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The OpenKIM processing pipeline: A cloud-based automatic material property computation engine. J Chem Phys 2020; 153:064104. [DOI: 10.1063/5.0014267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Imaging Atomic Rearrangements in Two-Dimensional Silica Glass: Watching Silica's Dance. Science 2013; 342:224-7. [DOI: 10.1126/science.1242248] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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4
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Intra-unit-cell electronic nematicity of the high-T(c) copper-oxide pseudogap states. Nature 2010; 466:347-51. [PMID: 20631795 DOI: 10.1038/nature09169] [Citation(s) in RCA: 436] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Accepted: 05/04/2010] [Indexed: 11/10/2022]
Abstract
In the high-transition-temperature (high-T(c)) superconductors the pseudogap phase becomes predominant when the density of doped holes is reduced. Within this phase it has been unclear which electronic symmetries (if any) are broken, what the identity of any associated order parameter might be, and which microscopic electronic degrees of freedom are active. Here we report the determination of a quantitative order parameter representing intra-unit-cell nematicity: the breaking of rotational symmetry by the electronic structure within each CuO(2) unit cell. We analyse spectroscopic-imaging scanning tunnelling microscope images of the intra-unit-cell states in underdoped Bi(2)Sr(2)CaCu(2)O(8 +) (delta) and, using two independent evaluation techniques, find evidence for electronic nematicity of the states close to the pseudogap energy. Moreover, we demonstrate directly that these phenomena arise from electronic differences at the two oxygen sites within each unit cell. If the characteristics of the pseudogap seen here and by other techniques all have the same microscopic origin, this phase involves weak magnetic states at the O sites that break 90 degrees -rotational symmetry within every CuO(2) unit cell.
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Optimal experimental design in an epidermal growth factor receptor signalling and down-regulation model. IET Syst Biol 2007; 1:190-202. [PMID: 17591178 DOI: 10.1049/iet-syb:20060065] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We apply the methods of optimal experimental design to a differential equation model for epidermal growth factor receptor signalling, trafficking and down-regulation. The model incorporates the role of a recently discovered protein complex made up of the E3 ubiquitin ligase, Cbl, the guanine exchange factor (GEF), Cool-1 (beta -Pix) and the Rho family G protein Cdc42. The complex has been suggested to be important in disrupting receptor down-regulation. We demonstrate that the model interactions can accurately reproduce the experimental observations, that they can be used to make predictions with accompanying uncertainties, and that we can apply ideas of optimal experimental design to suggest new experiments that reduce the uncertainty on unmeasurable components of the system.
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Bayesian error estimation in density-functional theory. PHYSICAL REVIEW LETTERS 2005; 95:216401. [PMID: 16384163 DOI: 10.1103/physrevlett.95.216401] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2005] [Indexed: 05/05/2023]
Abstract
We present a practical scheme for performing error estimates for density-functional theory calculations. The approach, which is based on ideas from Bayesian statistics, involves creating an ensemble of exchange-correlation functionals by comparing with an experimental database of binding energies for molecules and solids. Fluctuations within the ensemble can then be used to estimate errors relative to experiment on calculated quantities such as binding energies, bond lengths, and vibrational frequencies. It is demonstrated that the error bars on energy differences may vary by orders of magnitude for different systems in good agreement with existing experience.
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Abstract
The inherent complexity of cellular signaling networks and their importance to a wide range of cellular functions necessitates the development of modeling methods that can be applied toward making predictions and highlighting the appropriate experiments to test our understanding of how these systems are designed and function. We use methods of statistical mechanics to extract useful predictions for complex cellular signaling networks. A key difficulty with signaling models is that, while significant effort is being made to experimentally measure the rate constants for individual steps in these networks, many of the parameters required to describe their behavior remain unknown or at best represent estimates. To establish the usefulness of our approach, we have applied our methods toward modeling the nerve growth factor (NGF)-induced differentiation of neuronal cells. In particular, we study the actions of NGF and mitogenic epidermal growth factor (EGF) in rat pheochromocytoma (PC12) cells. Through a network of intermediate signaling proteins, each of these growth factors stimulates extracellular regulated kinase (Erk) phosphorylation with distinct dynamical profiles. Using our modeling approach, we are able to predict the influence of specific signaling modules in determining the integrated cellular response to the two growth factors. Our methods also raise some interesting insights into the design and possible evolution of cellular systems, highlighting an inherent property of these systems that we call 'sloppiness.'
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Abstract
We measure electron tunneling in transistors made from C(140), a molecule with a mass-spring-mass geometry chosen as a model system to study electron-vibration coupling. We observe vibration-assisted tunneling at an energy corresponding to the stretching mode of C(140). Molecular modeling provides explanations for why this mode couples more strongly to electron tunneling than to the other internal modes of the molecule. We make comparisons between the observed tunneling rates and those expected from the Franck-Condon model.
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Fracture in mode I using a conserved phase-field model. PHYSICAL REVIEW E 2002; 65:036117. [PMID: 11909175 DOI: 10.1103/physreve.65.036117] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2001] [Revised: 10/30/2001] [Indexed: 11/07/2022]
Abstract
We present a continuum phase-field model of crack propagation. It includes a phase-field that is proportional to the mass density and a displacement field that is governed by linear elastic theory. Generic macroscopic crack growth laws emerge naturally from this model. In contrast to classical continuum fracture mechanics simulations, our model avoids numerical front tracking. The added phase-field smooths the sharp interface, enabling us to use equations of motion for the material (grounded in basic physical principles) rather than for the interface (which often are deduced from complicated theories or empirical observations). The interface dynamics thus emerges naturally. In this paper, we look at stationary solutions of the model, mode I fracture, and also discuss numerical issues. We find that the Griffith's threshold underestimates the critical value at which our system fractures due to long wavelength modes excited by the fracture process.
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Abstract
Crackling noise arises when a system responds to changing external conditions through discrete, impulsive events spanning a broad range of sizes. A wide variety of physical systems exhibiting crackling noise have been studied, from earthquakes on faults to paper crumpling. Because these systems exhibit regular behaviour over a huge range of sizes, their behaviour is likely to be independent of microscopic and macroscopic details, and progress can be made by the use of simple models. The fact that these models and real systems can share the same behaviour on many scales is called universality. We illustrate these ideas by using results for our model of crackling noise in magnets, explaining the use of the renormalization group and scaling collapses, and we highlight some continuing challenges in this still-evolving field.
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Calculation of quantum tunneling for a spatially extended defect: the dislocation kink in copper has a low effective mass. PHYSICAL REVIEW LETTERS 2001; 86:1546-1549. [PMID: 11290189 DOI: 10.1103/physrevlett.86.1546] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2000] [Indexed: 05/23/2023]
Abstract
Several experiments indicate that there are atomic tunneling defects in plastically deformed metals. How this is possible has not been clear, given the large mass of the metal atoms. Using a classical molecular-dynamics calculation, we determine the structures, energy barriers, effective masses, and quantum tunneling rates for dislocation kinks and jogs in copper screw dislocations. We find that jogs are unlikely to tunnel, but the kinks should have large quantum fluctuations. The kink motion involves hundreds of atoms each shifting a tiny amount, leading to a small effective mass and tunneling barrier.
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Acoustic emission from crumpling paper. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1996; 54:278-283. [PMID: 9965070 DOI: 10.1103/physreve.54.278] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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14
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Hysteresis, avalanches, and disorder-induced critical scaling: A renormalization-group approach. PHYSICAL REVIEW. B, CONDENSED MATTER 1996; 53:14872-14905. [PMID: 9983282 DOI: 10.1103/physrevb.53.14872] [Citation(s) in RCA: 201] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Avalanches, Barkhausen noise, and plain old criticality. PHYSICAL REVIEW LETTERS 1995; 75:4528-4531. [PMID: 10059931 DOI: 10.1103/physrevlett.75.4528] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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16
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Disorder-driven pretransitional tweed pattern in martensitic transformations. PHYSICAL REVIEW. B, CONDENSED MATTER 1995; 52:803-822. [PMID: 9980656 DOI: 10.1103/physrevb.52.803] [Citation(s) in RCA: 104] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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17
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Fast domain growth through density-dependent diffusion in a driven lattice gas. PHYSICAL REVIEW. B, CONDENSED MATTER 1995; 51:15017-15026. [PMID: 9978456 DOI: 10.1103/physrevb.51.15017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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18
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Atomic tunneling from a scanning-tunneling or atomic-force microscope tip: dissipative quantum effects from phonons. PHYSICAL REVIEW LETTERS 1995; 74:1363-1366. [PMID: 10059001 DOI: 10.1103/physrevlett.74.1363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Real-space renormalization group for the random-field Ising model. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 48:16533-16538. [PMID: 10008236 DOI: 10.1103/physrevb.48.16533] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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21
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Hysteresis loop critical exponents in 6- epsilon dimensions. PHYSICAL REVIEW LETTERS 1993; 71:3222-3225. [PMID: 10054888 DOI: 10.1103/physrevlett.71.3222] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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22
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Erratum: Scaling theory for the glass transition. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 47:14661. [PMID: 10005841 DOI: 10.1103/physrevb.47.14661] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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23
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Hysteresis and hierarchies: Dynamics of disorder-driven first-order phase transformations. PHYSICAL REVIEW LETTERS 1993; 70:3347-3350. [PMID: 10053845 DOI: 10.1103/physrevlett.70.3347] [Citation(s) in RCA: 228] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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24
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Collective dynamics in a model of sliding charge-density waves. I. Critical behavior. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 47:11171-11193. [PMID: 10005252 DOI: 10.1103/physrevb.47.11171] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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25
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Collective dynamics in a model of sliding charge-density waves. II. Finite-size effects. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 47:11194-11203. [PMID: 10005253 DOI: 10.1103/physrevb.47.11194] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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26
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Derivation of a general three-dimensional crack-propagation law: A generalization of the principle of local symmetry. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 47:4831-4840. [PMID: 10006639 DOI: 10.1103/physrevb.47.4831] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Logarithmically slow domain growth in nonrandomly frustrated systems: Ising models with competing interactions. PHYSICAL REVIEW. B, CONDENSED MATTER 1992; 46:11376-11404. [PMID: 10003024 DOI: 10.1103/physrevb.46.11376] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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28
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Spin-glass nature of tweed precursors in martensitic transformations. PHYSICAL REVIEW LETTERS 1991; 67:3630-3633. [PMID: 10044784 DOI: 10.1103/physrevlett.67.3630] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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29
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Persistent infrared spectral hole burning of NO−2ions in potassium halide crystals. I. Principle and satellite hole generation. J Chem Phys 1991. [DOI: 10.1063/1.461216] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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30
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Fock's expansion, Kato's cusp conditions, and the exponential ansatz. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1991; 44:5537-5546. [PMID: 9906612 DOI: 10.1103/physreva.44.5537] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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31
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Scaling theory for the glass transition. PHYSICAL REVIEW. B, CONDENSED MATTER 1991; 44:4943-4959. [PMID: 9998301 DOI: 10.1103/physrevb.44.4943] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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32
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Evolving numerical enzymes: Accelerating relaxation in the Frenkel-Kontorova model. PHYSICAL REVIEW LETTERS 1991; 67:995-998. [PMID: 10045043 DOI: 10.1103/physrevlett.67.995] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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33
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Prediction of logarithmic growth in a quenched Ising model. PHYSICAL REVIEW. B, CONDENSED MATTER 1991; 43:3782-3785. [PMID: 9997719 DOI: 10.1103/physrevb.43.3782] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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34
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History dependence of a two-level system. PHYSICAL REVIEW. B, CONDENSED MATTER 1991; 43:3245-3254. [PMID: 9997633 DOI: 10.1103/physrevb.43.3245] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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35
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Infrared spectroscopic study of the dressed rotations of CN- isotopes in alkali halide crystals. PHYSICAL REVIEW. B, CONDENSED MATTER 1991; 43:43-61. [PMID: 9996189 DOI: 10.1103/physrevb.43.43] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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36
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Constrained spin model of phason dynamics in quasicrystals. PHYSICAL REVIEW. B, CONDENSED MATTER 1990; 42:8517-8536. [PMID: 9995028 DOI: 10.1103/physrevb.42.8517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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37
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38
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Low-temperature properties of a model glass. II. Specific heat and thermal transport. PHYSICAL REVIEW. B, CONDENSED MATTER 1990; 41:7799-7821. [PMID: 9993078 DOI: 10.1103/physrevb.41.7799] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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39
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Low-temperature properties of a model glass. I. Elastic dipole model. PHYSICAL REVIEW. B, CONDENSED MATTER 1990; 41:7784-7798. [PMID: 9993077 DOI: 10.1103/physrevb.41.7784] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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40
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Nonequilibrium entropy and entropy distributions. PHYSICAL REVIEW. B, CONDENSED MATTER 1990; 41:2261-2278. [PMID: 9993961 DOI: 10.1103/physrevb.41.2261] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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41
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Reply to "Neutral-fermion-soliton statistics in the short-range resonating-valence-bond state: A reevaluation". PHYSICAL REVIEW. B, CONDENSED MATTER 1989; 40:7343-7344. [PMID: 9991137 DOI: 10.1103/physrevb.40.7343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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42
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Entropy distribution of a two-level system: An asymptotic analysis. PHYSICAL REVIEW. B, CONDENSED MATTER 1989; 40:345-352. [PMID: 9990920 DOI: 10.1103/physrevb.40.345] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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43
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Density of states in a vortex core and the zero-bias tunneling peak. PHYSICAL REVIEW LETTERS 1989; 62:3089-3092. [PMID: 10040175 DOI: 10.1103/physrevlett.62.3089] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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44
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Resonant scattering and thermal transport in orientational glasses. PHYSICAL REVIEW. B, CONDENSED MATTER 1988; 38:12607-12614. [PMID: 9946206 DOI: 10.1103/physrevb.38.12607] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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45
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Electron-energy-loss spectroscopy of H adsorbed on Rh(100): Interpretation of overtone spectra as two-phonon bound states. PHYSICAL REVIEW. B, CONDENSED MATTER 1988; 38:10403-10420. [PMID: 9945891 DOI: 10.1103/physrevb.38.10403] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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46
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47
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48
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Theory of the ripple phase in hydrated phospholipid bilayers. PHYSICAL REVIEW. A, GENERAL PHYSICS 1987; 36:3359-3374. [PMID: 9899255 DOI: 10.1103/physreva.36.3359] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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49
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Topology of the resonating valence-bond state: Solitons and high-Tc superconductivity. PHYSICAL REVIEW. B, CONDENSED MATTER 1987; 35:8865-8868. [PMID: 9941277 DOI: 10.1103/physrevb.35.8865] [Citation(s) in RCA: 382] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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50
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Textures in a chiral smectic liquid-crystal film. PHYSICAL REVIEW. A, GENERAL PHYSICS 1986; 34:5035-5046. [PMID: 9897889 DOI: 10.1103/physreva.34.5035] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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