Article
Multidisciplinary Sciences
Volker L. Deringer, Noam Bernstein, Gabor Csanyi, Chiheb Ben Mahmoud, Michele Ceriotti, Mark Wilson, David A. Drabold, Stephen R. Elliott
Summary: This study investigates the structural transitions of amorphous silicon under increasing external pressure, revealing a three-step transformation sequence and demonstrating the transient nature of the VHDA phase, which rapidly nucleates crystallites. The machine learning model for electronic density of states provides support for the onset of metallicity during VHDA formation and subsequent crystallization, showcasing a machine learning-driven approach to predictive materials modeling.
Article
Materials Science, Multidisciplinary
Dihui Ruan, Sylvain Patinet, Michael L. Falk
Summary: By applying the local yield stress (LYS) method to probe local regions of three-dimensional computational glass models, high correlations were confirmed between the measured local yield stress (Delta tau(c)) and plastic events when the method was properly optimized. The optimal probing region was found to be around 5 sigma in radius, with the averaged correlation remaining positive through the first 200 identified plastic events or 1/3 of the yielding strain.
JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS
(2022)
Article
Nanoscience & Nanotechnology
Anna B. Stephenson, Ming Xiao, Victoria Hwang, Liangliang Qu, Paul A. Odorisio, Michael Burke, Keith Task, Ted Deisenroth, Solomon Barkley, Rupa H. Darji, Vinothan N. Manoharan
Summary: Photonic balls are spheres that contain nanoparticles or nanopores, with a diameter comparable to the wavelength of light. They can exhibit structural color due to their disordered but correlated nanoscale features, making them a promising type of pigment for various applications. However, predicting the color of materials made from photonic balls is challenging due to the need to account for sphere geometry and multiple scattering. In this study, a multiscale modeling approach involving Monte Carlo simulations is developed to address these challenges.
Article
Optics
Dian Wan, Ting Li, Si Chen, Weicheng Chen, Haofeng Hu, Sze Yun Set, Shinji Yamashita, Li Shen, Yi Zou, Tiegen Liu, Zhenzhou Cheng
Summary: Hyperuniform disordered solid (HUDS) structures provide large, uniform, complete, and isotropic light confinement at the nanoscale. In this study, a morphology engineering method is used to tailor HUDS photonic bandgaps (PBGs) and improve HUDS waveguide devices. Results show that Bezier-curve-decorated HUDS devices achieve increased PBG widths, improved transmittance, and enhanced quality factors, with compatibility for device fabrication.
LASER & PHOTONICS REVIEWS
(2023)
Article
Multidisciplinary Sciences
Hongyi Xiao, Ge Zhang, Entao Yang, Robert Ivancic, Sean Ridout, Robert Riggleman, Douglas J. Durian, Andrea J. Liu
Summary: This study introduces a new structuro-elastoplastic (StEP) model to tune the degree of strain localization in disordered solids, based on the stability of the disordered local structure represented by a machine learning-based descriptor called softness. The model exhibits semiquantitative agreement with experimental results for different disordered solids and provides a microscopic understanding of the interplay between structure, plasticity, and elasticity in strain localization.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Laszlo Dobson, Gabor E. Tusnady
Summary: Transmembrane proteins play crucial roles in cells, with their functions often mediated by intrinsically disordered regions. MemDis, a novel prediction method utilizing convolutional neural network and long short-term memory networks, achieved the highest prediction accuracy on a specific dataset of TMPs. By defining TMP-specific features, MemDis further enhanced the accuracy of predicting disordered regions in TMPs compared to other popular IDR prediction methods.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Materials Science, Ceramics
Karina Gonzalez-Lopez, Eran Bouchbinder, Edan Lerner
Summary: Quantifying mechanical disorder in solids, such as disordered crystals and glassy solids, is crucial for understanding their structure-properties relations. However, the bounds and variability of mechanical fluctuations in these disordered solids, as well as their dependence on formation history, remain unknown. In this study, a quantifier of mesoscopic mechanical disorder x, based on shear modulus fluctuations, is investigated in various disordered computer solids. The results reveal important relationships between x and fundamental properties of disordered solids, and highlight the potential divergent behavior of x in systems approaching the critical unjamming point.
JOURNAL OF NON-CRYSTALLINE SOLIDS
(2023)
Article
Physics, Multidisciplinary
Norihiro Oyama, Hideyuki Mizuno, Atsushi Ikeda
Summary: This letter reports that the instantaneous normal modes with negative eigenvalues, or so-called imaginary modes, serve as the structural signatures for the Herschel-Bulkley rheology in sheared glasses, providing new insights into the structural origins of the Herschel-Bulkley law.
PHYSICAL REVIEW LETTERS
(2021)
Article
Chemistry, Physical
Qianxiang Ai, Davion Marquise Williams, Matthew Danielson, Liam G. Spooner, Joshua A. Engler, Zihui Ding, Matthias Zeller, Alexander J. Norquist, Joshua Schrier
Summary: By studying the dataset of amine-templated metal oxides, it was found that predicting the dimensionality of products accurately can be achieved using only reactant identity information without stoichiometric information, with the amine identity playing a minor role in most cases. The generalization of this model was demonstrated on a time held-out test set with high predictive accuracy.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biology
Utsab R. Shrestha, Jeremy C. Smith, Loukas Petridis
Summary: The study demonstrates that enhancing the sampling using Hamiltonian replica exchange molecular simulation (HREMD) leads to accurate unbiased ensembles of intrinsically disordered proteins. Standard molecular simulation cannot reproduce small-angle scattering data as well as HREMD, highlighting the utility of the suggested approach.
COMMUNICATIONS BIOLOGY
(2021)
Article
Chemistry, Medicinal
Dominique Sydow, Eva Assmann, Albert J. Kooistra, Friedrich Rippmann, Andrea Volkamer
Summary: Protein kinases are important drug targets, but developing selective inhibitors is challenging due to their structural conservation. This study presents a kinase fingerprint based on structural similarity that can predict off-targets. The fingerprint is a valuable tool in kinase research for guiding off-target and polypharmacology prediction.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Multidisciplinary Sciences
Prakash Kulkarni, Ravi Salgia, Govindan Rangarajan
Summary: Phenotypic plasticity refers to the ability of individual genotypes to produce different phenotypes in response to environmental changes. Previous research has proposed that conformational noise derived from the conformational dynamics of intrinsically disordered proteins (IDPs) can contribute to phenotypic switching by altering the cellular protein interaction network. This review article discusses the progress in understanding this hypothesis, presents empirical evidence supporting it, and identifies key areas for future research.
Article
Chemistry, Physical
Y. Miyazaki, M. Nakano, A. Krivchikov, O. A. Koroyuk, J. F. Gebbia, C. Cazorla, J. Ll Tamarit
Summary: By measuring the specific heat of normal and deuterated thiophene, we found a large heat capacity bump at low temperatures for both stable and metastable phases, deviating significantly from the expected Debye temperature behavior. This anomaly, typically known as a Boson-peak in glassy crystals, is not exclusive to disordered materials.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Kui Wang, Xin Meng, Xue-Jiao Zhang
Summary: In this study, calixpyridinium was identified as a suitable component for constructing an artificial dissipative system. By utilizing an alkali as the fuel, the structural evolution of the calixpyridinium-indigo carmine system from disorder to fibrous assembly was achieved via a dual visual dissipative pathway. Moreover, this method was successfully applied to mimic the alkaline biological molecule-driven dissipative process in real samples.
MATERIALS CHEMISTRY FRONTIERS
(2023)
Article
Chemistry, Physical
Suleiman Mousa, Kyro Baron, Robin S. Fletcher, Sean P. Rigby
Summary: The key issue in using indirect pore structure characterization methods for disordered materials is the need for physical assumptions to probe pore size. This work introduces dual-liquid thermoporometry and dual-probe experiments to overcome this issue, providing more comprehensive information through triangulating data from three different porosimetries.
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS
(2022)
Article
Materials Science, Multidisciplinary
Z. Fan, E. Ma, M. L. Falk
Summary: We report atomistic simulation results showing that the location of shear banding in a metallic glass can be accurately determined from the undeformed static structure. Our findings demonstrate a correlation between the initiation of shear bands and the initial distribution of density of fertile sites for stress-driven shear transformations. Furthermore, we show that the initial distribution of density of fertile sites can be used to determine whether a glass is brittle or ductile. These results validate the existence of nonlinear instabilities in shear bands of metallic glass and highlight the influence of inhomogeneities in the as-quenched glass structure. Additionally, we reveal an important detail regarding the nondeterministic nature of athermal quasistatic shear simulations.
PHYSICAL REVIEW MATERIALS
(2022)
Article
Chemistry, Physical
Yagyik Goswami, Srikanth Sastry
Summary: This paper presents a method to estimate free energy surfaces with respect to multiple order parameters from a steady state ensemble of trajectories, and applies it to reconstruct the free energy surface for supercooled liquid silicon. The results are consistent with previous findings from umbrella sampling.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Editorial Material
Chemistry, Physical
Sidney R. Nagel, Srikanth Sastry, Zorana Zeravcic, Murugappan Muthukumar
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Physics, Multidisciplinary
M. Lisa Manning
Summary: The field of soft matter physics has expanded rapidly in recent decades, revealing the importance of entropy, elasticity, and geometry in understanding various materials and systems. Similarly, the fields of biological physics and the physics of living systems have gained recognition as independent areas of study, aided by tools from molecular and cell biology and optical physics. This Essay explores two future challenges at the intersection of these two fields: the characterization of emergent behavior and the manipulation of highly deformable active objects. Progress in these areas holds the potential for creating adaptive smart materials and advancing our understanding of biological function, particularly in the fight against disease.
PHYSICAL REVIEW LETTERS
(2023)
Article
Engineering, Mechanical
C. Turbil, J. Cabrero, I Simonsen, D. Vandembroucq, I Gozhyk
Summary: The topography of a rough surface plays a crucial role in determining its physical properties, and a deep understanding of these phenomena requires knowledge of the topography at appropriate length scales. This study presents a multi-scale and statistical analysis of the surface topography of blasted aluminum samples with different visual appearances. The analysis reveals a scale separation between micro-scale roughness inherited from the initial aluminum surface and large-scale roughness controlled by the blasting process. The study highlights the crucial importance of length scales in estimating local slopes and establishes a quantitative link between surface topography and the blasting process.
SURFACE TOPOGRAPHY-METROLOGY AND PROPERTIES
(2023)
Article
Chemistry, Multidisciplinary
Xiuyang Xia, Ge Zhang, Massimo Pica Ciamarra, Yang Jiao, Ran Ni
Summary: Multivalency is widely observed in biological systems and applications, and it offers superselectivity through the cooperativity of multivalent binding. Traditionally, weak individual binding was believed to enhance selectivity in multivalent targeting. However, our study using theoretical modeling and simulations reveals that the highest selectivity occurs at an intermediate binding energy, which can be even higher than the weak binding limit, for receptors that are highly uniformly distributed. This unexpected finding is attributed to an exponential relationship between the bound fraction and receptor concentration, which is influenced by both the strength and combinatorial entropy of binding. Our findings provide new guidelines for rational design of biosensors using multivalent nanoparticles and offer a fresh perspective on understanding biological processes involving multivalency.
Article
Thermodynamics
Xing Xiang, Sylvain Patinet, Sebastian Volz, Yanguang Zhou
Summary: Quasilocalized vibrational modes (QVMs) in glassy solids, although known to populate the low-frequency spectrum, have not been well explored in terms of their thermal transport properties. This study demonstrates that the modal thermal conductivity of QVMs is comparable to that of delocalized vibrational modes, indicating that QVMs can be efficient heat carriers. The high thermal exchange performance of QVMs is attributed to the mutual coherence between QVMs and other modes. These findings provide new insights into the thermal transport behavior of QVMs in glassy solids.
INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER
(2023)
Editorial Material
Chemistry, Physical
Emanuela Del Gado, Andrea Liu, C. Patrick Royall
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Physics, Multidisciplinary
Monoj Adhikari, Smarajit Karmakar, Srikanth Sastry
Summary: We investigated the dynamics of soft sphere liquids through computer simulations, finding ideal glass transition and crossover points in different dimensions and temperature-density ranges. Additionally, we observed an increasing difference between the ideal glass transition density and the athermal jamming density as the dimensionality increases.
PHYSICAL REVIEW LETTERS
(2023)
Article
Multidisciplinary Sciences
Hongyi Xiao, Ge Zhang, Entao Yang, Robert Ivancic, Sean Ridout, Robert Riggleman, Douglas J. Durian, Andrea J. Liu
Summary: This study introduces a new structuro-elastoplastic (StEP) model to tune the degree of strain localization in disordered solids, based on the stability of the disordered local structure represented by a machine learning-based descriptor called softness. The model exhibits semiquantitative agreement with experimental results for different disordered solids and provides a microscopic understanding of the interplay between structure, plasticity, and elasticity in strain localization.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Physics, Applied
Andrea J. Liu, Sidney R. Nagel
Summary: In this article, the authors discuss the proposal of a jamming phase diagram from twenty-five years ago and how linking jammed granular materials with glasses can enhance our understanding of the physics of various systems.
NATURE REVIEWS PHYSICS
(2023)
Article
Chemistry, Physical
Varghese Babu, H. A. Vinutha, Dapeng Bi, Srikanth Sastry
Summary: The rigidity transition associated with shear jamming is discontinuous, whether for frictionless or frictional systems, in both the quasi-static and low shear rate regimes.
Article
Physics, Fluids & Plasmas
Ojan Khatib Damavandi, Varda F. Hagh, Christian D. Santangelo, M. Lisa Manning
Summary: Rigidity plays a crucial role in the integrity and function of various physical and biological systems. This paper introduces the concept of energetic rigidity, which is a more practical notion of rigidity compared to commonly used rigidity tests. The formalism of energetic rigidity not only unifies our understanding of mechanical stability but also opens up new avenues for material design.
