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Graphs serve as fundamental descriptors for systems composed of interacting elements, capturing a wide array of data types, from molecular interactions to social networks and knowledge graphs. In this paper, we present an exhaustive review…

Machine Learning · Computer Science 2024-11-13 Chenqing Hua

The pebble-motion on graphs is a subcategory of multi-agent pathfinding problems dealing with moving multiple pebble-like objects from a node to a node in a graph with a constraint that only one pebble can occupy one node at a given time.…

Robotics · Computer Science 2020-07-21 Miroslav Kulich , Tomáš Novák , Libor Přeucil

Humans have a remarkable capacity to understand the physical dynamics of objects in their environment, flexibly capturing complex structures and interactions at multiple levels of detail. Inspired by this ability, we propose a hierarchical…

Artificial Intelligence · Computer Science 2018-10-30 Damian Mrowca , Chengxu Zhuang , Elias Wang , Nick Haber , Li Fei-Fei , Joshua B. Tenenbaum , Daniel L. K. Yamins

We simulate the granulation process of solid spherical particles in the presence of a viscous liquid in a horizontal rotating drum by using molecular dynamics simulations in three dimensions. The numerical approach accounts for the cohesive…

Capturing scene dynamics and predicting the future scene state is challenging but essential for robotic manipulation tasks, especially when the scene contains both rigid and deformable objects. In this work, we contribute a simulation…

Robotics · Computer Science 2021-03-05 Zehang Weng , Fabian Paus , Anastasiia Varava , Hang Yin , Tamim Asfour , Danica Kragic

We present a graph neural network (GNN) based surrogate framework for molecular dynamics simulations that directly predicts atomic displacements and learns the underlying evolution operator of an atomistic system. Unlike conventional…

Materials Science · Physics 2025-12-29 Judah Immanuel , Avik Mahata , Aniruddha Maiti

Many real-world phenomena can be modeled as a graph, making them extremely valuable due to their ubiquitous presence. GNNs excel at capturing those relationships and patterns within these graphs, enabling effective learning and prediction…

Machine Learning · Computer Science 2023-11-28 Abhinav Raghuvanshi , Kushal Sokke Malleshappa

The simulation of microcirculatory blood flow in realistic vascular architectures poses significant challenges due to the multiscale nature of the problem and the topological complexity of capillary networks. In this work, we propose a…

Numerical Analysis · Mathematics 2025-12-12 Paolo Botta , Piermario Vitullo , Thomas Ventimiglia , Andreas Linninger , Paolo Zunino

Many physical systems can be best understood as sets of discrete data with associated relationships. Where previously these sets of data have been formulated as series or image data to match the available machine learning architectures,…

Granular materials such as gravel, cereals, or pellets, are ubiquitous in nature, daily life, and industry. While sharing some characteristics with gases, liquids, and solids, granular matter exhibits a wealth of phenomena that defy these…

Soft Condensed Matter · Physics 2025-03-31 Mathieu Suter , Jens P. Metzger , Andreas Port , Christoph R. Müller , Klaas P. Pruessmann

Graph Neural Networks (GNNs) are powerful and flexible neural networks that use the naturally sparse connectivity information of the data. GNNs represent this connectivity as sparse matrices, which have lower arithmetic intensity and thus…

Machine Learning · Computer Science 2020-09-04 Alok Tripathy , Katherine Yelick , Aydin Buluc

Graph neural networks (GNNs), which are capable of learning representations from graphical data, are naturally suitable for modeling molecular systems. This review introduces GNNs and their various applications for small organic molecules.…

Machine Learning · Computer Science 2023-10-10 Yuyang Wang , Zijie Li , Amir Barati Farimani

The aim of the paper is to show algorithms for geometrical manipulations on NURBS surfaces. These include generating NURBS surfaces that pass through given points, calculating the minimum distance to a point and include line to surface and…

Numerical Analysis · Mathematics 2022-10-25 Gernot Beer

Molecular dynamics (MD) simulation predicts the trajectory of atoms by solving Newton's equation of motion with a numeric integrator. Due to physical constraints, the time step of the integrator need to be small to maintain sufficient…

Computational Physics · Physics 2021-12-22 Tianze Zheng , Weihao Gao , Chong Wang

Soft tissue simulation in virtual environments is becoming increasingly important for medical applications. However, the high deformability of soft tissue poses significant challenges. Existing methods rely on segmentation, meshing and…

Machine Learning · Computer Science 2025-08-08 Madina Kojanazarova , Florentin Bieder , Robin Sandkühler , Philippe C. Cattin

Grasping objects of different shapes and sizes - a foundational, effortless skill for humans - remains a challenging task in robotics. Although model-based approaches can predict stable grasp configurations for known object models, they…

Robotics · Computer Science 2022-11-22 Malte Mosbach , Sven Behnke

Entity interaction prediction is essential in many important applications such as chemistry, biology, material science, and medical science. The problem becomes quite challenging when each entity is represented by a complex structure,…

Machine Learning · Computer Science 2021-04-13 Hanchen Wang , Defu Lian , Ying Zhang , Lu Qin , Xuemin Lin

Nonlinear frequency response analysis is a widely used method for determining system dynamics in the presence of nonlinearities. In dusty plasmas, the plasma-grain interaction (e.g., grain charging fluctuations) can be characterized by a…

Plasma Physics · Physics 2020-10-26 Zhiyue Ding , Lorin S. Matthews , Truell W. Hyde

Impact of a solid object onto a small-body surface can be modeled by the solid impact onto a hierarchically structured granular target. Impact drag force model for the hierarchically structured granular target is developed based on the…

Earth and Planetary Astrophysics · Physics 2022-08-24 F. Okubo , H. Katsuragi

Accurately simulating real world object dynamics is essential for various applications such as robotics, engineering, graphics, and design. To better capture complex real dynamics such as contact and friction, learned simulators based on…

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