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OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

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arXiv 2023年

作者： Eastman, Peter Galvelis, Raimondas Peláez, Raúl P. Abreu, Charlles R.A. Farr, Stephen E. Gallicchio, Emilio Gorenko, Anton Henry, Michael M. Hu, Frank Huang, Jing Krämer, Andreas Michel, Julien Mitchell, Joshua A. Pande, Vijay S. Rodrigues, João P.G.L.M. Rodriguez-Guerra, Jaime Simmonett, Andrew C. Singh, Sukrit Swails, Jason Turner, Philip Wang, Yuanqing Zhang, Ivy Chodera, John D. De Fabritiis, Gianni Markland, Thomas E. Department of Chemistry Stanford University StanfordCA94305 United States Acellera Labs C Dr Trueta 183 Barcelona08005 Spain C Dr. Aiguader 88 Barcelona08003 Spain Chemical Engineering Department School of Chemistry Federal University of Rio de Janeiro Rio de Janeiro68542 Brazil Redesign Science Inc. 180 Varick St. New YorkNY10014 United States EaStCHEM School of Chemistry University of Edinburgh EH9 3FJ United Kingdom Department of Chemistry and Biochemistry Brooklyn College The City University of New York NY United States Ph.D. Program in Chemistry Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New YorkNY United States Stream HPC Koningin Wilhelminaplein 1 - 40601 Amsterdam1062 HG Netherlands Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University 18 Shilongshan Road Zhejiang Hangzhou310024 China Department of Mathematics and Computer Science Freie Universität Berlin Arnimallee 12 Berlin14195 Germany The Open Force Field Initiative Open Molecular Software Foundation DavisCA95616 United States Andreessen Horowitz 2865 Sand Hill Rd Menlo ParkCA94025 United States Department of Structural Biology Stanford University StanfordCA94305 United States Charité Universitätsmedizin Berlin In silico Toxicology and Structural Bioinformatics Virchowweg 6 Berlin10117 Germany Laboratory of Computational Biology National Heart Lung and Blood Institute National Institutes of Health BethesdaMD20892 United States Entos Inc. 9310 Athena Circle La Jolla CA92037 United States College of Engineering Virginia Polytechnic Institute State University BlacksburgVA24061 United States Simons Center for Computational Physical Chemistry Center for Data Science New York University 24 Waverly Place New YorkNY10004 United States T

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features on simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein (GFP) chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations at only a modest increase in cost. Copyright © 2023, The Authors. All rights reserved.

关键词： Machine learning

Using measurement and simulation for understanding distributed development processes in the cloud 17

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Using measurement and simulation for understanding distribut...

27th International Workshop on software Measurement and 12th International Conference on software Process and Product Measurement, IWSM Mensura 2017

作者： Lunesu, Ilaria Marchesi, Michele Münch, Jürgen Kuhrmann, Marco University of Cagliari Department of Electrical and Electronic Engineering Italy University of Cagliari Department of Mathematics and Computer Science Italy Reutlingen University Business Informatics and Herman Hollerith Center Germany Clausthal University of Technology Institute for Applied Software Systems Engineering Germany

ISBN: (纸本)9781450348539

Organizations increasingly develop software in a distributed manner. The Cloud provides an environment to create and maintain software-based products and services. Currently, it is widely unknown which software processes are suited for Cloud-based development and what their effects in specific contexts are. This paper presents a process simulation to study distributed development in the Cloud. We contribute a simulation model, which helps analyzing different project parameters and their impact on projects carried out in the Cloud. The simulator helps reproducing activities, developers, issues and events in the project, and it generates statistics, e.g., on throughput, total time, and lead and cycle time. The aim of this simulation model is thus to analyze the tradeoffs regarding throughput, total time, project size, and team size. Furthermore, the modified simulation model aims to help project managers select the most suitable planning alternative. Based on observed projects in Finland and Spain, we simulated a distributed project using artificial and real data. Particularly, we studied the variables project size, team size, throughput, and total project duration. A comparison of the real project data with the results obtained from the simulation shows the simulation producing results close to the real data, and we could successfully replicate a distributed software project. By improving the understanding of distributed development processes, our simulation model thus supports project managers in their decision-making. © 2017 Association for Computing Machinery.

关键词： Throughput

Conducting Online Lab Experiments with Blockly

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IFAC-PapersOnLine 2017年第1期50卷 13474-13479页

作者： Galan, Daniel Heradio, Ruben de la Torre, Luis Dormido, Sebastian Esquembre, Francisco Dept. of Computer Science and Automatic Control Universidad Nacional de Educación a Distancia Juan del Rosal 16 MadridE-28040 Spain Dept. of Software Engineering and Computer Systems Universidad Nacional de Educación a Distancia Juan del Rosal 16 MadridE-28040 Spain Dept. of Mathematics Universidad de Murcia Campus de Espinardo MurciaE-30071 Spain

Laboratory experimentation plays an essential role in control education. To reduce the high costs of maintaining apparatus in traditional labs and to support distance and blended learning, online laboratories are used as a possible alternative to conventional hands-on labs. In these labs it is often desirable to allow students to define their own experiments. This paper presents the definition and implementation of a generic experimentation language for conducting automatic experiments on existing online laboratories. The main objective is to use an online lab, created independently, as a component in which users can perform experiments. To achieve it, authors present the Experiment Application. It is composed by Blockly, to define and design the experiments, and Google Chart, review and visualize the experiment results. This tool offers benefits to students, teachers and, even, lab designers. For the moment, it can be used with any existing lab or simulation created with the authoring tool Easy Java(script) Simulations. Since there are repositories with hundreds of free available labs created with this tool, the potential applicability of the described tool is considerable. To illustrate the utility of the Experiment Application a very well-known system is used: the Simple Harmonic Oscillator system. © 2017

关键词： computer software Experiments Research laboratories Teaching Blockly Easy java(script) Simulations Experimentation Language Javascript Remote laboratories Virtual laboratories

Random asynchronous iterations in distributed coordination algorithms

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arXiv 2018年

作者： Chen, Yao Xia, Weiguo Cao, Ming Lü, Jinhu Department of Computer Science Southwestern University of Finance and Economics Chengdu611130 China School of Control Science and Engineering Dalian University of Technology Dalian116024 China Faculty of Science and Engineering ENTEG University of Groningen Groningen9747 AG Netherlands School of Automation Science and Electrical Engineering State Key Laboratory of Software Development Environment Beijing Advanced Innovation Center for Big Data and Brain Computing Beihang University Beijing100191 China Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing100190 China

Distributed coordination algorithms (DCA) carry out information processing processes among a group of networked agents without centralized information fusion. Though it is well known that DCA characterized by an SIA (stochastic, indecomposable, aperiodic) matrix generate consensus asymptotically via synchronous iterations, the dynamics of DCA with asynchronous iterations have not been studied extensively, especially when viewed as stochastic processes. This paper aims to show that for any given irreducible stochastic matrix, even non-SIA, the corresponding DCA lead to consensus successfully via random asynchronous iterations under a wide range of conditions on the transition probability. Particularly, the transition probability is neither required to be independent and identically distributed, nor characterized by a Markov chain. Copyright © 2018, The Authors. All rights reserved.

关键词： Stochastic systems

Joint product numerical range and geometry of reduced density matrices

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science China(Physics,Mechanics & Astronomy) 2017年第2期60卷 9-17页

作者： Jianxin Chen Cheng Guo Zhengfeng Ji Yiu-Tung Poon Nengkun YU Bei Zeng Jie Zhou Joint Center for Quantum Information and Computer Science University of Maryland College Park 20740 USA Institute for Advanced Study Tsinghua University Beijing 100084 China Centre for Quantum Computation ＆ Intelligent Systems School of Software Faculty of Engineering and Information Technology University of Technology Sydney Sydney 2007 Australia State Key Laboratory of Computer Science.Institute of Software Chinese Academy of Sciences Beijing 100084 China Department of Mathematics Iowa State University Ames 50011-2140 USA Institute for Quantum Computing University of Waterloo Waterloo N2L 3G1 Canada Department of Mathematics ＆ Statistics University of Guelph Guelph N1G 2 W1 Canada Perimeter Institute for Theoretical Physics Waterloo N2L 2Y5 Canada

The reduced density matrices of a many-body quantum system form a convex set, whose three-dimensional projection is convex in R3. The boundary of may exhibit nontrivial geometry, in particular ruled surfaces. Two physical mechanisms are known for the origins of ruled surfaces： symmetry breaking and gapless. In this work, we study the emergence of ruled surfaces for systems with local Hamiltonians in infinite spatial dimension, where the reduced density matrices are known to be separable as a consequence of the quantum de Finetti＇s theorem. This allows us to identify the reduced density matrix geometry with joint product numerical range II of the Hamiltonian interaction terms. We focus on the case where the interaction terms have certain structures, such that a ruled surface emerges naturally when taking a convex hull of ∏. We show that, a ruled surface on sitting in ∏ has a gapless origin, otherwise it has a symmetry breaking origin. As an example, we demonstrate that a famous ruled surface, known as the oloid, is a possible shape of , with two boundary pieces of symmetry breaking origin separated by two gapless lines.

关键词： reduced density matrices quantum tomography numerical range quantum information oloid ruled surface

Sparse weighted canonical correlation analysis

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arXiv 2017年

作者： Min, Wenwen Liu, Juan Zhang, Shihua State Key Laboratory of Software Engineering School of Computer Wuhan University National Center for Mathematics and Interdisciplinary Sciences Academy of Mathematics and Systems Science Chinese Academy of Sciences School of Mathematics Sciences University of Chinese Academy of Sciences

Given two data matrices X and Y, Sparse canonical correlation analysis (SCCA) is to seek two sparse canonical vectors u and v to maximize the correlation between Xu and Y v. However, classical and sparse CCA models consider the contribution of all the samples of data matrices and thus cannot identify an underlying specific subset of samples. To this end, we propose a novel Sparse weighted canonical correlation analysis (SWCCA), where weights are used for regularizing different samples. We solve the L0-regularized SWCCA (L0-SWCCA) using an alternating iterative algorithm. We apply L0-SWCCA to synthetic data and real-world data to demonstrate its effectiveness and superiority compared to related methods. Lastly, we consider also SWCCA with different penalties like LASSO (Least absolute shrinkage and selection operator) and Group LASSO, and extend it for integrating more than three data matrices. Copyright © 2017, The Authors. All rights reserved.

关键词： Iterative methods

Physical origins of ruled surfaces on the reduced density matrices geometry

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science China(Physics,Mechanics & Astronomy) 2017年第2期60卷 1-8页

作者： Ji-Yao Chen Zhengfeng Ji Zheng-Xin Liu Xiaofei Qi Nengkun Yu Bei Zeng Duanlu Zhou State Key Laboratory of Low Dimensional Quantum Physics Department of Physics Tsinghua University Beijing 100084 China Perimeter Institute for Theoretical Physics Waterloo N2L 2Y5 Canada Centre for Quantum Computation ＆ Intelligent Systems School of Software Faculty of Engineering and Information Technology University of Technology Sydney Sydney 2007 Australia State Key Laboratory of Computer Science Institute of Software Chinese Academy of Sciences Beijing 100190 China Department of Physics Renmin University of China Beijing 100872 China Department of Mathematics Shanxi University Taiyuan 030000 China Institute for Quantum Computing University of Waterloo Waterloo N2L 3G1 Canada Department of Mathematics ＆ Statistics University of Guelph Guelph N1G 2W1 Canada Institute of Physics Chinese Academy of Sciences Beijing 100190 China

The reduced density matrices （RDMs） of many-body quantum states form a convex set. The boundary of low dimensional projections of this convex set may exhibit nontrivial geometry such as ruled surfaces. In this paper, we study the physical origins of these ruled surfaces for bosonic systems. The emergence of ruled surfaces was recently proposed as signatures of symmetry- breaking phase. We show that, apart from being signatures of symmetry-brealdng, ruled surfaces can also be the consequence of gapless quantum systems by demonstrating an explicit example in terms of a two-mode Ising model. Our analysis was largely simplified by the quantum de Finetti＇s theorem--in the limit of large system size, these RDMs are the convex set of all the symmetric separable states. To distinguish ruled surfaces originated from gapless systems from those caused by symmetry- breaking, we propose to use the finite size scaling method for the corresponding geometry. This method is then applied to the two-mode XY model, successfully identifying a ruled surface as the consequence of gapless systems.

关键词： ruled surfaces reduced density matrices bosonic system geometry

Achieving adaptation for adaptive systems via runtime verification: A model-driven approach

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arXiv 2017年

作者： Yang, Zhuoqun Jin, Zhi Li, Zhi Institute of Mathematics Academy of Mathematics and Systems Science Chinese Academy of Sciences Haidian Dstr. Beijing100190 China Peking University Haidian Dstr. Beijing100871 China Software Engineering Dept. College of Computer Science and Information Technology Guangxi Normal University Guilin Guangxi541004 China

Self-adaptive systems (SASs) are capable of adjusting its behavior in response to meaningful changes in the operational context and itself. The adaptation needs to be performed automatically through self-managed reactions and decision-making processes at runtime. To support this kind of automatic behavior, SASs must be endowed by a rich runtime support that can detect requirements violations and reason about adaptation decisions. Requirements engineering for SASs primarily aims to model adaptation logic and mechanisms. Requirements models will guide the design decisions and runtime behaviors of system-to-be. This paper proposes a model-driven approach for achieving adaptation against non-functional requirements (NFRs), i.e. reliability and performances. The approach begins with the models in RE stage and provides runtime support for self-adaptation. We capture adaptation mechanisms as graphical elements in the goal model. By assigning reliability and performance attributes to related system tasks, we derive the tagged sequential diagram for specifying the reliability and performances of system behaviors. To formalize system behavior, we transform the requirements model to the corresponding behavior model, expressed by Label Transition systems (LTS). To analyze the reliability requirements and performance requirements, we merged the sequential diagram and LTS to a variable Discrete-Time Markov Chains (DTMC) and a variable Continuous-Time Markov Chains (CTMC) respectively. Adaptation candidates are characterized by the variable states. The optimal decision is derived by verifying the concerned NFRs and reducing the decision space. Our approach is implemented through the demonstration of a mobile information *** Codes 68N30 Copyright © 2017, The Authors. All rights reserved.

关键词： Adaptive systems

Classification and retrieval of digital pathology scans: A new dataset

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arXiv 2017年

作者： Babaie, Morteza Kalra, Shivam Sriram, Aditya Mitcheltree, Christopher Zhu, Shujin Khatami, Amin Rahnamayan, Shahryar Tizhoosh, H.R. KIMIA Lab University of Waterloo Canada Mathematics and Computer Science Amirkabir University Tehran Iran Electrical and Computer Engineering University of Waterloo Canada School of Electronic & Optical Eng. Nanjing University of Science & Technology Jiangsu China Institute for Intelligent Systems Research and Innovation Deakin University Australia Electrical Computer and Software Engineering University of Ontario Institute of Technology Oshawa Canada

In this paper, we introduce a new dataset, Kimia Path24, for image classification and retrieval in digital pathology. We use the whole scan images of 24 different tissue textures to generate 1,325 test patches of size 1000×1000 (0.5mm×0.5mm). Training data can be generated according to preferences of algorithm designer and can range from approximately 27,000 to over 50,000 patches if the preset parameters are adopted. We propose a compound patch- and-scan accuracy measurement that makes achieving high accuracies quite challenging. In addition, we set the benchmarking line by applying LBP, dictionary approach and convolutional neural nets (CNNs) and report their results. The highest accuracy was 41.80% for CNN. Copyright © 2017, The Authors. All rights reserved.

关键词： Classification (of information)