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Assessment of scoring functions for computational models of protein-protein interfaces

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arXiv 2024年

作者： Sumner, Jacob Meng, Grace Brandt, Naomi Grigas, Alex T. Córdoba, Andrés 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 Chemistry Yale University New HavenCT06520 United States Department of Physics Yale University New HavenCT06520 United States Department of Chemistry Duke University DurhamNC27708 United States Department of Physics Duke University DurhamNC27708 United States Benjamin Levich Institute Physics Department City College of New York New YorkNY10031 United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States

A goal of computational studies of protein-protein interfaces (PPIs) is to predict the binding site between two monomers that form a heterodimer. The simplest version of this problem is to rigidly re-dock the bound forms of the monomers, which involves generating computational models of the heterodimer and then scoring them to determine the most native-like models. Scoring functions have been assessed previously using rank- and classification-based metrics, however, these methods are sensitive to the number and quality of models in the scoring function training set. We assess the accuracy of seven PPI scoring functions by comparing their scores to a measure of structural similarity to the x-ray crystal structure (i.e. the DockQ score) for a non-redundant set of heterodimers from the Protein Data Bank. For each heterodimer, we generate re-docked models uniformly sampled over DockQ and calculate the Spearman correlation between the PPI scores and DockQ. For some targets, the scores and DockQ are highly correlated;however, for many targets, there are weak correlations. Several physical features can explain the difference between difficult- and easy-to-score targets. For example, strong correlations exist between the score and DockQ for targets with highly intertwined monomers and many interface contacts. We also develop a new score based on only three physical features that matches or exceeds the performance of current PPI scoring functions. These results emphasize that PPI prediction can be improved by focusing on correlations between the PPI score and DockQ and incorporating more discriminating physical features into PPI scoring functions. © 2024, CC BY.

关键词： Monomers

High-Q unidirectional polarization singularities

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Physical Review applied 2025年第5期23卷 054020-054020页

作者： Chuanlin Li Wenhao Wang Jianfeng Chen Mengqi Liu Aobo Ren Cheng-Wei Qiu Hongxing Xu Zhiming Wang Jiang Wu Institute of Fundamental and Frontier Sciences University of Electronic Science and Technology of China Chengdu 610054 China Division of Physics and Applied Physics School of Physical and Mathematical Sciences Nanyang Technological University Singapore 637371 Singapore Centre for Disruptive Photonic Technologies The Photonics Institute Nanyang Technological University Singapore 637371 Singapore Department of Electrical and Computer Engineering National University of Singapore Singapore 117583 Singapore Institute of Engineering Thermophysics School of Mechanical Engineering Shanghai Jiao Tong University Shanghai 200240 China School of Physics and Technology Center for Nanoscience and Nanotechnology and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education Wuhan University Wuhan 430072 China

Unidirectional guided resonances (UGRs), which are eigenstates that radiate exclusively in a single channel, are promising for advancing diverse photonic devices. However, existing approaches face an inherent trade-off between achieving high-Q factors and maximizing the radiation-asymmetry ratios. To address this challenge, we propose a scheme that exploits both out-of-plane and in-plane couplings to generate bound states in the continuum with precise radial and rotational control in momentum space. This approach effectively decouples the Q factors of UGRs from their radiation-asymmetry ratios. As a result, we achieve UGRs with Q factors exceeding 104, which is 1–2 orders of magnitude higher than traditional UGRs. Furthermore, we demonstrate the ability to reverse the emission direction of these UGRs, leading to a broad range of radiation-asymmetry ratios from −53 to 55 dB. We further validate the practical realization of high-Q UGRs using a silicon-on-silica system. Our findings provide a versatile method for generating high-Q UGRs, offering alternative pathways for innovations in nonlinear optics, light-matter interactions, and advanced optoelectronic applications.

关键词： Nonlinear optics

A Pretraining-Finetuning Computational Framework for Material Homogenization

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arXiv 2024年

作者： Wang, Yizheng Li, Xiang Yan, Ziming Ma, Shuaifeng Bai, Jinshuai Liu, Bokai Rabczuk, Timon Liu, Yinghua Zhuang, Xiaoying Department of Engineering Mechanics Tsinghua University Beijing China School of Information Science and Technology Hainan Normal University Haikou China Institute of Structural Mechanics Bauhaus-Universität Weimar Marienstr. 15 Weimar Germany Institute of Photonics Department of Mathematics and Physics Leibniz University Hannover Germany School of Mechanical Medical and Process Engineering Queensland University of Technology Brisbane Australia Department of Applied Physics and Electronics Umeå University Umea Sweden

Homogenization is a fundamental tool for studying multiscale physical phenomena. Traditional numerical homogenization methods, heavily reliant on finite element analysis, demand significant computational resources, especially for complex geometries, materials, and high-resolution problems. To address these challenges, we propose PreFine-Homo, a novel numerical homogenization framework comprising two phases: pretraining and fine-tuning. In the pretraining phase, a Fourier Neural Operator (FNO) is trained on large datasets to learn the mapping from input geometries and material properties to displacement fields. In the fine-tuning phase, the pretrained predictions serve as initial solutions for iterative algorithms, drastically reducing the number of iterations needed for convergence. The pretraining phase of PreFine-Homo delivers homogenization results up to 1000 times faster than conventional methods, while the fine-tuning phase further enhances accuracy. Moreover, the fine-tuning phase grants PreFine-Homo unlimited generalization capabilities, enabling continuous learning and improvement as data availability increases. We validate PreFine-Homo by predicting the effective elastic tensor for 3D periodic materials, specifically Triply Periodic Minimal Surfaces (TPMS). The results demonstrate that PreFine-Homo achieves high precision, exceptional efficiency, robust learning capabilities, and strong extrapolation ability, establishing it as a powerful tool for multiscale homogenization tasks. Copyright © 2024, The Authors. All rights reserved.

关键词： Iterative methods

Ultra-Cold Cryogenic TEM with Liquid Helium and High Stability

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arXiv 2024年

作者： Rennich, Emily Sung, Suk Hyun Agarwal, Nishkarsh Gates, Maya Kerns, Robert Hovden, Robert Baggari, Ismail El The Rowland Institute at Harvard Harvard University CambridgeMA02142 United States Department of Mechanical Engineering University of Michigan Ann ArborMI48109 United States Department of Materials Science and Engineering University of Michigan Ann ArborMI48109 United States Michigan Center for Materials Char-acterization University of Michigan Ann ArborMI48109 United States Applied Physics Program University of Michigan Ann ArborMI48109 United States

Cryogenic transmission electron microscopy has revolutionized structural biology and materials science, but achieving temperatures below the boiling point of liquid nitrogen remains a long-standing aspiration. We introduce an ultra-cold liquid helium transmission electron microscope specimen holder, featuring continuous cryogen flow and vibration decoupling. This instrument is compatible with modern aberration-corrected microscopes and achieves sub-25 K base temperature, ±2 mK thermal stability over many hours, and atomic resolution—setting the stage for a new era of cryogenic electron microscopy. © 2024, CC BY.

关键词： High resolution transmission electron microscopy

Study of background from accidental coincidence signals in the PandaX-Ⅱexperiment

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Chinese physics C 2022年第10期46卷 11-24页

作者： Abdusalam Abdukerim Wei Chen Xun Chen Yunhua Chen Chen Cheng Xiangyi Cui Yingjie Fan Deqing Fang Changbo Fu Mengting Fu Lisheng Geng Karl Giboni Linhui Gu Xuyuan Guo Ke Han Changda He Di Huang Yan Huang Yanlin Huang Zhou Huang Xiangdong Ji Yonglin Ju Shuaijie Li Huaxuan Liu Jianglai Liu Wenbo Ma Yugang Ma Yajun Mao Yue Meng Kaixiang Ni Jinhua Ning Xuyang Ning Xiangxiang Ren Changsong Shang Lin Si Guofang Shen Andi Tan Anqing Wang Hongwei Wang Meng Wang Qiuhong Wang Siguang Wang Wei Wang Xiuli Wang Zhou Wang Mengmeng Wu Shiyong Wu Weihao Wu Jingkai Xia Mengjiao Xiao Pengwei Xie Binbin Yan Jijun Yang Yong Yang Chunxu Yu Jumin Yuan Ying Yuan Xinning Zeng Dan Zhang Tao Zhang Li Zhao Qibin Zheng Jifang Zhou Ning Zhou Xiaopeng Zhou School of Physics and Astronomy Shanghai Jiao Tong UniversityMOE Key Laboratory for Particle Astrophysics and CosmologyShanghai Key Laboratory for Particle Physics and CosmologyShanghai 200240China Shanghai Jiao Tong University Sichuan Research Institute Chengdu 610213China Yalong River Hydropower Development Company Ltd.288 Shuanglin RoadChengdu 610051China School of Physics Sun Yat-Sen UniversityGuangzhou 510275China Tsung-Dao Lee Institute Shanghai 200240China School of Physics Nankai UniversityTianjin 300071China Key Laboratory of Nuclear Physics and Ion-beam Application(MOE) Institute of Modern PhysicsFudan UniversityShanghai 200433China School of Physics Peking UniversityBeijing 100871China School of Physics Beihang UniversityBeijing 102206China Beijing Key Laboratory of Advanced Nuclear Materials and Physics Beihang UniversityBeijing102206China School of Physics and Microelectronics Zhengzhou UniversityZhengzhouHenan 450001China School of Medical Instrument and Food Engineering University of Shanghai for Science and TechnologyShanghai 200093China Department of Physics University of MarylandCollege ParkMaryland 20742USA School of Mechanical Engineering Shanghai Jiao Tong UniversityShanghai 200240China School of Physics and Key Laboratory of Particle Physics and Particle Irradiation(MOE) Shandong UniversityJinan 250100China Shanghai Institute of Applied Physics Chinese Academy of SciencesShanghai 201800China Shanghai Advanced Research Institute Chinese Academy of SciencesShanghai 201210China Center for High Energy Physics Peking UniversityBeijing 100871China

Ⅰ.INTRODUCTION The direct detection of dark matter particles,especially the weakly interacting massive particles(WIMPs),is being actively carried out by a couple of experiments worldwide[1].In recent years,the PandaX-Ⅱ experiment located in the China Jinping Underground Laboratory(CJPL)[1-3],which uses the technology of dual phase liquid xenon time projection chambers(TPCs),has pushed the limits of the cross section between WIMPs and nucleons to a new level for most of the possible WIMP masses;other experiments of the same type are also being performed[4–10].

关键词： dark matter xenon detector background accidental coincidence machine learning

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

Nonlinear time series computing using a linear optical microcavity

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Optics Express 2025年第12期33卷 24982-24994页

作者： Mengyu You Kohei Arai Satoshi Sunada Department of Applied Physics School of Advanced Science and Engineering Waseda University 3-4-1 Okubo Shinjuku-ku Tokyo 169-8555 Japan mengyuyou@akane.waseda.jp Graduate School of Natural Science and Technology Kanazawa University Kakuma-machi Kanazawa Ishikawa 920-1192 Japan Faculty of Mechanical Engineering Institute of Science and Engineering Kanazawa University Kanazawa Ishikawa 920-1192 Japan sunada@se.kanazawa-u.ac.jp

Photonic systems excel at performing linear computations, such as matrix-vector multiplications, in a highly parallel and energy-efficient manner. However, implementing nonlinear computations in photonic systems remains challenging without relying on optoelectronic conversions or nonlinear/active materials, both of which are energy-intensive. Here, we present a nonlinear computing approach for time series processing. This approach enables energy-efficient and nonlinear computations of large-scale optical networks within a single linear (passive) microcavity by leveraging the interplay between cavity modes and an optical phase-encoded input signal and facilitates an on-chip implementation on a silicon photonic platform. We experimentally demonstrate higher-order nonlinear computational capacity using a silicon photonic microcavity, achieving superior performance in time-dependent processing tasks, such as chaotic time-series prediction and nonlinear observer tasks.

关键词： Integrated photonics Integrating spheres Optical networks Phase modulation Spatial light modulators Vertical cavity surface emitting lasers

Promises and technological prospects of two-dimensional Rashba materials

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arXiv 2024年

作者： Bordoloi, Arjyama Garcia-Castro, A.C. Romestan, Zachary Romero, Aldo H. Singh, Sobhit Department of Mechanical Engineering University of Rochester RochesterNY14627 United States School of Physics Universidad Industrial de Santander Carrera 27 Calle 9 Bucaramanga680002 Colombia Department of Physics and Astronomy West Virginia University MorgantownWV26505-6315 United States Materials Science Program University of Rochester RochesterNY14627 United States

The Rashba spin-orbit coupling effect, primarily arising from structural-inversion asymmetry in periodic crystals, has garnered considerable attention due to its tunability and potential applications in spintronics. Its capability to manipulate electron spin without an external magnetic field opens new avenues for spintronic device design, particularly in semiconductor technology. Within this framework, 2D Rashba materials hold special interest due to their inherent characteristics, which facilitate miniaturization and engineering capabilities. In this Perspective article, we provide an overview of recent advancements in the research of 2D Rashba materials, aiming to offer a comprehensive understanding of the diverse manifestations and multifaceted implications of the Rashba effect in material science. Rather than merely presenting a list of materials, our approach involves synthesizing various viewpoints, assessing current trends, and addressing challenges within the field. Our objective is to bridge the gap between fundamental research and practical applications by correlating each material with the necessary advancements required to translate theoretical concepts into tangible technologies. Furthermore, we highlight promising avenues for future research and development, drawing from insights gleaned from the current state of the field. © 2024, CC BY.

关键词： Magnetic moments

Electroweak, QCD and flavour physics studies with ATLAS data from Run 2 of the LHC

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physics Reports 2025年 1116卷 57-126页

作者： Aad, G. Aakvaag, E. Abbott, B. Abdelhameed, S. Abeling, K. Abicht, N.J. Abidi, S.H. Aboelela, M. Aboulhorma, A. Abramowicz, H. Abreu, H. Abulaiti, Y. Acharya, B.S. Ackermann, A. Adam Bourdarios, C. Adamczyk, L. Addepalli, S.V. Addison, M.J. Adelman, J. Adiguzel, A. Adye, T. Affolder, A.A. Afik, Y. Agaras, M.N. Agarwala, J. Aggarwal, A. Agheorghiesei, C. Ahmad, A. Ahmadov, F. Ahmed, W.S. Ahuja, S. Ai, X. Aielli, G. Aikot, A. Ait Tamlihat, M. Aitbenchikh, B. Akbiyik, M. Åkesson, T.P.A. Akimov, A.V. Akiyama, D. Akolkar, N.N. Aktas, S. Al Khoury, K. Alberghi, G.L. Albert, J. Albicocco, P. Albouy, G.L. Alderweireldt, S. Alegria, Z.L. Aleksa, M. Aleksandrov, I.N. Alexa, C. Alexopoulos, T. Alfonsi, F. Algren, M. Alhroob, M. Ali, B. Ali, H.M.J. Ali, S. Alibocus, S.W. Aliev, M. Alimonti, G. Alkakhi, W. Allaire, C. Allbrooke, B.M.M. Allen, J.F. Allendes Flores, C.A. Allport, P.P. Aloisio, A. Alonso, F. Alpigiani, C. Alsolami, Z.M.K. Alvarez Estevez, M. Alvarez Fernandez, A. Alves Cardoso, M. Alviggi, M.G. Aly, M. Amaral Coutinho, Y. Ambler, A. Amelung, C. Amerl, M. Ames, C.G. Amidei, D. Amirie, K.J. Amor Dos Santos, S.P. Amos, K.R. An, S. Ananiev, V. Anastopoulos, C. Andeen, T. Anders, J.K. Andrean, S.Y. Andreazza, A. Angelidakis, S. Angerami, A. Anisenkov, A.V. Annovi, A. Antel, C. Antipov, E. Antonelli, M. Anulli, F. Aoki, M. Aoki, T. Aparo, M.A. Aperio Bella, L. Appelt, C. Apyan, A. Arbiol Val, S.J. Arcangeletti, C. Arce, A.T.H. Arena, E. Arguin, J.-F. Argyropoulos, S. Arling, J.-H. Arnaez, O. Arnold, H. Artoni, G. Asada, H. Asai, K. Asai, S. Asbah, N.A. Ashby Pickering, R.A. Assamagan, K. Astalos, R. Astrand, K.S.V. Atashi, S. Atkin, R.J. Atkinson, M. Atmani, H. Atmasiddha, P.A. Augsten, K. Auricchio, S. Auriol, A.D. Austrup, V.A. Avolio, G. Axiotis, K. Azuelos, G. Babal, D. Bachacou, H. Bachas, K. Bachiu, A. Backman, F. Badea, A. Baer, T.M. Bagnaia, P. Bahmani, M. Bahner, D. Bai, K. Baines, J.T. Baines, L. Baker, O.K. Bakos, E. Bakshi Gupta, D. Balakrishnan, V. Balasubramanian, R. Baldin, E.M. Balek, P. Ballabene, E. CPPM Aix-Marseille Université CNRS IN2P3 Marseille France Department for Physics and Technology University of Bergen Bergen Norway Homer L. Dodge Department of Physics and Astronomy University of Oklahoma Norman OK United States New York University Abu Dhabi Abu Dhabi United Arab Emirates II. Physikalisches Institut Georg-August-Universität Göttingen Göttingen Germany Fakultät Physik Technische Universität Dortmund Dortmund Germany Physics Department Brookhaven National Laboratory Upton NY United States Physics Department Southern Methodist University Dallas TX United States Faculté des sciences Université Mohammed V Rabat Morocco Raymond and Beverly Sackler School of Physics and Astronomy Tel Aviv University Tel Aviv Israel Department of Physics Technion Israel Institute of Technology Haifa Israel Department of Physics New York University New York NY United States INFN Gruppo Collegato di Udine Sezione di Trieste Udine Italy ICTP Trieste Italy Department of Physics King's College London London United Kingdom Kirchhoff-Institut für Physik Ruprecht-Karls-Universität Heidelberg Heidelberg Germany LAPP Université Savoie Mont Blanc CNRS IN2P3 Annecy France AGH University of Krakow Faculty of Physics and Applied Computer Science Krakow Poland Department of Physics Brandeis University Waltham MA United States School of Physics and Astronomy University of Manchester Manchester United Kingdom Department of Physics Northern Illinois University DeKalb IL United States Department of Physics Istanbul University Istanbul Turkey Particle Physics Department Rutherford Appleton Laboratory Didcot United Kingdom Santa Cruz Institute for Particle Physics University of California Santa Cruz Santa Cruz CA United States Enrico Fermi Institute University of Chicago Chicago IL United States Institut de Física d'Altes Energies (IFAE) Barcelona Institute of Science and Technology Barcelona Spain INFN Sezione di Pavia Italy Dipartimento di Fisica Uni

A summary of precision measurements sensitive to electroweak, QCD and quark-flavour effects performed by the ATLAS Collaboration at the Large Hadron Collider is reported. The measurements are predominantly performed on proton–proton (pp) collision data recorded at a centre-of-mass energy of 13 TeV taken from 2015 to 2018, with an integrated luminosity of up to 140 fb⁻¹, with some results based on pp and Pb+Pb data recorded at lower nucleon centre-of-mass energies. The results cover a wide range of topics, from strong production of particles at low energies and the spectroscopy of hadrons to perturbative QCD with hadronic jets and electroweak and strong production of single and multiple vector bosons. They provide precise measurements of fundamental constants and stringent tests of the Standard Model with unprecedented precision and in energy ranges never explored before. They are also used to explore the proton structure and to perform model-independent searches for new physics. © 2024 CERN for the benefit of the ATLAS Collaboration

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