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The connection between polymer collapse and the onset of jamming

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arXiv 2023年

作者： Grigas, Alex T. Fisher, Aliza Shattuck, Mark D. O’Hern, Corey S. Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Benjamin Levich Institute and Physics Department The City College of New York New YorkNY10031 United States Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States

Previous studies have shown that the interiors of proteins are densely packed, reaching packing fractions that are as large as those found for static packings of individual amino-acid-shaped particles. How can the interiors of proteins take on such high packing fractions given that amino acids are connected by peptide bonds and many amino acids are hydrophobic with attractive interactions? We investigate this question by comparing the structural and mechanical properties of collapsed attractive disk-shaped bead-spring polymers to those of three reference systems: static packings of repulsive disks, of attractive disks, and of repulsive disk-shaped bead-spring polymers. We show that attractive systems quenched to temperatures below the glass transition T Tg and static packings of both repulsive disks and bead-spring polymers possess similar interior packing fractions. Previous studies have shown that static packings of repulsive disks are isostatic at jamming onset, i.e. the number of contacts Nc matches the number of degrees of freedom, which strongly influences their mechanical properties. We find that repulsive polymers are hypostatic at jamming onset, but effectively isostatic when including quartic modes. While attractive disk and polymer packings are hyperstatic, we identify a definition for interparticle contacts for which they can also be considered as effectively isostatic. As a result, we show that the mechanical properties (e.g. scaling of the potential energy with excess contact number and low-frequency contribution to the density of vibrational modes) of weakly attractive disk and polymer packings are similar to those of isostatic repulsive disk and polymer packings. Our results demonstrate that static packings generated via attractive collapse or compression of repulsive particles possess similar structural and mechanical properties. © 2023, CC BY.

关键词： Amino acids

Challenges in Developing Materials for Microreactors: A Case-Study of Yttrium Dihydride in Extreme Conditions

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SSRN

SSRN 2023年

作者： Tunes, Matheus Araujo Parkison, Darren Huang, Yuqing Chancey, M.R. Vogel, Sven C. Mehta, Vedant K. Torrez, Michael A. Luther, E.P. Valdez, James A. Wang, Yongqiang Yu, Jianguo Cinbiz, Mahmut Nedim Shivprasad, Aditya P. Kohnert, Cailtin A. Montanuniversität Leoben Austria Materials Science and Technology Division Los Alamos National Laboratory United States Department of Nuclear Engineering University of California Berkeley United States Department of Nuclear Engineering North Carolina State University United States Irradiated Fuels and Materials Idaho National Laboratory United States Program Project Interface Division Los Alamos National Laboratory United States Sigma Division Los Alamos National Laboratory United States Computational Mechanics and Materials Idaho National Laboratory United States Materials Science and Technology Division Oak Ridge National Laboratory United States

The development of microreactor technology presents an efficient solution for providing portable electricity, catering to both human space exploration needs within our solar system and supplying power to remote Earth-bound areas. The miniaturization of nuclear reactors poses immediate new challenges for materials science with respect to the capability for controlling nuclear reactions via thermalization of highly-energetic neutrons. In a microreactor, neutron moderation takes place in compact geometries, therefore new moderator materials are required to exhibit high moderating power per unit of volume. This challenge is currently being addressed through the advancement of hydrogen technology and materials science, particularly focusing on development of transition metal hydrides, but to date, research on their irradiation response, specifically regarding phase stability, hydrogen in-lattice retention, and their dependence on irradiation temperature and dose, is limited. Herein, we present a detailed investigation on the response of yttrium dihydride (\ce{YH2}) - the most suitable moderator candidate with respect to its high operational temperature - to heavy ion irradiation. A combination of multiple experimental techniques indicate that \ce{YH2} is stable up to an irradiation dose of 2 dpa and below 800$^{\circ}$C, identified as a critical temperature for \ce{YH2}. Our study unravels that voids emerge as the major form of radiation damage. Below the critical temperature no phase change, precipitation or amorphization was observed to occur. Experimental results from ion beam and neutron scattering techniques with concomitant density functional theory calculations have allowed us to elaborate and propose new strategies to enhance the metal hydride performance in extreme environments. © 2023, The Authors. All rights reserved.

关键词： Hydrides

Molecular interaction volume model of mixing enthalpy for molten salt system: An integrated calorimetry-model case study of LaCl3-(LiCl-KCl)

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arXiv 2024年

作者： Goncharov, Vitaliy G. Smith, William Li, Jiahong Eakin, Jeffrey A. Reinhart, Erik D. Boncella, James Gibson, Luke D. Bryantsev, Vyacheslav S. Gong, Rushi Shang, Shun-Li Liu, Zi-Kui Xu, Hongwu Clark, Aurora Guo, Xiaofeng Department of Chemistry Washington State University PullmanWA99164 United States Materials Science and Engineering Program Washington State University PullmanWA99164 United States Computational Sciences and Engineering Division Oak Ridge National Laboratory P.O. Box 2008 Oak RidgeTN37831 United States Chemical Science Division Oak Ridge National Laboratory P.O. Box 2008 Oak RidgeTN37831 United States Department of Materials Science and Engineering Pennsylvania State University University ParkPA16802 United States Earth and Environmental Sciences Division Los Alamos National Laboratory Los Alamos New MexicoNM87545 United States Arizona State University TempeAZ United States Department of Chemistry The University of Utah Salt Lake CityUT84112 United States

Calorimetric determination of enthalpies of mixing (ΔHmix) of multicomponent molten salts often employs empirical models that lack parameters with clear physical interpretation (e.g., coordination numbers, molar volumes, and pair potentials). Although such physics informed models are not always needed, a thermodynamic understanding of the relationships between excess energies of mixing and local to intermediate solvation structures is particularly important for pyrochemical separation, as is the case for lanthanides (Ln), which are common neutron poisons and critical industrial elements found in spent nuclear fuels. Here we implement the molecular interaction volume model (MIVM) to synthesize information from experimentally measured ΔHmix (using high temperature melt drop calorimetry) and the distribution of solvation structures from ab initio molecular dynamics (AIMD) simulations. This was demonstrated by a case study of molten salt system consisted of LaCl3 mixing with a eutectic LiCl-KCl (58mol% - 42mol%) at 873 K and 1133 K. The parameters modelled from MIVM were used to extrapolate excess Gibbs energy (ΔGmix), and compositional dependence of La3+ activity in the LaCl3-(LiCl-KCl) system. In contrast, by AIMD or polarizable ion model (PIM) simulations, a significant deviation regarding the predicted ΔHmix was seen if computed directly from the molecular dynamic trajectories. The integrated experimental and simulation data within the MIVM formalism are generalizable to a wide variety of molten salts and demonstrate a significant improvement over currently employed methods to study molten salts for nuclear and separations sciences. Copyright © 2024, The Authors. All rights reserved.

关键词： Enthalpy

Epidemic dynamics on metapopulation networks with node2vec mobility

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arXiv 2021年

作者： Meng, Lingqi Masuda, Naoki Department of Mathematics State University of New York BuffaloNY14260-2900 United States Computational and Data-Enabled Science and Engineering Program State University of New York BuffaloNY14260-5030 United States Faculty of Science and Engineering Waseda University Tokyo169-8555 Japan

Metapopulation models have been a powerful tool for both theorizing and simulating epidemic dynamics. In a metapopulation model, one considers a network composed of subpopulations and their pairwise connections, and individuals are assumed to migrate from one subpopulation to another obeying a given mobility rule. While how different mobility rules affect epidemic dynamics in metapopulation models has been studied, there have been relatively few efforts on comparison of the effects of simple (i.e., unbiased) random walks and more complex mobility rules. Here we study a susceptible-infectious-susceptible (SIS) dynamics in a metapopulation model, in which individuals obey a parametric second-order random-walk mobility rule called the node2vec. We map the second-order mobility rule of the node2vec to a first-order random walk in a network whose each node is a directed edge connecting a pair of subpopulations and then derive the epidemic threshold. For various networks, we find that the epidemic threshold is large (therefore, epidemic spreading tends to be suppressed) when the individuals infrequently backtrack or infrequently visit the common neighbors of the currently visited and the last visited subpopulations than when the individuals obey the simple random walk. The amount of change in the epidemic threshold induced by the node2vec mobility is in general not as large as, but is sometimes comparable with, the one induced by the change in the diffusion rate for individuals. Copyright © 2021, The Authors. All rights reserved.

关键词： Random processes

Machine-learning-based non-Newtonian fluid model with molecular fidelity

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Physical Review E 2020年第4期102卷 043309-043309页

作者： Huan Lei Lei Wu Weinan E Department of Computational Mathematics Science & Engineering and Department of Statistics & Probability Michigan State University East Lansing Michigan 48824 USA Department of Mathematics and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

We introduce a machine-learning-based framework for constructing continuum a non-Newtonian fluid dynamics model directly from a microscale description. Dumbbell polymer solutions are used as examples to demonstrate the essential ideas. To faithfully retain molecular fidelity, we establish a micro-macro correspondence via a set of encoders for the microscale polymer configurations and their macroscale counterparts, a set of nonlinear conformation tensors. The dynamics of these conformation tensors can be derived from the microscale model, and the relevant terms can be parametrized using machine learning. The final model, named the deep non-Newtonian model (DeePN2), takes the form of conventional non-Newtonian fluid dynamics models, with a generalized form of the objective tensor derivative that retains the microscale interpretations. Both the formulation of the dynamic equation and the neural network representation rigorously preserve the rotational invariance, which ensures the admissibility of the constructed model. Numerical results demonstrate the accuracy of DeePN2 where models based on empirical closures show limitations.

关键词： Learning Neuronal networks Complex fluids Non-Newtonian fluids Rheology Viscoelasticity Multiscale modeling

computational design of anisotropic stealthy hyperuniform composites with engineered directional scattering properties

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Physical Review E 2023年第4期108卷 045306-045306页

作者： Wenlong Shi David Keeney Duyu Chen Yang Jiao Salvatore Torquato Materials Science and Engineering Arizona State University Tempe Arizona 85287 USA Materials Research Laboratory University of California Santa Barbara California 93106 USA Department of Physics Arizona State University Tempe Arizona 85287 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Department of Physics Princeton University Princeton New Jersey 08544 USA Princeton Institute of Materials Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

Disordered hyperuniform materials are an emerging class of exotic amorphous states of matter that endow them with singular physical properties, including large isotropic photonic band gaps, superior resistance to fracture, and nearly optimal electrical and thermal transport properties, to name but a few. Here we generalize the Fourier-space-based numerical construction procedure for designing and generating digital realizations of isotropic disordered hyperuniform two-phase heterogeneous materials (i.e., composites) developed by Chen and Torquato [Acta Mater. 142, 152 (2018)] to anisotropic microstructures with targeted spectral densities. Our generalized construction procedure explicitly incorporates the vector-dependent spectral density function χ̃V(k) of arbitrary form that is realizable. We demonstrate the utility of the procedure by generating a wide spectrum of anisotropic stealthy hyperuniform microstructures with χ̃V(k)=0 for k∈Ω, i.e., complete suppression of scattering in an “exclusion” region Ω around the origin in Fourier space. We show how different exclusion-region shapes with various discrete symmetries, including circular-disk, elliptical-disk, square, rectangular, butterfly-shaped, and lemniscate-shaped regions of varying size, affect the resulting statistically anisotropic microstructures as a function of the phase volume fraction. The latter two cases of Ω lead to directionally hyperuniform composites, which are stealthy hyperuniform only along certain directions and are nonhyperuniform along others. We find that while the circular-disk exclusion regions give rise to isotropic hyperuniform composite microstructures, the directional hyperuniform behaviors imposed by the shape asymmetry (or anisotropy) of certain exclusion regions give rise to distinct anisotropic structures and degree of uniformity in the distribution of the phases on intermediate and large length scales along different directions. Moreover, while the anisotropic exclusion regions

关键词： Amorphous materials Complex materials Simulated annealing

A Human-Centered Design Approach to SOVTE Straw Phonation Instruction

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Journal of Voice 2023年

作者： Bhatt, Sandeep Scearce, Leda Frank-Ito, Dennis Nixon, Tara Umstead, Kelly A. Department of Industrial Design North Carolina State University Raleigh NC United States Department of Head and Neck Surgery & Communication Sciences Duke University School of Medicine Durham NC United States Computational Biology and Bioinformatics Program Duke University Durham NC United States Department of Mechanical Engineering and Materials Science Duke University Durham NC United States

Objectives: Extensive research has demonstrated that straw/tube phonation exercises produce positive effects on the voice quality of the user. The purpose of this study was to explore pedagogical practices employed by a range of voice professionals when using SOVTEs by applying human-centered design approaches to examine workflow and communication between teachers and students. Method/Design: The researchers conducted a series of five participatory role-playing workshop activities at a multi-disciplinary vocology conference that included speech-language pathologists, voice scientists, physicians, singing teachers, acting voice teachers, choral directors, and singers. Volunteers were asked to assume the role of teaching or learning straw phonation exercises. The other participants from each workshop were asked to provide written and verbal feedback regarding the teacher/student dynamics and what they found most important and relevant in terms of best practices for SOVTEs. Expert evaluators subsequently provided similar feedback based on video recordings of the workshops. Results: While there was variability noted in teaching techniques and results, common themes emerged in the analysis. Successful and unsuccessful student and teacher techniques were identified by the workshop participants. Through the video analysis, the research team identified themes in instructional teaching, experiential learning, and straw articulation and mechanics. Conclusions: The benefits of straw/tube phonation exercises on voice quality have been well-established and are clear. As we continue to refine best practices in SOVTEs and, in particular, straw phonation, involvement of experts in HCD as part of multidisciplinary teams may lead to the eventual design of SOVTE tools that provide greater precision, consistency, and effectiveness both in clinical and pedagogical settings, and aid in the differentiation of SOVTE approaches within the taxonomy of vocal habilitation and rehabilitation te

关键词： Voice disorder Voice habilitation Voice pedagogy Voice rehabilitation Voice therapy Voice training

Improving debris flow evacuation alerts in Taiwan using machine learning

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arXiv 2022年

作者： Tsai, Yi-Lin Irvin, Jeremy Chundi, Suhas Ng, Andrew Y. Field, Christopher B. Kitanidis, Peter K. Department of Civil and Environmental Engineering Stanford University StanfordCA United States Department of Computer Science Stanford University StanfordCA United States Woods Institute for the Environment Stanford University StanfordCA United States Interdisciplinary Environmental Studies Program Stanford University StanfordCA United States Department of Earth System Science Stanford University StanfordCA United States Institute for Computational and Mathematical Engineering Stanford University StanfordCA United States

Taiwan has the highest susceptibility to and fatalities from debris flows worldwide. The existing debris flow warning system in Taiwan, which uses a time-weighted measure of rainfall, leads to alerts when the measure exceeds a predefined threshold. However, this system generates many false alarms and misses a substantial fraction of the actual debris flows. Towards improving this system, we implemented five machine learning models that input historical rainfall data and predict whether a debris flow will occur within a selected time. We found that a random forest model performed the best among the five models and outperformed the existing system in Taiwan. Furthermore, we identified the rainfall trajectories strongly related to debris flow occurrences and explored trade-offs between the risks of missing debris flows versus frequent false alerts. These results suggest the potential for machine learning models trained on hourly rainfall data alone to save lives while reducing false alerts. Copyright © 2022, The Authors. All rights reserved.

关键词： Rain

Deep learning inter-atomic potential for thermal and phonon behaviour of silicon carbide with quantum accuracy

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arXiv 2021年

作者： Fu, Baoqin Sun, Yandong Zhang, Linfeng Wang, Han Xu, Ben Key Laboratory of Radiation Physics and Technology of the Ministry of Education Institute of Nuclear Science and Technology Sichuan University Chengdu610064 China Graduate School China Academy of Engineering Physics Beijing100193 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ United States Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Beijing100088 China

Silicon carbide (SiC) is an essential material for next generation semiconductors and components for nuclear plants. It’s applications are strongly dependent on its thermal conductivity, which is highly sensitive to microstructures. Molecular dynamics (MD) simulation is the most used methods to address thermal transportation mechanisms in devices or microstructures of nano-meters. However, the implementation of MD is limited in SiC because of lacking accurate inter-atomic potentials. In this work, using the Deep Potential (DP) methodology, we developed two inter-atomic potentials (DP-*Corresponding author. IAPs) for SiC based on two adaptively generated datasets within the density functional approximations at the local density and the generalized gradient levels. These two DP-IAPs manifest their speed with quantum accuracy in lattice dynamics simulations as well as scattering rate analysis of phonon transportation. Combining with molecular dynamics simulations, the thermal transport and mechanical properties were systematically investigated. The presented methodology and the inter-atomic potentials pave the way for a systematic approach to model heat transport in SiC related devices using multiscale modelling. Copyright © 2021, The Authors. All rights reserved.

关键词： Silicon carbide