scholarly journals Nature of excitations and defects in structural glasses

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Camille Scalliet ◽  
Ludovic Berthier ◽  
Francesco Zamponi
Keyword(s):  
Amorphous Materials ◽  
Energy Landscape ◽  
Three Dimensional ◽  
Collective Excitations ◽  
Molecular Glasses ◽  
Physical Conditions ◽  
Temperature Scales ◽  
Model Glass ◽  
Localized Defects ◽  
Glassy Materials

Abstract The nature of defects in amorphous materials, analogous to vacancies and dislocations in crystals, remains elusive. Here, we explore their nature in a three-dimensional microscopic model glass-former that describes granular, colloidal, atomic and molecular glasses by changing the temperature and density. We find that all glasses evolve in a very rough energy landscape, with a hierarchy of barrier sizes corresponding to both localized and delocalized excitations. Collective excitations dominate in the jamming regime relevant for granular and colloidal glasses. By moving gradually to larger densities describing atomic and molecular glasses, the system crosses over to a regime dominated by localized defects and relatively simpler landscapes. We quantify the energy and temperature scales associated to these defects and their evolution with density. Our results pave the way to a systematic study of low-temperature physics in a broad range of physical conditions and glassy materials.

scholarly journals An energy landscape approach to locomotor transitions in complex 3D terrain

2020 ◽  
Vol 117 (26) ◽  
pp. 14987-14995 ◽  
Author(s):  
Ratan Othayoth ◽  
George Thoms ◽  
Chen Li
Keyword(s):  
Potential Energy ◽  
Complex Terrain ◽  
Statistical Physics ◽  
Energy Landscape ◽  
Three Dimensional ◽  
Single Mode ◽  
Physical Interaction ◽  
Landscape Approach ◽  
3D Terrain ◽  
Potential Energy Landscape

Effective locomotion in nature happens by transitioning across multiple modes (e.g., walk, run, climb). Despite this, far more mechanistic understanding of terrestrial locomotion has been on how to generate and stabilize around near–steady-state movement in a single mode. We still know little about how locomotor transitions emerge from physical interaction with complex terrain. Consequently, robots largely rely on geometric maps to avoid obstacles, not traverse them. Recent studies revealed that locomotor transitions in complex three-dimensional (3D) terrain occur probabilistically via multiple pathways. Here, we show that an energy landscape approach elucidates the underlying physical principles. We discovered that locomotor transitions of animals and robots self-propelled through complex 3D terrain correspond to barrier-crossing transitions on a potential energy landscape. Locomotor modes are attracted to landscape basins separated by potential energy barriers. Kinetic energy fluctuation from oscillatory self-propulsion helps the system stochastically escape from one basin and reach another to make transitions. Escape is more likely toward lower barrier direction. These principles are surprisingly similar to those of near-equilibrium, microscopic systems. Analogous to free-energy landscapes for multipathway protein folding transitions, our energy landscape approach from first principles is the beginning of a statistical physics theory of multipathway locomotor transitions in complex terrain. This will not only help understand how the organization of animal behavior emerges from multiscale interactions between their neural and mechanical systems and the physical environment, but also guide robot design, control, and planning over the large, intractable locomotor-terrain parameter space to generate robust locomotor transitions through the real world.

scholarly journals Multi-Funnel Landscape of the Fold-Switching Protein RfaH-CTD

2017 ◽  
Author(s):  
Nathan A. Bernhardt ◽  
Ulrich H.E. Hansmann
Keyword(s):  
Free Energy ◽  
Transcription Factor ◽  
Biological Function ◽  
Double Helix ◽  
Energy Landscape ◽  
Three Dimensional ◽  
Conversion Process ◽  
Free Energy Landscape ◽  
Enhanced Sampling ◽  
Helix Bundle

AbstractProteins such as the transcription factor RfaH can change biological function by switching between distinct three-dimensional folds. RfaH regulates transcription if the C-terminal domain folds into a double helix bundle, and promotes translation when this domain assumes a β-barrel form. This fold-switch has been also observed for the isolated domain, dubbed by us RfaH-CTD, and is studied here with a variant of the RET approach recently introduced by us. We use the enhanced sampling properties of this technique to map the free energy landscape of RfaH-CTD and to propose a mechanism for the conversion process.TOC Image

scholarly journals Computational Protein Stabilization Can Affect Folding Energy Landscapes and Lead to Domain-Swapped Dimers

2021 ◽  
Author(s):  
Klara Markova ◽  
Antonin Kunka ◽  
Klaudia Chmelova ◽  
Martin Havlasek ◽  
Petra Babkova ◽  
...  
Keyword(s):  
Protein Folding ◽  
Protein Design ◽  
Energy Landscape ◽  
Single Point ◽  
Three Dimensional ◽  
Protein Stabilization ◽  
Dimensional Structure ◽  
Evolutionary Analysis ◽  
Folding Energy

<p>The functionality of a protein depends on its unique three-dimensional structure, which is a result of the folding process when the nascent polypeptide follows a funnel-like energy landscape to reach a global energy minimum. Computer-encoded algorithms are increasingly employed to stabilize native proteins for use in research and biotechnology applications. Here, we reveal a unique example where the computational stabilization of a monomeric α/β-hydrolase enzyme (<i>T</i><sub>m</sub> = 73.5°C; Δ<i>T</i><sub>m</sub> > 23°C) affected the protein folding energy landscape. Introduction of eleven single-point stabilizing mutations based on force field calculations and evolutionary analysis yielded catalytically active domain-swapped intermediates trapped in local energy minima. Crystallographic structures revealed that these stabilizing mutations target cryptic hinge regions and newly introduced secondary interfaces, where they make extensive non-covalent interactions between the intertwined misfolded protomers. The existence of domain-swapped dimers in a solution is further confirmed experimentally by data obtained from SAXS and crosslinking mass spectrometry. Unfolding experiments showed that the domain-swapped dimers can be irreversibly converted into native-like monomers, suggesting that the domain-swapping occurs exclusively <i>in vivo</i>. Our findings uncovered hidden protein-folding consequences of computational protein design, which need to be taken into account when applying a rational stabilization to proteins of biological and pharmaceutical interest.</p>

scholarly journals Computational Protein Stabilization Can Affect Folding Energy Landscapes and Lead to Domain-Swapped Dimers

2021 ◽  
Author(s):  
Klara Markova ◽  
Antonin Kunka ◽  
Klaudia Chmelova ◽  
Martin Havlasek ◽  
Petra Babkova ◽  
...  
Keyword(s):  
Protein Folding ◽  
Protein Design ◽  
Energy Landscape ◽  
Single Point ◽  
Three Dimensional ◽  
Protein Stabilization ◽  
Dimensional Structure ◽  
Evolutionary Analysis ◽  
Folding Energy

<p>The functionality of a protein depends on its unique three-dimensional structure, which is a result of the folding process when the nascent polypeptide follows a funnel-like energy landscape to reach a global energy minimum. Computer-encoded algorithms are increasingly employed to stabilize native proteins for use in research and biotechnology applications. Here, we reveal a unique example where the computational stabilization of a monomeric α/β-hydrolase enzyme (<i>T</i><sub>m</sub> = 73.5°C; Δ<i>T</i><sub>m</sub> > 23°C) affected the protein folding energy landscape. Introduction of eleven single-point stabilizing mutations based on force field calculations and evolutionary analysis yielded catalytically active domain-swapped intermediates trapped in local energy minima. Crystallographic structures revealed that these stabilizing mutations target cryptic hinge regions and newly introduced secondary interfaces, where they make extensive non-covalent interactions between the intertwined misfolded protomers. The existence of domain-swapped dimers in a solution is further confirmed experimentally by data obtained from SAXS and crosslinking mass spectrometry. Unfolding experiments showed that the domain-swapped dimers can be irreversibly converted into native-like monomers, suggesting that the domain-swapping occurs exclusively <i>in vivo</i>. Our findings uncovered hidden protein-folding consequences of computational protein design, which need to be taken into account when applying a rational stabilization to proteins of biological and pharmaceutical interest.</p>

scholarly journals New Insights into the Electrocatalytic Mechanism of Methanol Oxidation on Amorphous Ni-B-Co Nanoparticles in Alkaline Media

Catalysts ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 749 ◽  
Author(s):  
Wu ◽  
Zhang ◽  
Zhang ◽  
Duan ◽  
Li ◽  
...  
Keyword(s):  
Methanol Oxidation ◽  
Amorphous Materials ◽  
Reaction Order ◽  
Chemical Reduction ◽  
Three Dimensional ◽  
Kinetic Studies ◽  
Alkaline Media ◽  
Methanol Oxidation Reaction ◽  
Oxidation Reactions ◽  
Co Nanoparticles

Despite an increased interest in sustainable energy conversion systems, there have been limited studies investigating the electrocatalytic reaction mechanism of methanol oxidation on Ni-based amorphous materials in alkaline media. A thorough understanding of such mechanisms would aid in the development of amorphous catalytic materials for methanol oxidation reactions. In the present work, amorphous Ni-B and Ni-B-Co nanoparticles were prepared by a simple chemical reduction, and their electrocatalytic properties were investigated by cyclic voltammetry measurements. The diffusion coefficients (D0) for Ni-B, Ni-B-Co0.02, Ni-B-Co0.05, and Ni-B-Co0.1 nanoparticles were calculated to be 1.28 × 10−9, 2.35 × 10−9, 4.48 × 10−9 and 2.67 × 10−9 cm2 s−1, respectively. The reaction order of methanol in the studied transformation was approximately 0.5 for all studied catalysts, whereas the reaction order of the hydroxide ion was nearly 1. The activation energy (Ea) values of the reaction were also calculated for the Ni-B and Ni-B-Co nanoparticle systems. Based on our kinetic studies, a mechanism for the methanol oxidation reaction was proposed which involved formation of an electrocatalytic layer on the surface of amorphous Ni–B and Ni-B-Co nanoparticles. And methanol and hydroxide ions could diffuse freely through this three-dimensional porous conductive layer.

Energy landscape in molecular glasses probed by high-resolution dielectric experiments

2010 ◽  
Vol 82 (10) ◽  
Author(s):  
Catalin Gainaru ◽  
Roland Böhmer ◽  
Robert Kahlau ◽  
Ernst Rössler
Keyword(s):  
High Resolution ◽  
Energy Landscape ◽  
Molecular Glasses

scholarly journals Off-equilibrium dynamics in the energy landscape of a simple model glass

2002 ◽  
Vol 82 (2) ◽  
pp. 163-169 ◽  
Author(s):  
R. Di Leonardo ◽  
L. Angelani ◽  
G. Parisi ◽  
G. Ruocco ◽  
A. Scala ◽  
...  
Keyword(s):  
Simple Model ◽  
Energy Landscape ◽  
Equilibrium Dynamics ◽  
Model Glass

scholarly journals Geometry and mechanics of two-dimensional defects in amorphous materials

2015 ◽  
Vol 112 (35) ◽  
pp. 10873-10878 ◽  
Author(s):  
Michael Moshe ◽  
Ido Levin ◽  
Hillel Aharoni ◽  
Raz Kupferman ◽  
Eran Sharon
Keyword(s):  
Amorphous Materials ◽  
Flexible Substrate ◽  
Large Family ◽  
Multipole Expansion ◽  
Inelastic Behavior ◽  
Intrinsic Metric ◽  
Elastic Interactions ◽  
Dipole Term ◽  
Localized Defects ◽  
Analytical Tools

We study the geometry of defects in amorphous materials and their elastic interactions. Defects are defined and characterized by deviations of the material’s intrinsic metric from a Euclidian metric. This characterization makes possible the identification of localized defects in amorphous materials, the formulation of a corresponding elastic problem, and its solution in various cases of physical interest. We present a multipole expansion that covers a large family of localized 2D defects. The dipole term, which represents a dislocation, is studied analytically and experimentally. Quadrupoles and higher multipoles correspond to fundamental strain-carrying entities. The interactions between those entities, as well as their interaction with external stress fields, are fundamental to the inelastic behavior of solids. We develop analytical tools to study those interactions. The model, methods, and results presented in this work are all relevant to the study of systems that involve a distribution of localized sources of strain. Examples are plasticity in amorphous materials and mechanical interactions between cells on a flexible substrate.

scholarly journals Potential energy landscape and long-time dynamics in a simple model glass

2000 ◽  
Vol 61 (2) ◽  
pp. 1681-1691 ◽  
Author(s):  
L. Angelani ◽  
G. Parisi ◽  
G. Ruocco ◽  
G. Viliani
Keyword(s):  
Simple Model ◽  
Potential Energy ◽  
Energy Landscape ◽  
Time Dynamics ◽  
Model Glass ◽  
Potential Energy Landscape ◽  
Long Time ◽  
Long Time Dynamics
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