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Theoretical study on adsorption and reaction of polymeric formic acid on the Cu(111) surface

Physical Review Materials 2021年第7期5卷 075801-075801页

作者： Septia Eka Marsha Putra Fahdzi Muttaqien Yuji Hamamoto Kouji Inagaki Akitoshi Shiotari Jun Yoshinobu Yoshitada Morikawa Ikutaro Hamada Department of Precision Engineering Graduate School of Engineering Osaka University 2-1 Yamada-oka Suita Osaka 565-0871 Japan Department of Engineering Physics Institut Teknologi Sumatera Jalan Terusan Ryacudu Way Hui Jati Agung South Lampung 35365 Indonesia Instrumentation and Computational Physics Research Group Faculty of Mathematics and Natural Sciences Institut Teknologi Bandung Jalan Ganesha 10 Bandung West Java 40132 Indonesia Master Program in Computational Science Faculty of Mathematics and Natural Sciences Institut Teknologi Bandung Jalan Ganesha 10 Bandung West Java 40132 Indonesia Elements Strategy Initiative for Catalysts and Batteries (ESICB) Kyoto University Goryo-Ohara Nishikyou-ku Katsura Kyoto 615-8245 Japan Department of Advanced Materials Science The University of Tokyo 5-1-5 Kashiwanoha Kashiwa Chiba 277-8561 Japan The Institute for Solid State Physics The University of Tokyo 5-1-5 Kashiwanoha Kashiwa Chiba 277-8581 Japan Research Center for Precision Engineering Graduate School of Engineering Osaka University 2-1 Yamada-oka Suita Osaka 565-0871 Japan

We investigate the polymeric adsorption of formic acid (HCOOH) on the Cu(111) surface by means of density functional theory. We present structural models for the polymeric form of HCOOH on Cu(111) and characterize their stability, electronic, and vibrational properties. Based on the energetics and dynamics, as well as simulated scanning tunneling microscopy and atomic force microscopy images, we propose that the α polymorph is likely to be formed on the Cu(111) surface and can explain the experimental findings. We also study the initial step of the catalytic dehydrogenation of HCOOH and find that the O-H bond dissociation at the edge of the polymer is facilitated, rather than that forming hydrogen bonding, agreeing well with the experiments.

关键词： Adsorption Chemical bonding Chemical kinetics, dynamics & catalysis Electronic structure Surface & interfacial phenomena Surfaces Density functional theory First-principles calculations

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DeePMD-kit v2: A software package for Deep Potential models

arXiv

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arXiv 2023年

作者： Zeng, Jinzhe Zhang, Duo Lu, Denghui Mo, Pinghui Li, Zeyu Chen, Yixiao Rynik, Marián Huang, Li'ang Li, Ziyao Shi, Shaochen Wang, Yingze Ye, Haotian Tuo, Ping Yang, Jiabin Ding, Ye Li, Yifan Tisi, Davide Zeng, Qiyu Bao, Han Xia, Yu Huang, Jiameng Muraoka, Koki Wang, Yibo Chang, Junhan Yuan, Fengbo Bore, Sigbjørn Løland Cai, Chun Lin, Yinnian Wang, Bo Xu, Jiayan Zhu, Jia-Xin Luo, Chenxing Zhang, Yuzhi Goodall, Rhys E.A. Liang, Wenshuo Singh, Anurag Kumar Yao, Sikai Zhang, Jingchao Wentzcovitch, Renata Han, Jiequn Liu, Jie Jia, Weile York, Darrin M. Weinan, E. Car, Roberto Zhang, Linfeng Wang, Han Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China College of Electrical and Information Engineering Hunan University Changsha China Yuanpei College Peking University Beijing100871 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ08540 United States Department of Experimental Physics Comenius University Mlynská Dolina F2 Bratislava842 48 Slovakia Center for Quantum Information Institute for Interdisciplinary Information Sciences Tsinghua University Beijing100084 China Center for Data Science Peking University Beijing100871 China ByteDance Research Zhonghang Plaza No. 43 North 3rd Ring West Road Haidian District Beijing China College of Chemistry and Molecular Engineering Peking University Beijing100871 China Baidu Inc. Beijing China Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University Zhejiang Hangzhou China Westlake AI Therapeutics Lab Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Hangzhou China Department of Chemistry Princeton University PrincetonNJ08544 United States SISSA Scuola Internazionale Superiore di Studi Avanzati Trieste34136 Italy Laboratory of Computational Science and Modeling Institute of Materials École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Department of Physics National University of Defense Technology Hunan Changsha410073 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China School of Electronics Engineerin

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments. © 2023, CC BY-NC-ND.

关键词： Molecular dynamics

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Concurrency measures in the era of temporal network epidemiology: A review

arXiv

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arXiv 2020年

作者： Masuda, Naoki Miller, Joel C. Holme, Petter Department of Mathematics State University of New York Buffalo United States Computational and Data-Enabled Science and Engineering Program State University of New York Buffalo United States School of Engineering and Mathematical Sciences La Trobe University Australia Institute of Innovative Research Tokyo Institute of Technology Yokohama226-8503 Japan

Diseases spread over temporal networks of interaction events between individuals. Structures of these temporal networks hold the keys to understanding epidemic propagation. One early concept of the literature to aid in discussing these structures is concurrency-quantifying individuals' tendency to form time-overlapping "partnerships". Although conflicting evaluations and an overabundance of operational definitions have marred the history of concurrency, it remains important, especially in the area of sexually transmitted infections. Today, much of theoretical epidemiology uses more direct models of contact patterns, and there is an emerging body of literature trying to connect methods to the concurrency literature. In this review, we will cover the development of the concept of concurrency and these new approaches. © 2020, CC BY.

关键词： Epidemiology

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Effective Elastic Wave Characteristics of Composite Media

arXiv

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arXiv 2020年

作者： Kim, Jaeuk Torquato, S. Department of Physics Princeton University PrincetonNJ08544 United States Department of Chemistry Princeton University PrincetonNJ08544 United States Princeton Institute for the Science and Technology of Materials Princeton University PrincetonNJ08544 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

We derive exact expressions for effective elastodynamic properties of two-phase composites in the long-wavelength (quasistatic) regime via homogenized constitutive relations that are local in space. This is accomplished by extending the "strong-contrast" expansion formalism that was previously applied to the static problem. These strong-contrast expansions explicitly incorporate complete microstructural information of the composite via an infinite set of n-point correlation functions. Utilizing the rapid-convergence properties of these series expansions (even for extreme contrast ratios), we extract accurate approximations that depend on the microstructure via the spectral density, which is easy to compute or measure for any composite. We also investigate the predictive power of modifications of such approximation formulas postulated elsewhere [J. Kim and S. Torquato, Proc. Nat. Acad. Sci. 117, 8764 (2020)] to extend their applicability beyond the quasistatic regime. The accuracy of these nonlocal microstructure-dependent approximations is validated by comparison to full-waveform simulation results for certain models of dispersions. We apply our formulas to a variety of models of nonhyperuniform and hyperuniform disordered composites. We demonstrate that hyperuniform systems are less lossy than their nonhyperuniform counterparts in the quasistatic regime, and stealthy hyperuniform media can be perfectly transparent for a wide range of wavenumbers. Finally, we discuss how to utilize our approximations for engineering composites with prescribed elastic wave characteristics. Copyright © 2020, The Authors. All rights reserved.

关键词： Microstructure

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Quantum phase transitions in long-range interacting hyperuniform spin chains in a transverse field

arXiv

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arXiv 2020年

作者： Bose, Amartya Torquato, Salvatore Department of Chemistry Princeton University PrincetonNJ08544 United States Department of Physics Princeton University PrincetonNJ08544 United States Princeton Institute for the Science and Technology of Materials Princeton University PrincetonNJ08544 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

Hyperuniform states of matter are characterized by anomalous suppression of long-wavelength density fluctuations. While most of the interesting cases of disordered hyperuniformity are provided by complex many-body systems like liquids or amorphous solids, classical spin chains with certain long-range interactions have been shown to demonstrate the same phenomenon. Such systems involving spin chains are ideal models for exploring the effects of quantum mechanics on hyperuniformity. It is well-known that the transverse field Ising model shows a quantum phase transition (QPT) at zero temperature. Under the quantum effects of a transverse magnetic field, classical hyperuniform spin chains are expected to lose their hyperuniformity. High-precision simulations of these cases are complicated because of the presence of highly nontrivial long-range interactions. We perform extensive analysis of these systems using density matrix renormalization group (DMRG) to study the possibilities of phase transitions and the mechanism by which they lose hyperuniformity. Even for a spin chain of length 30, we see discontinuous changes in properties like the "τ order metric" of the ground state, the measure of hyperuniformity and the second cumulant of the total magnetization along the x-direction, all suggestive of first-order QPTs. An interesting feature of the phase transitions in these disordered hyperuniform spin chains is that, depending on the parameter values, the presence of transverse magnetic field may remarkably lead to increase in the order of the ground state as measured by the "τ order metric," even if hyperuniformity is lost. Therefore, it would be possible to design materials to target specific novel quantum behaviors in the presence of a transverse magnetic field. Our numerical investigations suggest that these spin chains can show no more than two QPTs. We further analyze the long-range interacting spin chains via the Jordan-Wigner mapping on to a system of spinless ferm

关键词： Phase transitions

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Nonlocal effective electromagnetic wave characteristics of composite media: Beyond the quasistatic regime

arXiv

引用

arXiv 2020年

作者： Torquato, Salvatore Kim, Jaeuk Department of Physics Princeton University PrincetonNJ08544 United States Department of Chemistry Princeton University PrincetonNJ08544 United States Princeton Institute Science and Technology of Materials Princeton University PrincetonNJ08544 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

We derive exact nonlocal homogenized constitutive relations for the effective electromagnetic wave properties of disordered two-phase composites and metamaterials from first principles. This exact formalism enables us to extend the long-wavelength limitations of conventional homogenization estimates of the effective dynamic dielectric constant tensor Εe(kI, ω) for arbitrary microstructures so that it can capture spatial dispersion well beyond the quasistatic regime (where ω and kI are the frequency and wave vector of the incident radiation). We accomplish this task by deriving nonlocal strong-contrast expansions that exactly account for complete microstructural information (infinite set of n-point correlation functions) and hence multiple scattering to all orders for the range of wave numbers for which our extended homogenization theory applies, i.e., 0 ≤ |kI|. 1 (where is a characteristic heterogeneity length scale). Because of the fast-convergence properties of such expansions, their lower-order truncations yield accurate closed-form approximate formulas for Εe(kI, ω) that apply for a wide class of microstructures. These nonlocal formulas are resummed representations of the strong-contrast expansions that still accurately capture multiple scattering to all orders via the microstructural information embodied in the spectral density, which is easy to compute for any composite. The accuracy of these microstructure-dependent approximations is validated by comparison to full-waveform simulation computations for both 2D and 3D ordered and disordered models of composite media. Thus, our closed-form formulas enable one to predict accurately and efficiently the effective wave characteristics well beyond the quasistatic regime for a wide class of composite microstructures without having to perform full-blown simulations. We find that disordered hyperuniform media are generally less lossy than their nonhyperuniform counterparts. We also show that certain disordered hyperunif

关键词： Microstructure

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Characterizing the hyperuniformity of ordered and disordered two-phase media

arXiv

引用

arXiv 2020年

作者： Kim, Jaeuk Torquato, Salvatore Department of Physics Princeton University PrincetonNJ08544 United States Department of Chemistry Princeton University PrincetonNJ08544 United States Princeton Institute for the Science and Technology of Materials Princeton University PrincetonNJ08544 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

The hyperuniformity concept provides a unified means to classify all perfect crystals, perfect quasicrystals, and exotic amorphous states of matter according to their capacity to suppress large-scale density fluctuations. While the classification of hyperuniform point configurations has received considerable attention, much less is known about the classification of hyperuniform heterogeneous two-phase media, which include composites, porous media, foams, cellular solids, colloidal suspensions and polymer blends. The purpose of this article is to begin such a program for certain two-dimensional models of hyperuniform two-phase media by ascertaining their local volume-fraction variances σV2 (R) and the associated hyperuniformity order metrics BV . This is a highly challenging task because the geometries and topologies of the phases are generally much richer and more complex than point-configuration arrangements and one must ascertain a broadly applicable length scale to make key quantities dimensionless. Therefore, we purposely restrict ourselves to a certain class of two-dimensional periodic cellular networks as well as periodic and disordered/irregular packings, some of which maximize their effective transport and elastic properties. Among the cellular networks considered, the honeycomb networks have the minimal value of the hyperuniformity order metrics BV across all volume fractions. On the other hand, among all packings considered, the triangular-lattice packings have the smallest values of BV for the possible range of volume fractions. Among all structures studied here, the triangular-lattice packing has the minimal order metric for almost all volume fractions. Our study provides a theoretical foundation for the establishment of hyperuniformity order metrics for general two-phase media and a basis to discover new hyperuniform two-phase systems by inverse design procedures. Copyright © 2020, The Authors. All rights reserved.

关键词： Wireless networks

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Investigating the sources of variable impact of pathogenic variants in monogenic metabolic conditions

引用

Nature Communications 2025年第1期16卷 1-13页

作者： Wei, Angela Border, Richard Fu, Boyang Cullina, Sinéad Brandes, Nadav Jang, Seon-Kyeong Sankararaman, Sriram Kenny, Eimear E. Udler, Miriam S. Ntranos, Vasilis Zaitlen, Noah Arboleda, Valerie A. Interdepartmental Bioinformatics Program UCLA Los Angeles CA United States Department of Pathology and Laboratory Medicine David Geffen School of Medicine UCLA Los Angeles CA United States Department of Computational Medicine David Geffen School of Medicine UCLA Los Angeles CA United States Department of Human Genetics David Geffen School of Medicine UCLA Los Angeles CA United States Department of Computer Science UCLA Los Angeles CA United States Department of Neurology David Geffen School of Medicine UCLA Los Angeles CA United States Institute for Genomic Health Icahn School of Medicine at Mount Sinai New York NY United States Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai New York NY United States Department of Epidemiology & Biostatistics UCSF San Francisco CA United States Department of Bioengineering & Therapeutic Sciences (HIVE) UCSF San Francisco CA United States Bakar Computational Health Sciences Institute UCSF San Francisco CA United States Division of Genomic Medicine Department of Medicine Icahn School of Medicine at Mount Sinai New York NY United States Center for Translational Genomics Icahn School of Medicine at Mount Sinai New York NY United States Center for Genomic Medicine Massachusetts General Hospital Boston MA United States The Broad Institute Boston MA United States

Over three percent of people carry a dominant pathogenic variant, yet only a fraction of carriers develop disease. Disease phenotypes from carriers of variants in the same gene range from mild to severe. Here, we investigate underlying mechanisms for this heterogeneity: variable variant effect sizes, carrier polygenic backgrounds, and modulation of carrier effect by genetic background (marginal epistasis). We leveraged exomes and clinical phenotypes from the UK Biobank and the Mt. Sinai BioMe Biobank to identify carriers of pathogenic variants affecting cardiometabolic traits. We employed recently developed methods to study these cohorts, observing strong statistical support and clinical translational potential for all three mechanisms of variable carrier penetrance and disease severity. For example, scores from our recent model of variant pathogenicity were tightly correlated with phenotype amongst clinical variant carriers, they predicted effects of variants of unknown significance, and they distinguished gain- from loss-of-function variants. We also found that polygenic scores modify phenotypes amongst pathogenic carriers and that genetic background additionally alters the effects of pathogenic variants through interactions. © The Author(s) 2025.

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A Parallel RatSlam C++ Library Implementation 2nd

A Parallel RatSlam C++ Library Implementation

引用

2nd Latin American Workshop on computational Neuroscience, LAWCN 2019

作者： de Souza Muñoz, Mauro Enrique Menezes, Matheus Chaves de Freitas, Edison Pignaton Cheng, Sen de Almeida Neto, Areolino de Oliveira, Alexandre César Muniz de Almeida Ribeiro, Paulo Rogério Federal University of Maranhão Av. dos Portugueses 1966 Bacanga São LuísMaranhão Brazil Graduate Program on Computer Science Federal University of Rio Grande do Sul Porto Alegre Brazil Computational Neuroscience Institute for Neural Computation Ruhr University Bochum Bochum Germany

ISBN: (纸本)9783030366353

RatSlam is a bio-inspired Simultaneous Location and Mapping (SLAM) algorithm used for autonomous mobile robots navigation tasks. This work presents a RatSlam algorithm implementation as a C++ library designed to take advantage of internal RatSlam modules parallelization. The RatSlam algorithm is presented with principal aspects of the library architecture design. Furthermore, its results using a well known RatSlam data set with a standard RatSlam implementation (OpenRatSLAM - Robot Operating System), and a Python implementation. The mapping found with the previous approaches and the proposed on this work were similar. Moreover, the execution times between the OpenRatSLAM and this C++ library was compared, with the proposed implementation having a lower execution time. Thus, the current implementation was validated and has some advantages against previous ones, which can be very relevant for real-time applications. © Springer Nature Switzerland AG 2019.

关键词： Robot Operating System

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Nearest-neighbor functions for disordered stealthy hyperuniform many-particle systems

arXiv

引用

arXiv 2020年

作者： Middlemas, Timothy M. Torquato, Salvatore Department of Chemistry Princeton University PrincetonNJ08544 United States Department of Physics Princeton University PrincetonNJ08544 United States Princeton Institute for the Science and Technology of Materials Princeton University PrincetonNJ08544 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

Disordered stealthy many-particle systems in d-dimensional Euclidean space Rd are exotic amorphous states of matter that suppress any single scattering events for a finite range of wavenumbers around the origin in reciprocal space. They are currently the subject of intense fundamental and practical interest. We derive analytical formulas for the nearest-neighbor functions of disordered stealthy many-particle systems. First, we analyze asymptotic small-r approximations and expansions of the nearest-neighbor functions based on the pseudo-hard-sphere ansatz. We then consider the problem of determining how many of the standard n-point correlation functions are needed to determine the nearest neighbor functions, and find that a finite number suffice. Via theoretical and computational methods, we are able to compare the large-r behavior of these functions for disordered stealthy systems to those belonging to crystalline lattices. Such ordered and disordered stealthy systems have bounded hole sizes, and thus compact support for their nearest-neighbor functions. However, we find that the approach to the critical-hole size can be quantitatively different, emphasizing the importance of hole statistics in distinguishing ordered and disordered stealthy configurations. We argue that the probability of finding a hole close to the critical-hole size should decrease as a power law with an exponent only dependent on the space dimension d for ordered systems, but that this probability decays asymptotically faster for disordered systems, with either an increase in the exponent of the power law or a crossover into a decay faster than any power law. This implies that holes close to the critical-hole size are rarer in disordered systems. The rarity of observing large holes in disordered systems creates substantial numerical difficulties in sampling the nearest neighbor distributions near the critical-hole size. This motivates both the need for new computational methods for efficient samp

关键词： computational methods

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