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Protein structure determination has long been one of the primary challenges of structural biology, to which deep machine learning (ML)-based approaches have increasingly been applied. However, these ML models generally do not incorporate…

Biological Physics · Physics 2025-11-14 Tom Pan , Evan Dramko , Mitchell D. Miller , Anastasios Kyrillidis , George N. Phillips

Crystal structure prediction is one of the major unsolved problems in materials science. Traditionally, this problem is formulated as a global optimization problem for which global search algorithms are combined with first principle free…

Materials Science · Physics 2023-06-13 Jianjun Hu , Yong Zhao , Qin Li , Yuqi Song , Rongzhi Dong , Wenhui Yang , Edirisuriya MD Siriwardane

A micromorphic computational homogenization framework has recently been developed to deal with materials showing long-range correlated interactions, i.e. displaying patterning modes. Typical examples of such materials are elastomeric…

Soft Condensed Matter · Physics 2024-06-21 S. Maraghechi , O. Rokoš , R. H. J. Peerlings , M. G. D. Geers , J. P. M. Hoefnagels

Autonomous agents face the challenge of coordinating multiple tasks (perception, motion planning, controller) which are computationally expensive on a single onboard computer. To utilize the onboard processing capacity optimally, it is…

Robotics · Computer Science 2023-05-09 Aditya Shirwatkar , Aman Singh , Jana Ravi Kiran

Machine learning (ML) models utilizing structure-based features provide an efficient means for accurate property predictions across diverse chemical spaces. However, obtaining equilibrium crystal structures typically requires expensive…

Materials Science · Physics 2021-04-22 Yunxing Zuo , Mingde Qin , Chi Chen , Weike Ye , Xiangguo Li , Jian Luo , Shyue Ping Ong

Crystal structure modeling with graph neural networks is essential for various applications in materials informatics, and capturing SE(3)-invariant geometric features is a fundamental requirement for these networks. A straightforward…

Machine Learning · Computer Science 2025-03-05 Yusei Ito , Tatsunori Taniai , Ryo Igarashi , Yoshitaka Ushiku , Kanta Ono

Crystal structure design is important for the discovery of new highly functional materials because crystal structure strongly influences material properties. Crystal structures are composed of space-filling polyhedra, which affect material…

Materials Science · Physics 2024-02-06 Tomoyasu Yokoyama , Kazuhide Ichikawa , Hisashi Naito

Most elemental metals under ambient conditions adopt simple structures such as BCC, FCC and HCP in specific groupings across the Periodic Table, and on compression, many of these elements undergo transitions to surprisingly complex…

Materials Science · Physics 2022-06-27 Yuanhui Sun , Lei Zhao , Chris J. Pickard , Russell J. Hemley , Yonghao Zheng , Maosheng Miao

Machine learning has the potential to accelerate materials discovery by accurately predicting materials properties at a low computational cost. However, the model inputs remain a key stumbling block. Current methods typically use…

Computational Physics · Physics 2021-01-07 Rhys E. A. Goodall , Alpha A. Lee

The detailed investigation of electronic and magnetic properties of polymeric coordination materials with accurate ab initio quantum mechanical methods is often computationally extremely demanding because of the large number of atoms in the…

Generative models for materials, especially inorganic crystals, hold potential to transform the theoretical prediction of novel compounds and structures. Advancement in this field depends on robust benchmarks and minimal, information-rich…

Successful scientific applications of large-scale molecular dynamics often rely on automated methods for identifying the local crystalline structure of condensed phases. Many existing methods for structural identification, such as Common…

Materials Science · Physics 2016-05-24 Peter Mahler Larsen , Søren Schmidt , Jakob Schiøtz

The modeling of solid-state transformations, such as polymorphic transitions and chemical reactions in molecular crystals, is vital for many applications including drug design or the development of new synthesis methods. However, a…

Chemical Physics · Physics 2025-06-17 Natalia Goncharova , Johannes Hoja

How long threadlike eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advances in experimental techniques. Several polymer models, which…

Soft Condensed Matter · Physics 2024-10-03 D. Thirumalai , Guang Shi , Sucheol Shin , Changbong Hyeon

Crystal structure prediction is a fundamental problem in materials science. We present CrystalFormer-CSP, an efficient framework that unifies data-driven heuristic and physics-driven optimization approaches to predict stable crystal…

Materials Science · Physics 2025-12-23 Zhendong Cao , Shigang Ou , Lei Wang

We derive a mode-coupling theory for the slow dynamics of fluids confined in disordered porous media represented by spherical particles randomly placed in space. Its equations display the usual nonlinear structure met in this theoretical…

Soft Condensed Matter · Physics 2007-05-23 V. Krakoviack

We have developed an efficient and reliable methodology for crystal structure prediction, merging ab initio total-energy calculations and a specifically devised evolutionary algorithm. This method allows one to predict the most stable…

Materials Science · Physics 2009-11-18 A. R. Oganov , C. W. Glass

Crystal-structure phase mapping is a core, long-standing challenge in materials science that requires identifying crystal structures, or mixtures thereof, in synthesized materials. Materials science experts excel at solving simple systems…

We demonstrate a new algorithm for finding protein conformations that minimize a non-bonded energy function. The new algorithm, called the difference map, seeks to find an atomic configuration that is simultaneously in two constraint…

Biomolecules · Quantitative Biology 2007-06-13 Ivan C. Rankenburg , Veit Elser

Many major cities suffer from severe traffic congestion. Road expansion in the cites is usually infeasible, and an alternative way to alleviate traffic congestion is to coordinate the route of vehicles. Various path selection and planning…

Physics and Society · Physics 2019-06-05 Hao Liao , Xingtong Wu , Mingyang Zhou , Chi Ho Yeung