检索结果-内蒙古大学图书馆

Ab initio phonon transport across grain boundaries in graphene using machine learning based on small dataset

学校读者我要写书评

暂无评论

Physical Review Materials 2022年第4期6卷 044004-044004页

作者： Amirreza Hashemi Ruiqiang Guo Keivan Esfarjani Sangyeop Lee Computational Modeling and Simulation Program University of Pittsburgh Pittsburgh Pennsylvania 15261 USA Department of Mechanical Engineering and Materials Science University of Pittsburgh Pittsburgh Pennsylvania 15261 USA Department of Mechanical and Aerospace Engineering University of Virginia Charlottesville Virginia 22904 USA Department of Materials Science and Engineering University of Virginia Charlottesville Virginia 22904 USA Department of Physics University of Virginia Charlottesville Virginia 22904 USA Department of Physics and Astronomy University of Pittsburgh Pittsburgh Pennsylvania 15261 USA

Establishing the structure-property relationship for grain boundaries (GBs) is critical for developing next-generation functional materials but has been severely hampered due to its extremely large configurational space. Atomistic simulations with low computational cost and high predictive power are strongly desirable, but the conventional simulations using empirical interatomic potentials and density functional theory suffer from the lack of predictive power and high computational cost, respectively. A machine learning interatomic potential (MLIP) recently emerged but often requires extensive size of the training dataset, making it a less feasible approach. Here, we demonstrate that an MLIP trained with a rationally designed small training dataset can predict thermal transport across GBs in graphene with ab initio accuracy at an affordable computational cost. We employed a rational approach based on the structural unit model to find a small set of GBs that can represent the entire configurational space and thus can serve as a cost-effective training dataset for the MLIP. Only 5 GBs were found to be enough to represent the entire configurational space of graphene GBs. Using the atomistic Green's function approach and the MLIP, we revealed that the structure-thermal resistance relation in graphene does not follow the common understanding that large dislocation density causes larger thermal resistance. In fact, thermal resistance is nearly independent of dislocation density at room temperature and is higher when the dislocation density is small at sub-room temperature. We explain this intriguing behavior with the buckling near a GB causing a strong scattering of flexural phonon modes. In this paper, we show that a machine learning technique combined with conventional wisdom (e.g., structural unit model) can extend the recent success of ab initio thermal transport simulation, which has been mostly limited to single crystals, to complex yet practically important polycry

关键词： Phonons Graphene Landauer formula Machine learning

Gumbel-Softmax Flow Matching with Straight-Through Guidance for Controllable Biological Sequence Generation

学校读者我要写书评

暂无评论

arXiv 2025年

作者： Tang, Sophia Zhang, Yinuo Tong, Alexander Chatterjee, Pranam Department of Biomedical Engineering Duke University United States Management and Technology Program University of Pennsylvania United States Center of Computational Biology Duke-NUS Medical School Singapore Mila Quebec AI Institute Canada Université de Montréal Canada Department of Computer Science Duke University United States Department of Biostatistics and Bioinformatics Duke University United States

Flow matching in the continuous simplex has emerged as a promising strategy for DNA sequence design, but struggles to scale to higher simplex dimensions required for peptide and protein generation. We introduce Gumbel-Softmax Flow and Score Matching, a generative framework on the simplex based on a novel Gumbel-Softmax interpolant with a time-dependent temperature. Using this interpolant, we introduce Gumbel-Softmax Flow Matching by deriving a parameterized velocity field that transports from smooth categorical distributions to distributions concentrated at a single vertex of the simplex. We alternatively present Gumbel-Softmax Score Matching which learns to regress the gradient of the probability density. Our framework enables high-quality, diverse generation and scales efficiently to higher-dimensional simplices. To enable training-free guidance, we propose Straight-Through Guided Flows (STGFlow), a classifier-based guidance method that leverages straight-through estimators to steer the unconditional velocity field toward optimal vertices of the simplex. STGFlow enables efficient inference-time guidance using classifiers pre-trained on clean sequences, and can be used with any discrete flow method. Together, these components form a robust framework for controllable de novo sequence generation. We demonstrate state-of-the-art performance in conditional DNA promoter design, sequence-only protein generation, and target-binding peptide design for rare disease treatment. © 2025, CC BY-NC-ND.

关键词： Velocity distribution

Embedding and trajectories of temporal networks

学校读者我要写书评

暂无评论

arXiv 2022年

作者： Thongprayoon, Chanon Livi, Lorenzo Masuda, Naoki Department of Mathematics State University of New York at Buffalo BuffaloNY United States Department of Computer Science University of Manitoba WinnipegMB Canada Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo BuffaloNY United States Faculty of Science and Engineering Waseda University Shinjuku Tokyo Japan

Temporal network data are increasingly available in various domains, and often represent highly complex systems with intricate structural and temporal evolutions. Due to the difficulty of processing such complex data, it may be useful to coarse grain temporal network data into a numeric trajectory embedded in a low-dimensional space. We refer to such a procedure as temporal network embedding, which is distinct from procedures that aim at embedding individual nodes. Temporal network embedding is a challenging task because we often have access only to discrete time-stamped events between node pairs, and, in general, the events occur with irregular intervals, making the construction of the network at a given time a nontrivial question already. We propose a method to generate trajectories of temporal networks embedded in a low-dimensional space given a sequence of time-stamped events as input. We realize this goal by combining the landmark multidimensional scaling, which is an out-of-sample extension of the well-known multidimensional scaling method, and the framework of tie-decay temporal networks. This combination enables us to obtain a continuous-time trajectory describing the evolution of temporal networks. We then study mathematical properties of the proposed temporal network embedding framework. Finally, we showcase the method with empirical data of social contacts to find temporal organization of contact events and loss of them over a single day and across different days. © 2022, CC BY.

关键词： Trajectories

A Method for Automatic Generation of 3D Background Models Using Fractal Models and Genetic Algorithms

学校读者我要写书评

暂无评论

A Method for Automatic Generation of 3D Background Models Us...

International Symposium on Computing and Networking Workshops (CANDARW)

作者： Kaito Watanabe Hirotaka Nakayama Atsushi Shiraki Tomoyoshi Ito Katsumi Hirata Naoto Hoshikawa Advanced Course General Engineering Program National Institute of Technology Oyama College Oyama Japan Center for Computational Astrophysics National Astronomical Observatory of Japan Mitaka Japan Graduate School of Engineering Chiba University Chiba Japan Department of Innovative Electrical and Electronic Engineering National Institute of Technology Oyama College Oyama Japan Graduate School of Science and Tecnology University of Tsukuba Tsukuba Japan

In recent years, 3DCG-related industries have grown rapidly and the demand for 3DCG content has increased. However, 3DCG production requires special skills and a lot of time. In particular, the creation of background data requires a lot of human resources at the production site because the data is huge and complex. Therefore, we propose an automatic creation system that generates 3D background data for 3DCG production. The proposed system consists of three functions: 3D model generation, generation parameter optimization, and fitness evaluation. The user inputs a landscape photograph as idea information into the system, and the system optimizes the generation parameters so that the 3D object shape approximates the input image. To evaluate the accuracy of the system's performance, we observe the optimization process and the 3D object output when a previously generated fractal image or landscape photos are input. Experimental results show that the system accurately optimizes the generation parameters and generates 3D objects that are almost identical to the shape of the fractal image. In addition, the parameters were also optimized with a certain degree of accuracy for landscape photographs for which no specific solution had been determined.

关键词：

Undersampled Magnetic Resonance Image Reconstructions Based on a Combination of U-Nets and L1, L2, and TV Optimizations

学校读者我要写书评

暂无评论

Undersampled Magnetic Resonance Image Reconstructions Based ...

IEEE International Workshop on Imaging Systems and Techniques (IST)

作者： Aline A.S. Thomaz Jonathan A.S. Lima Cristiano J. Miosso Mylé ne C.Q. Farias Andrey S. Krylov Yong Ding Department of Electrical Engineering University of Brasilia (UnB) Brasilia Brazil Biomedical Engineering Graduate Program University of Brasilia (UnB) Brasilia Brazil Faculty of Computational Mathematics and Cybernetics Lomonosov Moscow State University Moscow Russia College of Information Science and Electronic Engineering Zhejiang University Zhejiang China

Magnetic Resonance Imaging (MRI) plays a major role in the diagnosis of several diseases. However, the acquisition of measurements in the k-space domain, which is the basis for image reconstruction, takes a long time compared to other imaging modalities and is comparatively costly. In this context, undersampled MRI reconstruction is an approach for decreasing the acquisition duration and the exam's final cost. With this objective, both Compressed Sensing (CS) and Deep Learning (DL) provide techniques for generating good quality MRI images from undersampled measurements. In this paper, we combine CS and DL methods in order to investigate the potential increase in image quality over each isolated approach. We use reconstructions from from highly undersampled MRI signals using two CS approaches, the L1 and total minimizations, as inputs to a U-Net. We also use, for comparison, the reconstructions from the same undersampled signals using L2 minimization, and also test them as inputs to a U-net. The goal is to evaluate whether the the U-Net can improve the results of the CS reconstructions after learning from degraded and original image pairs. Our experimental results suggest that the combination of L1 or TV minimization with U-Nets can improve reconstruction, in terms of objective image quality, over each technique used in isolation.

关键词： Image quality TV Magnetic resonance imaging Magnetic resonance Minimization Time measurement Sensors

On Time Uniform Wong-Zakai Approximation Theorems

学校读者我要写书评

暂无评论

arXiv 2023年

作者： Del Moral, Pierre Hu, Shulan Jasra, Ajay Ruzayqat, Hamza Wang, Xinyu Institut de Mathematiques de Bordeaux Bordeaux33405 France School of Statistics and Mathematics Zhongnan University of Economics and Law China Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Wenlan School of Business Zhongnan University of Economics and Law China

We consider the long time behavior of Wong-Zakai approximations of stochastic differential equations. These piecewise smooth diffusion approximations are of great importance in many areas, such as those with ordinary differential equations associated to random smooth fluctuations;e.g. robust filtering problems. In many examples, the mean error estimate bounds that have been derived in the literature can grow exponentially with respect to the time horizon. We show in a simple example that indeed mean error estimates do explode exponentially in the time parameter, i.e. in that case a Wong-Zakai approximation is only useful for extremely short time intervals. Under spectral conditions, we present some quantitative time-uniform convergence theorems, i.e. time-uniform mean error bounds, yielding what seems to be the first results of this type for Wong-Zakai diffusion *** Codes 60H35(Primary), 65C30(Secondary) Copyright © 2023, The Authors. All rights reserved.

关键词： Brownian movement

Artificial neural network approach for turbulence models: A local framework

学校读者我要写书评

暂无评论

Physical Review Fluids 2021年第8期6卷 084612-084612页

作者： Chenyue Xie Xiangming Xiong Jianchun Wang Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA Department of Mechanics and Aerospace Engineering Southern University of Science and Technology Shenzhen 518055 People's Republic of China

A local artificial neural network (LANN) framework is developed for turbulence modeling. The Reynolds-averaged Navier-Stokes (RANS) unclosed terms are reconstructed by the artificial neural network based on the local coordinate system which is orthogonal to the curved walls. We verify the proposed model in the flows over periodic hills. The correlation coefficients of the RANS unclosed terms predicted by the LANN model can be made larger than 0.96 in an a priori analysis, and the relative error of the unclosed terms can be made smaller than 18%. In an a posteriori analysis, detailed comparisons are made on the results of RANS simulations using the LANN, global artificial neural network (GANN), Spalart-Allmaras (SA), and shear stress transport (SST) k−ω models. It is shown that the LANN model performs better than the GANN, SA, and SST k−ω models in the prediction of the average velocity, wall-shear stress, and average pressure, which gives the results that are essentially indistinguishable from the direct numerical simulation data. The LANN model trained at low Reynolds number, Re=2800, can be directly applied to the cases of high Reynolds numbers, Re=5600, 10 595, 19 000, and 37 000, with accurate predictions. Furthermore, the LANN model is verified for flows over periodic hills with varying slopes. These results suggest that the LANN framework has a great potential to be applied to complex turbulent flows with curved walls.

关键词： Compressible boundary layers Turbulence Artificial neural networks

Deep Potentials for Materials science

学校读者我要写书评

暂无评论

arXiv 2022年

作者： Wen, Tongqi Zhang, Linfeng Wang, Han Weinan, E. Srolovitz, David J. Department of Mechanical Engineering The University of Hong Kong Hong Kong DP Technology Beijing China AI for Science Institute Beijing China Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Beijing China HEDPS CAPT College of Engineering Peking University Beijing China School of Mathematical Sciences Peking University Beijing China Department of Mathematics and Program in Applied and Computational Mathematics Princeton University Princeton United States Shenzhen China

To fill the gap between accurate (and expensive) ab initio calculations and efficient atomistic simulations based on empirical interatomic potentials, a new class of descriptions of atomic interactions has emerged and been widely applied;i.e., machine learning potentials (MLPs). One recently developed type of MLP is the Deep Potential (DP) method. In this review, we provide an introduction to DP methods in computational materials science. The theory underlying the DP method is presented along with a step-by-step introduction to their development and use. We also review materials applications of DPs in a wide range of materials systems. The DP Library provides a platform for the development of DPs and a database of extant DPs. We discuss the accuracy and efficiency of DPs compared with ab initio methods and empirical potentials. Copyright © 2022, The Authors. All rights reserved.

关键词： Calculations

Cyclic ferroelectric switching and quantized charge transport in CuInP2S6

学校读者我要写书评

暂无评论

Physical Review B 2023年第18期108卷 L180101-L180101页

作者： Daniel Seleznev Sobhit Singh John Bonini Karin M. Rabe David Vanderbilt Department of Physics and Astronomy Center for Materials Theory Rutgers University Piscataway New Jersey 08854 USA Department of Mechanical Engineering University of Rochester Rochester New York 14627 USA Materials Science Program University of Rochester Rochester New York 14627 USA Center for Computational Quantum Physics Flatiron Institute 162 5th Avenue New York New York 10010 USA

The van der Waals layered ferroelectric CuInP2S6 has been found to exhibit a variety of intriguing properties arising from the fact that the Cu ions are unusually mobile in this system. While the polarization switching mechanism is usually understood to arise from Cu ion motion within the monolayers, a second switching path involving Cu motion across the van der Waals gaps has been suggested. In this work, we perform zero-temperature first-principles calculations on such switching paths, focusing on two types that preserve the periodicity of the primitive unit cell: “cooperative” paths preserving the system's glide mirror symmetry, and “sequential” paths in which the two Cu ions in the unit cell move independently of each other. We find that CuInP2S6 features a rich and varied energy landscape, and that sequential paths are clearly favored energetically both for cross-gap and through-layer paths. Importantly, these segments can be assembled to comprise a globally insulating cycle with the out-of-plane polarization evolving by a quantum as the Cu ions shift to neighboring layers. In this sense, we argue that CuInP2S6 embodies the physics of a quantized adiabatic charge pump.

关键词： Electric polarization Electronic structure Ferroelectricity Phonons Structural phase transition