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King EA, Sen S, Takeda W, Boussard-Pledel C, Bureau B, Guin JP, Lucas P. Extended aging of Ge-Se glasses below the glass transition temperature. J Chem Phys 2021; 154:164502. [PMID: 33940843 DOI: 10.1063/5.0050474] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Germanium selenide glasses of compositions spanning the whole glass-formation range are aged at room temperature for up to 20 years. A prominent enthalpy relaxation process is observed in all glasses, and its structural origin is analyzed by Raman spectroscopy. The structural relaxation is manifested in the Raman spectra as a decrease in the ratio of edge- to corner-sharing GeSe4/2 tetrahedral units. This structural evolution can be explained in terms of configurational entropy and density changes. Changes in Raman features and enthalpy follow an identical stretched exponential relaxation function characteristic of aging in glasses. The compositional dependence of enthalpy relaxation after 20 years is in agreement with kinetic considerations based on the glass transition temperature of each glass. The relaxation behavior and heat capacity curves are consistent with standard glass relaxation models for all compositions. These results indicate that the non-reversing enthalpy obtained by modulated differential scanning calorimetry (MDSC), which suggests the existence of non-aging glasses, is not a reliable measure of the ability of a glass to relax. Instead, it is suggested that an interpretation of MDSC data in terms of complex heat capacity provides a more complete and reliable assessment of the relaxation properties of glasses.
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Affiliation(s)
- Ellyn A King
- Department of Materials Science and Engineering, University of Arizona, Tucson, Arizona 85721, USA
| | - Sabyasachi Sen
- Department of Materials Science and Engineering, University of California, Davis, California 95616, USA
| | - Wataru Takeda
- Department of Materials Science and Engineering, University of Arizona, Tucson, Arizona 85721, USA
| | - Catherine Boussard-Pledel
- Univ. Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes) - UMR 6226, F-35000 Rennes, France
| | - Bruno Bureau
- Univ. Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes) - UMR 6226, F-35000 Rennes, France
| | - Jean-Pierre Guin
- Univ. Rennes, CNRS, IPR (Institut de Physique de Rennes) - UMR 6251, Rennes, France
| | - Pierre Lucas
- Department of Materials Science and Engineering, University of Arizona, Tucson, Arizona 85721, USA
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2
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Orientationally ordered glasses via controlled deposition. Proc Natl Acad Sci U S A 2019; 116:21341-21342. [PMID: 31578254 DOI: 10.1073/pnas.1915691116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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3
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Marple MAT, Yong V, Sen S. Fragility and aging behavior of Si xSe 1-x glasses and liquids. J Chem Phys 2019; 150:044506. [PMID: 30709249 DOI: 10.1063/1.5080225] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The composition dependence of the fragility of SixSe1-x liquids with 0.05 ≤ x ≤ 0.33 is determined using the calorimetric method and is found to be rather similar to that characteristic of their Ge analogues. In addition, the nature and the time scale of the structural relaxation of the Si25Se75 glass during aging at 40 K below Tg are measured using Raman spectroscopy. The structural relaxation in this glass, which belongs to the so-called intermediate phase, involves progressive conversion of the doubly edge-shared SiSe4/2 tetrahedra E2 into singly edge-shared E1 and corner-shared E0 tetrahedra upon lowering of temperature. This tetrahedral speciation can be expressed in the form of the reaction 2 E2 → E0 + E1. The time scale of this tetrahedral conversion reaction corresponds well with that of shear relaxation. This result is inconsistent with the claim made previously in the literature that intermediate phase compositions do not undergo aging. Moreover, when taken together, the fragility and the structural relaxation results suggest that the constraint counting scheme typically adopted in the literature for edge- vs. corner-shared tetrahedra in chalcogenide networks may need to be revised. A rigid-polytope based constraint counting approach is shown to be more consistent with the experimental results.
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Affiliation(s)
- Maxwell A T Marple
- Department of Materials Science and Engineering, University of California at Davis, Davis, California 95616, USA
| | - Vuthtyra Yong
- Department of Materials Science and Engineering, University of California at Davis, Davis, California 95616, USA
| | - Sabyasachi Sen
- Department of Materials Science and Engineering, University of California at Davis, Davis, California 95616, USA
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4
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Flores-Ruiz H, Micoulaut M. From elemental tellurium to Ge 2Sb 2Te 5 melts: High temperature dynamic and relaxation properties in relationship with the possible fragile to strong transition. J Chem Phys 2018; 148:034502. [PMID: 29352786 DOI: 10.1063/1.5013668] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate the dynamic properties of Ge-Sb-Te phase change melts using first principles molecular dynamics with a special emphasis on the effect of tellurium composition on melt dynamics. From structural models and trajectories established previously [H. Flores-Ruiz et al., Phys. Rev. B 92, 134205 (2015)], we calculate the diffusion coefficients for the different species, the activation energies for diffusion, the Van Hove correlation, and the intermediate scattering functions able to substantiate the dynamics and relaxation behavior of the liquids as a function of temperature and composition that is also compared to experiment whenever possible. We find that the diffusion is mostly Arrhenius-like and that the addition of Ge/Sb atoms leads to a global decrease of the jump probability and to an increase in activated dynamics for diffusion. Relaxation behavior is analyzed and used in order to evaluate the possibility of a fragile to strong transition that is evidenced from the calculated high fragility (M = 129) of Ge2Sb2Te5 at high temperatures.
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Affiliation(s)
- H Flores-Ruiz
- Laboratoire de Physique Théorique de la Matière Condensée, Paris Sorbonne Universités - UPMC, Boite 121, 4, Place Jussieu, 75252 Paris Cedex 05, France
| | - M Micoulaut
- Laboratoire de Physique Théorique de la Matière Condensée, Paris Sorbonne Universités - UPMC, Boite 121, 4, Place Jussieu, 75252 Paris Cedex 05, France
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5
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Bauchy M, Wang M, Yu Y, Wang B, Krishnan NMA, Masoero E, Ulm FJ, Pellenq R. Topological Control on the Structural Relaxation of Atomic Networks under Stress. PHYSICAL REVIEW LETTERS 2017; 119:035502. [PMID: 28777608 DOI: 10.1103/physrevlett.119.035502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Indexed: 06/07/2023]
Abstract
Upon loading, atomic networks can feature delayed irreversible relaxation. However, the effect of composition and structure on relaxation remains poorly understood. Herein, relying on accelerated molecular dynamics simulations and topological constraint theory, we investigate the relationship between atomic topology and stress-induced structural relaxation, by taking the example of creep deformations in calcium silicate hydrates (C─S─H), the binding phase of concrete. Under constant shear stress, C─S─H is found to feature delayed logarithmic shear deformations. We demonstrate that the propensity for relaxation is minimum for isostatic atomic networks, which are characterized by the simultaneous absence of floppy internal modes of relaxation and eigenstress. This suggests that topological nanoengineering could lead to the discovery of nonaging materials.
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Affiliation(s)
- Mathieu Bauchy
- Physics of AmoRphous and Inorganic Solids Laboratory (PARISlab), Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095, USA
| | - Mengyi Wang
- Physics of AmoRphous and Inorganic Solids Laboratory (PARISlab), Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095, USA
| | - Yingtian Yu
- Physics of AmoRphous and Inorganic Solids Laboratory (PARISlab), Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095, USA
| | - Bu Wang
- Physics of AmoRphous and Inorganic Solids Laboratory (PARISlab), Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095, USA
| | - N M Anoop Krishnan
- Physics of AmoRphous and Inorganic Solids Laboratory (PARISlab), Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095, USA
| | - Enrico Masoero
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Franz-Joseph Ulm
- Concrete Sustainability Hub, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- MIT-CNRS joint laboratory at Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Roland Pellenq
- Concrete Sustainability Hub, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- MIT-CNRS joint laboratory at Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Centre Interdisciplinaire des Nanosciences de Marseille, CNRS and Aix-Marseille University, Campus de Luminy, Marseille, 13288 Cedex 09, France
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6
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Pignatelli I, Kumar A, Alizadeh R, Le Pape Y, Bauchy M, Sant G. A dissolution-precipitation mechanism is at the origin of concrete creep in moist environments. J Chem Phys 2016; 145:054701. [DOI: 10.1063/1.4955429] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Isabella Pignatelli
- Laboratory for the Chemistry of Construction Materials (LC2), Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095, USA
| | - Aditya Kumar
- Materials Science and Engineering Department, Missouri University of Science and Technology, Rolla, Missouri 65409, USA
| | | | - Yann Le Pape
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Mathieu Bauchy
- Physics of AmoRphous and Inorganic Solids Laboratory (PARISlab), Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095, USA
| | - Gaurav Sant
- Laboratory for the Chemistry of Construction Materials (LC2), Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095, USA
- California Nanosystems Institute (CNSI), University of California, Los Angeles, California 90095, USA
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7
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Micoulaut M. Relaxation and physical aging in network glasses: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2016; 79:066504. [PMID: 27213928 DOI: 10.1088/0034-4885/79/6/066504] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Recent progress in the description of glassy relaxation and aging are reviewed for the wide class of network-forming materials such as GeO2, Ge x Se1-x , silicates (SiO2-Na2O) or borates (B2O3-Li2O), all of which have an important usefulness in domestic, geological or optoelectronic applications. A brief introduction of the glass transition phenomenology is given, together with the salient features that are revealed both from theory and experiments. Standard experimental methods used for the characterization of the slowing down of the dynamics are reviewed. We then discuss the important role played by aspects of network topology and rigidity for the understanding of the relaxation of the glass transition, while also permitting analytical predictions of glass properties from simple and insightful models based on the network structure. We also emphasize the great utility of computer simulations which probe the dynamics at the molecular level, and permit the calculation of various structure-related functions in connection with glassy relaxation and the physics of aging which reveal the non-equilibrium nature of glasses. We discuss the notion of spatial variations of structure which leads to the concept of 'dynamic heterogeneities', and recent results in relation to this important topic for network glasses are also reviewed.
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Affiliation(s)
- Matthieu Micoulaut
- Paris Sorbonne Universités, LPTMC-UPMC, 4 place Jussieu, 75252 Paris cedex 05, France
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Yu Y, Wang M, Zhang D, Wang B, Sant G, Bauchy M. Stretched Exponential Relaxation of Glasses at Low Temperature. PHYSICAL REVIEW LETTERS 2015; 115:165901. [PMID: 26550886 DOI: 10.1103/physrevlett.115.165901] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Indexed: 06/05/2023]
Abstract
The question of whether glass continues to relax at low temperature is of fundamental and practical interest. Here, we report a novel atomistic simulation method allowing us to directly access the long-term dynamics of glass relaxation at room temperature. We find that the potential energy relaxation follows a stretched exponential decay, with a stretching exponent β=3/5, as predicted by Phillips's diffusion-trap model. Interestingly, volume relaxation is also found. However, it is not correlated to the energy relaxation, but it is rather a manifestation of the mixed alkali effect.
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Affiliation(s)
- Yingtian Yu
- Physics of AmoRphous and Inorganic Solids Laboratory (PARISlab), Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095, USA
| | - Mengyi Wang
- Physics of AmoRphous and Inorganic Solids Laboratory (PARISlab), Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095, USA
| | - Dawei Zhang
- Physics of AmoRphous and Inorganic Solids Laboratory (PARISlab), Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095, USA
| | - Bu Wang
- Physics of AmoRphous and Inorganic Solids Laboratory (PARISlab), Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095, USA
| | - Gaurav Sant
- Laboratory for the Chemistry of Construction Materials (LC2), Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095, USA
- California Nanosystems Institute (CNSI), University of California, Los Angeles, California 90095, USA
| | - Mathieu Bauchy
- Physics of AmoRphous and Inorganic Solids Laboratory (PARISlab), Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095, USA
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9
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Bauchy M, Qomi MJA, Bichara C, Ulm FJ, Pellenq RJM. Rigidity transition in materials: hardness is driven by weak atomic constraints. PHYSICAL REVIEW LETTERS 2015; 114:125502. [PMID: 25860757 DOI: 10.1103/physrevlett.114.125502] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Indexed: 06/04/2023]
Abstract
Understanding the composition dependence of the hardness in materials is of primary importance for infrastructures and handled devices. Stimulated by the need for stronger protective screens, topological constraint theory has recently been used to predict the hardness in glasses. Herein, we report that the concept of rigidity transition can be extended to a broader range of materials than just glass. We show that hardness depends linearly on the number of angular constraints, which, compared to radial interactions, constitute the weaker ones acting between the atoms. This leads to a predictive model for hardness, generally applicable to any crystalline or glassy material.
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Affiliation(s)
- Mathieu Bauchy
- Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095, USA
| | - Mohammad Javad Abdolhosseini Qomi
- Concrete Sustainability Hub, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Christophe Bichara
- Centre Interdisciplinaire des Nanosciences de Marseille, CNRS and Aix-Marseille University, Campus de Luminy, Marseille, 13288 Cedex 09, France
| | - Franz-Josef Ulm
- Concrete Sustainability Hub, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- MIT-CNRS joint laboratory at Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Roland J-M Pellenq
- Concrete Sustainability Hub, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Centre Interdisciplinaire des Nanosciences de Marseille, CNRS and Aix-Marseille University, Campus de Luminy, Marseille, 13288 Cedex 09, France
- MIT-CNRS joint laboratory at Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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10
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Densified network glasses and liquids with thermodynamically reversible and structurally adaptive behaviour. Nat Commun 2015; 6:6398. [DOI: 10.1038/ncomms7398] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 01/25/2015] [Indexed: 11/08/2022] Open
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11
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Yan L, Wyart M. Evolution of covalent networks under cooling: contrasting the rigidity window and jamming scenarios. PHYSICAL REVIEW LETTERS 2014; 113:215504. [PMID: 25479505 DOI: 10.1103/physrevlett.113.215504] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Indexed: 06/04/2023]
Abstract
We study the evolution of structural disorder under cooling in supercooled liquids, focusing on covalent networks. We introduce a model for the energy of networks that incorporates weak noncovalent interactions. We show that at low temperature these interactions considerably affect the network topology near the rigidity transition that occurs as the coordination increases. As a result, this transition becomes mean field and does not present a line of critical points previously argued for, the "rigidity window." Vibrational modes are then not fractons but instead are similar to the anomalous modes observed in packings of particles near jamming. These results suggest an alternative interpretation for the intermediate phase observed in chalcogenides.
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Affiliation(s)
- Le Yan
- Department of Physics, Center for Soft Matter Research, New York University, 4 Washington Place, New York, New York 10003, USA
| | - Matthieu Wyart
- Department of Physics, Center for Soft Matter Research, New York University, 4 Washington Place, New York, New York 10003, USA
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12
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Chen P, Boolchand P, Georgiev DG. Long term aging of selenide glasses: evidence of sub-Tg endotherms and pre-Tg exotherms. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:065104. [PMID: 21389364 DOI: 10.1088/0953-8984/22/6/065104] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Long term aging, extending from months to several years, is studied on several families of chalcogenide glasses including the Ge-Se, As-Se, and Ge-As-Se systems. Special attention is given to the As-Se binary, a system that displays a rich variety of aging behavior intimately tied to sample synthesis conditions and the ambient environment in which samples are aged. Calorimetric (modulated DSC) and Raman scattering experiments are undertaken. Our results show all samples display a sub-Tg endotherm typically 10-70 °C below Tg in glassy networks possessing a mean coordination number r in the 2.25 < r < 2.45 range. Two sets of As(x)Se(100-x) samples aged for eight years were compared, set A consisted of slow cooled samples aged in the dark, and set B consisted of melt-quenched samples aged at laboratory environment. Samples of set B in the As concentration range, 35% < x < 60%, display a pre-T(g) exotherm, but the feature is not observed in samples of set A. The aging behavior of set A presumably represents intrinsic aging in these glasses, while that of set B is extrinsic due to the presence of light. The reversibility window persists in both sets of samples, but is less well defined in set B. These findings contrast with a recent study by Golovchak et al (2008 Phys. Rev. B 78 014202), which finds the onset of the reversibility window moved up to the stoichiometric composition (x = 40%). Here we show that the up-shifted window is better understood as resulting due to demixing of As4Se4 and As4Se3 molecules from the backbone, i.e., nanoscale phase separation (NSPS). We attribute sub-Tg endotherms to compaction of the flexible part of the networks upon long term aging, while the pre-Tg exotherm is to NSPS. The narrowing and sharpening of the reversibility window upon aging is interpreted as the slow 'self-organizing' stress relaxation of the phases just outside the intermediate phase, which itself is stress free and displays little aging.
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Affiliation(s)
- Ping Chen
- Department of Electrical and Computer Engineering, University of Cincinnati, Cincinnati, OH 45221-0030, USA
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13
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Phillips JC. Scaling and self-organized criticality in proteins: Lysozyme c. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:051916. [PMID: 20365015 DOI: 10.1103/physreve.80.051916] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Revised: 07/29/2009] [Indexed: 05/29/2023]
Abstract
Proteins appear to be the most dramatic natural example of self-organized criticality (SOC), a concept that explains many otherwise apparently unlikely phenomena. Protein functionality is often dominated by long-range hydro(phobic/philic) interactions, which both drive protein compaction and mediate protein-protein interactions. In contrast to previous reductionist short-range hydrophobicity scales, the holistic Moret-Zebende hydrophobicity scale [Phys. Rev. E 75, 011920 (2007)] represents a hydroanalytic tool that bioinformatically quantifies SOC in a way fully compatible with evolution. Hydroprofiling identifies chemical trends in the activities and substrate binding abilities of model enzymes and antibiotic animal lysozymes c , as well as defensins, which have been the subject of tens of thousands of experimental studies. The analysis is simple and easily performed and immediately yields insights not obtainable by traditional methods based on short-range real-space interactions, as described either by classical force fields used in molecular-dynamics simulations, or hydrophobicity scales based on transference energies from water to organic solvents or solvent-accessible areas.
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Affiliation(s)
- J C Phillips
- Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08854, USA
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14
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Phillips JC. Scaling and self-organized criticality in proteins I. Proc Natl Acad Sci U S A 2009; 106:3107-12. [PMID: 19218446 PMCID: PMC2651243 DOI: 10.1073/pnas.0811262106] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Indexed: 11/18/2022] Open
Abstract
The complexity of proteins is substantially simplified by regarding them as archetypical examples of self-organized criticality (SOC). To test this idea and elaborate on it, this article applies the Moret-Zebende SOC hydrophobicity scale to the large-scale scaffold repeat protein of the HEAT superfamily, PR65/A. Hydrophobic plasticity is defined and used to identify docking platforms and hinges from repeat sequences alone. The difference between the MZ scale and conventional hydrophobicity scales reflects long-range conformational forces that are central to protein functionality.
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Affiliation(s)
- J C Phillips
- Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854, USA.
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15
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A stringent test for hydrophobicity scales: two proteins with 88% sequence identity but different structure and function. Proc Natl Acad Sci U S A 2008; 105:9233-7. [PMID: 18591657 DOI: 10.1073/pnas.0803264105] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. In their classic article, Kyte and Doolittle (KD) concluded that the "simplicity and graphic nature of hydrophobicity scales make them very useful tools for the evaluation of protein structures." In practice, however, attempts to develop hydrophobicity scales (for example, compatible with classical force fields (CFF) in calculating the energetics of protein folding) have encountered many difficulties. Here, we suggest an entirely different approach based on the idea that proteins are self-organized networks, subject to evolving finite-scale criticality (like some network glasses). We test this proposal against two small proteins that are delicately balanced between alpha and alpha/beta structures, with different functions encoded with only 12% of their amino acids. This example explains why protein structure prediction is so challenging, and it provides a severe test for the accuracy and content of hydrophobicity scales. This method confirms KD's evaluation and at the same time suggests that protein structure, dynamics, and function can be best discussed without using CFF.
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16
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Rompicharla K, Novita DI, Chen P, Boolchand P, Micoulaut M, Huff W. Abrupt boundaries of intermediate phases and space filling in oxide glasses. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2008; 20:202101. [PMID: 21694230 DOI: 10.1088/0953-8984/20/20/202101] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Modulated differential scanning calorimetry measurements on bulk (Na(2)O)(x)(GeO(2))(1-x) glasses show a sharp reversibility window in the 14%<x<19% soda range, which correlates well with a broad global minimum in molar volumes. Raman and IR reflectance transverse- and longitudinal-optic mode frequencies exhibit anomalies between x(c)(1) = 14% (stress transition) and x(c)(2) = 19% (rigidity transition), with optical elasticity power laws confirming the nature of the transitions. Birefringence measurements dramatize the macroscopically stress-free nature of the intermediate phase in the reversibility window.
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Affiliation(s)
- K Rompicharla
- Department of Electrical and Computer Engineering, University of Cincinnati, Cincinnati, OH 45221-0030, USA
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17
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Novita DI, Boolchand P, Malki M, Micoulaut M. Fast-ion conduction and flexibility of glassy networks. PHYSICAL REVIEW LETTERS 2007; 98:195501. [PMID: 17677626 DOI: 10.1103/physrevlett.98.195501] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Indexed: 05/16/2023]
Abstract
We observe two thresholds in the variations of electrical conductivity of dry (AgI)_{x}(AgPO3)_{1-x} solid electrolyte glasses, when the AgI additive concentration x increases to 9.5% and to 37.8%. Raman scattering complemented by calorimetric measurements confirms that these thresholds are signatures of the rigidity phase transitions at x=9.5% from a stressed rigid to an isostatically (stress-free) rigid phase, and at x=37.8% from isostatically rigid to a flexible phase. In the flexible phase, the electrical conductivity seems to increase as a power of x. This is in good agreement with the theoretical prediction based on 3D percolation.
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Affiliation(s)
- Deassy I Novita
- Department of Electrical and Computer Engineering, University of Cincinnati, Cincinnati, OH 45221-0030, USA
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18
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Brière MA, Chubynsky MV, Mousseau N. Self-organized criticality in the intermediate phase of rigidity percolation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 75:056108. [PMID: 17677134 DOI: 10.1103/physreve.75.056108] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2006] [Indexed: 05/16/2023]
Abstract
Experimental results for covalent glasses have highlighted the existence of a self-organized phase due to the tendency of glass networks to minimize internal stress. Recently, we have shown that an equilibrated self-organized two-dimensional lattice-based model also possesses an intermediate phase in which a percolating rigid cluster exists with a probability between zero and one, depending on the average coordination of the network. In this paper, we study the properties of this intermediate phase in more detail. We find that microscopic perturbations, such as the addition or removal of a single bond, can affect the rigidity of macroscopic regions of the network, in particular, creating or destroying percolation. This, together with a power-law distribution of rigid cluster sizes, suggests that the system is maintained in a critical state on the rigid-floppy boundary throughout the intermediate phase, a behavior similar to self-organized criticality, but, remarkably, in a thermodynamically equilibrated state. The distinction between percolating and nonpercolating networks appears physically meaningless, even though the percolating cluster, when it exists, takes up a finite fraction of the network. We point out both similarities and differences between the intermediate phase and the critical point of ordinary percolation models without self-organization. Our results are consistent with an interpretation of recent experiments on the pressure dependence of Raman frequencies in chalcogenide glasses in terms of network homogeneity.
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Affiliation(s)
- M-A Brière
- Département de Physique and Regroupement Québécois sur les Matériaux de Pointe, Université de Montréal, Case Postale 6128, Succursale Centre-ville, Montréal, Québec, Canada H3C 3J7
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Chubynsky MV, Brière MA, Mousseau N. Self-organization with equilibration: a model for the intermediate phase in rigidity percolation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 74:016116. [PMID: 16907160 DOI: 10.1103/physreve.74.016116] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2006] [Indexed: 05/11/2023]
Abstract
Recent experimental results for covalent glasses suggest the existence of an intermediate phase attributed to the self-organization of the glass network resulting from the tendency to minimize its internal stress. However, the exact nature of this experimentally measured phase remains unclear. We modified a previously proposed model of self-organization by generating a uniform sampling of stress-free networks. In our model, studied on a diluted triangular lattice, an unusual intermediate phase appears, in which both rigid and floppy networks have a chance to occur, a result also observed in a related model on a Bethe lattice by Barré et al[Phys. Rev. Lett. 94, 208701 (2005)]. Our results for the bond-configurational entropy of self-organized networks, which turns out to be only about 2% lower than that of random networks, suggest that a self-organized intermediate phase could be common in systems near the rigidity percolation threshold.
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Affiliation(s)
- M V Chubynsky
- Département de Physique, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, Québec, Canada H3C 3J7.
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De Michele C, Gabrielli S, Tartaglia P, Sciortino F. Dynamics in the Presence of Attractive Patchy Interactions. J Phys Chem B 2006; 110:8064-79. [PMID: 16610908 DOI: 10.1021/jp056380y] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report extensive Monte Carlo and event-driven molecular dynamics simulations of a liquid composed of particles interacting via hard-sphere interactions complemented by four tetrahedrally coordinated short-range attractive ("sticky") spots, a model introduced several years ago by Kolafa and Nezbeda (Kolafa, J.; Nezbeda, I. Mol. Phys. 1987, 87, 161). To access the dynamic properties of the model, we introduce and implement a new event-driven molecular dynamics algorithm suited to study the evolution of hard bodies interacting, beside the repulsive hard-core, with a short-ranged interpatch square well potential. We evaluate the thermodynamic properties of the model in deep supercooled states, where the bond network is fully developed, providing evidence of density anomalies. Different from models of spherically symmetric interacting particles, the liquid can be supercooled without encountering the gas-liquid spinodal in a wide region of packing fractions phi. Around an optimal phi, a stable fully connected tetrahedral network of bonds develops. By analyzing the dynamics of the model we find evidence of anomalous behavior: around the optimal packing, dynamics accelerate on both increasing and decreasing phi. We locate the shape of the isodiffusivity lines in the (phi - T) plane and establish the shape of the dynamic arrest line in the phase diagram of the model. Results are discussed in connection with colloidal dispersions of sticky particles and gel-forming proteins and their ability to form dynamically arrested states.
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Affiliation(s)
- Cristiano De Michele
- Dipartimento di Fisica and INFM-CRS-SOFT, Università di Roma La Sapienza, Piazzale A. Moro 2, 00185 Rome, Italy
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