to perform their function properly. Herein, we discuss the problem whether the extent of changes of the mean properties of solvation water can be connected with the antifreeze activity of the protein. To this aim, the structure of solvation water of a type III antifreeze protein from Macrozoarces americanus (eel pout) is investigated. A wild type of the protein is used, along with its three mutants, with antifreeze activities equal to 54% or 10% of the activity of the native form. The solvation water of the ice-binding surface and the rest of the protein are analyzed separately. To characterize the structure of solvation shell, parameters describing radial and angular characteristics of the mutual arrangement of the molecules were employed. They take into account short-distance (first hydration shell) or long-distance (two solvation shells) effects. The obtained results and the comparison with the results obtained previously for a hyperactive antifreeze protein from Choristoneura fumiferana lead to the conclusion that the structure and amino acid composition of the active region of the protein evolved to achieve two goals. The first one is the modification of the properties of the solvation water. The second one is the geometrical adjustment of the protein surface to the specific crystallographic plane of ice. Both of these goals have to be achieved simultaneously in order for the protein to perform its function properly. However, they seem to be independent from one another in a sense that very small antifreeze activity does not imply that properties of water become different from the ones observed for the wild type. The proteins with significantly lower activity still modify the mean properties of solvation water in a right direction, in spite of the fact that the accuracy of the geometrical match with the ice lattice is lost because of the mutations. Therefore, we do not observe any correlation between the antifreeze activity and the extent of modification of the properties of solvation water.
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Affiliation(s)
- Joanna Grabowska
- Faculty of Chemistry, Department of Physical Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Anna Kuffel
- Faculty of Chemistry, Department of Physical Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Jan Zielkiewicz
- Faculty of Chemistry, Department of Physical Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
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Relationship between structural order and water-like anomalies in metastable liquid silicon: Ab initio molecular dynamics. Sci Rep 2017; 7:39952. [PMID: 28054595 PMCID: PMC5215308 DOI: 10.1038/srep39952] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/30/2016] [Indexed: 11/28/2022] Open
Abstract
The relationship between structural order and water-like anomalies in tetrahedral liquids is still open. Here, first-principle molecular dynamics are performed to study it in metastable liquid Si. It is found that in T-P phase diagram, there indeed exists a structural anomaly region, which encloses density anomaly but not diffusivity anomaly. This is consistent with that of SW Si and BKS SiO2 but different from that of SPC/E water. Two-body excess entropy anomaly can neither capture the diffusivity, structural, and density anomalies, as it can in a two-scale potential fluid. In structural anomaly region, tetrahedrality order qtetra (measuring the extent to which an atom and its four nearest neighbours adopt tetrahedral arrangement) and translational order ttrans (measuring the tendency of two atoms to adopt preferential separation) are not perfectly correlated, which is different from that in SW Si and renders it impossible to use the isotaxis line to quantify the degree of structural order needed for water-like anomalies to occur. Along the isotherm of critical temperature Tc, ttrans/qtetra is approximately linear with pressure. With decreasing pressure along the isotherm below Tc, ttrans/qtetra departs downward from the line, while it is the opposite case above Tc.
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46
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Erramreddy VV, Tu S, Ghosh S. Rheological reversibility and long-term stability of repulsive and attractive nanoemulsion gels. RSC Adv 2017. [DOI: 10.1039/c7ra09605d] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The storage modulus (G′) of a canola oil nanoemulsion gel depends on the storage time and SDS emulsifier concentration.
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Affiliation(s)
| | - Sylvana Tu
- Department of Food and Bioproduct Sciences
- University of Saskatchewan
- Saskatoon
- Canada
| | - Supratim Ghosh
- Department of Food and Bioproduct Sciences
- University of Saskatchewan
- Saskatoon
- Canada
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47
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Gnan N, Sciortino F, Zaccarelli E. Discontinous change from thermally- to geometrically-dominated effective interactions in colloidal solutions. SOFT MATTER 2016; 12:9649-9656. [PMID: 27869285 PMCID: PMC5640983 DOI: 10.1039/c6sm01872f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report numerical results for the effective potential arising between two colloids immersed in a self-assembling cosolute which forms reversible clusters. The potential is evaluated at cosolute state points with different densities and temperatures but with the same connectivity properties. We find that the range of the resulting effective potential is controlled only by the cosolute thermal correlation length rather than by its connectivity length. We discuss the significant differences from previous results focusing on the cosolute forming irreversible clusters and we show that the irreversible bond case represents a singular limit which cannot be accessed in equilibrium by continuously increasing the bond lifetime.
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Affiliation(s)
- Nicoletta Gnan
- CNR-ISC UOS Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy and Dipartimento di Fisica, "Sapienza" Universita' di Roma, Piazzale A. Moro 2, 00185 Roma, Italy.
| | - Francesco Sciortino
- CNR-ISC UOS Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy and Dipartimento di Fisica, "Sapienza" Universita' di Roma, Piazzale A. Moro 2, 00185 Roma, Italy.
| | - Emanuela Zaccarelli
- CNR-ISC UOS Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy and Dipartimento di Fisica, "Sapienza" Universita' di Roma, Piazzale A. Moro 2, 00185 Roma, Italy.
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48
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Jadrich RB, Lindquist BA, Bollinger JA, Truskett TM. Consequences of minimising pair correlations in fluids for dynamics, thermodynamics and structure. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1159742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- R. B. Jadrich
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - B. A. Lindquist
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - J. A. Bollinger
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - T. M. Truskett
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
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49
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Atkinson S, Stillinger FH, Torquato S. Static structural signatures of nearly jammed disordered and ordered hard-sphere packings: Direct correlation function. Phys Rev E 2016; 94:032902. [PMID: 27739707 DOI: 10.1103/physreve.94.032902] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Indexed: 06/06/2023]
Abstract
The nonequilibrium process by which hard-particle systems may be compressed into disordered, jammed states has received much attention because of its wide utility in describing a broad class of amorphous materials. While dynamical signatures are known to precede jamming, the task of identifying static structural signatures indicating the onset of jamming have proven more elusive. The observation that compressing hard-particle packings towards jamming is accompanied by an anomalous suppression of density fluctuations (termed "hyperuniformity") has paved the way for the analysis of jamming as an "inverted critical point" in which the direct correlation function c(r), rather than the total correlation function h(r), diverges. We expand on the notion that c(r) provides both universal and protocol-specific information as packings approach jamming. By considering the degree and position of singularities (discontinuities in the nth derivative) as well as how they are changed by the convolutions found in the Ornstein-Zernike equation, we establish quantitative statements about the structure of c(r) with regards to singularities it inherits from h(r). These relations provide a concrete means of identifying features that must be expressed in c(r) if one hopes to reproduce various details in the pair correlation function accurately and provide stringent tests on the associated numerics. We also analyze the evolution of systems of three-dimensional monodisperse hard spheres of diameter D as they approach ordered and disordered jammed configurations. For the latter, we use the Lubachevsky-Stillinger (LS) molecular dynamics and Torquato-Jiao (TJ) sequential linear programming algorithms, which both generate disordered packings, but can show perceptible structural differences. We identify a short-ranged scaling c(r)∝-1/r as r→0 that accompanies the formation of the delta function at c(D) that indicates the formation of contacts in all cases, and show that this scaling behavior is, in this case, a consequence of the growing long rangedness in c(r), e.g., c∝-1/r^{2} as r→∞ for disordered packings. At densities in the vicinity of the freezing density, we find striking qualitative differences in the structure factor S(k) as well as c(r) between TJ- and LS-generated configurations, including the early formation of a delta function at c(D) in the TJ algorithm's packings, indicating the early formation of clusters of particles in near contact. Both algorithms yield structure factors that tend towards zero in the low-wave-number limit as jamming is approached. Correspondingly, we observe the expected power-law decay in c(r) for large r, in agreement with previous theoretical work. Our work advances the notion that static signatures are exhibited by hard-particle packings as they approach jamming and underscores the utility of the direct correlation function as a sensitive means of monitoring for the appearance of an incipient rigid network.
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Affiliation(s)
- Steven Atkinson
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Frank H Stillinger
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Salvatore Torquato
- Department of Chemistry, Department of Physics, Princeton Center for Theoretical Science, Program of Applied and Computational Mathematics, Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, New Jersey 08544, USA
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50
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Ryltsev RE, Klumov BA, Chtchelkatchev NM, Shunyaev KY. Cooling rate dependence of simulated Cu64.5Zr35.5 metallic glass structure. J Chem Phys 2016; 145:034506. [DOI: 10.1063/1.4958631] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- R. E. Ryltsev
- Institute of Metallurgy, Ural Branch of Russian Academy of Sciences, 101 Amundsen Str., 620016 Ekaterinburg, Russia
- Ural Federal University, 19 Mira Str., 620002 Ekaterinburg, Russia
- L.D. Landau Institute for Theoretical Physics, Russian Academy of Sciences, 2 Kosygina Str., 119334 Moscow, Russia
| | - B. A. Klumov
- L.D. Landau Institute for Theoretical Physics, Russian Academy of Sciences, 2 Kosygina Str., 119334 Moscow, Russia
- Aix-Marseille-Université, CNRS, Laboratoire PIIM, UMR 7345, 13397 Marseille Cedex 20, France
- High Temperature Institute, Russian Academy of Sciences, 13/2 Izhorskaya Str., 125412 Moscow, Russia
| | - N. M. Chtchelkatchev
- Institute of Metallurgy, Ural Branch of Russian Academy of Sciences, 101 Amundsen Str., 620016 Ekaterinburg, Russia
- L.D. Landau Institute for Theoretical Physics, Russian Academy of Sciences, 2 Kosygina Str., 119334 Moscow, Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy Per., Dolgoprudny, 141700 Moscow Region, Russia
- All-Russia Research Institute of Automatics, 22 Sushchevskaya, 127055 Moscow, Russia
| | - K. Yu. Shunyaev
- Institute of Metallurgy, Ural Branch of Russian Academy of Sciences, 101 Amundsen Str., 620016 Ekaterinburg, Russia
- Ural Federal University, 19 Mira Str., 620002 Ekaterinburg, Russia
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