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The folding structure of the DNA molecule combined with helper molecules, also referred to as the chromatin, is highly relevant for the functional properties of DNA. The chromatin structure is largely determined by the underlying primary…

Machine Learning · Computer Science 2018-06-14 Bojian Yin , Marleen Balvert , Davide Zambrano , Alexander Schönhuth , Sander Bohte

The computational prediction of the structure and stability of hybrid organic-inorganic interfaces provides important insights into the measurable properties of electronic thin film devices, coatings, and catalyst surfaces and plays an…

The design of fluid channel structures of reactors or separators of chemical processes is key to enhancing the mass transfer processes inside the devices. However, the systematic design of channel topological structures is difficult for…

Fluid Dynamics · Physics 2025-03-07 Chenhui Kou , Yuhui Yin , Min Zhu , Shengkun Jia , Yiqing Luo , Xigang Yuana , Lu Lu

Solving the intricate quantum behavior of interacting particles is key to unlocking the mysteries of condensed matter, but capturing their complex correlations across different scales remains a monumental challenge. We introduce a neural…

Electron microscopy is a powerful tool for studying the properties of materials down to their atomic structure. In many cases, the quantitative interpretation of images requires simulations based on atomistic structure models. These…

An interacting lattice model describing the subspace spanned by a set of strongly-correlated bands is rigorously coupled to density functional theory to enable ab initio calculations of geometric and topological material properties. The…

Strongly Correlated Electrons · Physics 2019-03-26 Ryan Requist , E. K. U. Gross

We introduce a deep neural network to model in a symmetry preserving way the environmental dependence of the centers of the electronic charge. The model learns from ab-initio density functional theory, wherein the electronic centers are…

Computational Physics · Physics 2020-07-29 Linfeng Zhang , Mohan Chen , Xifan Wu , Han Wang , Weinan E , Roberto Car

Descriptors play an important role in data-driven materials design. While most descriptors of crystalline materials emphasize structure and composition, they often neglect the electron density - a complex yet fundamental quantity that…

Materials Science · Physics 2025-06-18 Nathan J. Szymanski , Alexander Smith , Prodromos Daoutidis , Christopher J. Bartel

Graph neural networks (GNNs) demonstrate great performance in compound property and activity prediction due to their capability to efficiently learn complex molecular graph structures. However, two main limitations persist including…

Biomolecules · Quantitative Biology 2023-10-10 Apakorn Kengkanna , Masahito Ohue

A deep understanding of the intricate interactions between particles within a system is a key approach to revealing the essential characteristics of the system, whether it is an in-depth analysis of molecular properties in the field of…

High Energy Physics - Lattice · Physics 2024-12-17 Ru Geng , Yixian Gao , Jian Zu , Hong-Kun Zhang

Many patterns in nature exhibit self-similarity: they can be compactly described via self-referential transformations. Said patterns commonly appear in natural and artificial objects, such as molecules, shorelines, galaxies and even images.…

Machine Learning · Computer Science 2022-04-19 Michael Poli , Winnie Xu , Stefano Massaroli , Chenlin Meng , Kuno Kim , Stefano Ermon

Identifying the dynamics of physical systems requires a machine learning model that can assimilate observational data, but also incorporate the laws of physics. Neural Networks based on physical principles such as the Hamiltonian or…

Machine Learning · Statistics 2021-11-22 Jonas Eichelsdörfer , Sebastian Kaltenbach , Phaedon-Stelios Koutsourelakis

Using the message-passing mechanism in machine learning (ML) instead of self-consistent iterations to directly build the mapping from structures to electronic Hamiltonian matrices will greatly improve the efficiency of density functional…

Computational Physics · Physics 2023-10-19 Yang Zhong , Hongyu Yu , Mao Su , Xingao Gong , Hongjun Xiang

Nonlinear metamaterials with tailored mechanical properties have applications in engineering, medicine, robotics, and beyond. While modeling their macromechanical behavior is challenging in itself, finding structure parameters that lead to…

Graphics · Computer Science 2023-09-20 Yue Li , Stelian Coros , Bernhard Thomaszewski

Neural network force fields have significantly advanced ab initio atomistic simulations across diverse fields. However, their application in the realm of magnetic materials is still in its early stage due to challenges posed by the subtle…

Materials Science · Physics 2024-02-08 Zilong Yuan , Zhiming Xu , He Li , Xinle Cheng , Honggeng Tao , Zechen Tang , Zhiyuan Zhou , Wenhui Duan , Yong Xu

Deep potentials for molecular dynamics (MD) achieve first-principles accuracy at much lower computational cost. However, their use in large length- and time-scale simulations is limited by their lower speeds compared to analytical atomistic…

Materials Science · Physics 2023-06-19 Or Shafir , Ilya Grinberg

We push the boundaries of electronic structure-based \textit{ab-initio} molecular dynamics (AIMD) beyond 100 million atoms. This scale is otherwise barely reachable with classical force-field methods or novel neural network and machine…

Constitutive models that describe the mechanical behavior of soft tissues have advanced greatly over the past few decades. These expert models are generalizable and require the calibration of a number of parameters to fit experimental data.…

Quantitative Methods · Quantitative Biology 2021-07-13 Vahidullah Tac , Vivek D. Sree , Manuel K. Rausch , Adrian B. Tepole

Networks of silicon nanowires possess intriguing electronic properties surpassing the predictions based on quantum confinement of individual nanowires. Employing large-scale atomistic pseudopotential computations, as yet unexplored branched…

Mesoscale and Nanoscale Physics · Physics 2013-11-18 Ümit Keleş , Bartosz Liedke , Karl-Heinz Heinig , Ceyhun Bulutay

The quantitative description of correlated electron materials remains a modern computational challenge. We demonstrate a numerical strategy to simulate correlated materials at the fully ab initio level beyond the solution of effective…

Superconductivity · Physics 2022-09-19 Zhi-Hao Cui , Huanchen Zhai , Xing Zhang , Garnet Kin-Lic Chan
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