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Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…

Soft Condensed Matter · Physics 2021-05-26 Marco Oestereich , Jürgen Gauss , Gregor Diezemann

This paper considers the problem of distributed model fitting using the alternating directions method of multipliers (ADMM). ADMM splits the learning problem into several smaller subproblems, usually by partitioning the data samples. The…

Optimization and Control · Mathematics 2022-03-04 Dinesh Krishnamoorthy , Vyacheslav Kungurtsev

Backward compatible representation learning enables updated models to integrate seamlessly with existing ones, avoiding to reprocess stored data. Despite recent advances, existing compatibility approaches in Euclidean space neglect the…

Machine Learning · Computer Science 2025-06-09 Ngoc Bui , Menglin Yang , Runjin Chen , Leonardo Neves , Mingxuan Ju , Rex Ying , Neil Shah , Tong Zhao

We present a hybrid continuum-atomistic scheme which combines molecular dynamics (MD) simulations with on-the-fly machine learning techniques for the accurate and efficient prediction of multiscale fluidic systems. By using a Gaussian…

Fluid Dynamics · Physics 2016-03-16 David Stephenson , James R Kermode , Duncan A Lockerby

Automatic differentiation (AD) is a set of techniques that systematically applies the chain rule to compute the gradients of functions without requiring human intervention. Although the fundamentals of this technology were established…

Machine Learning · Computer Science 2025-09-03 Afif Boudaoud , Alexandru Calotoiu , Marcin Copik , Torsten Hoefler

This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…

Chemical Physics · Physics 2025-04-01 Cheng Fan , Maodong Li , Sihao Yuan , Zhaoxin Xie , Dechin Chen , Yi Isaac Yang , Yi Qin Gao

Dynamic Mode Decomposition (DMD) is a data based modeling tool that identifies a matrix to map a quantity at some time instant to the same quantity in future. We design a new version which we call Adaptive Dynamic Mode Decomposition (ADMD)…

Signal Processing · Electrical Eng. & Systems 2020-12-16 Mohammad N. Murshed , M. Monir Uddin

We present a new software system PETSc TSAdjoint for first-order and second-order adjoint sensitivity analysis of time-dependent nonlinear differential equations. The derivative calculation in PETSc TSAdjoint is essentially a high-level…

Mathematical Software · Computer Science 2021-10-28 Hong Zhang , Emil M. Constantinescu , Barry F. Smith

We develop a multiscale hybrid scheme for simulations of soft condensed matter systems, which allows one to treat the system at the particle level in selected regions of space, and at the continuum level elsewhere. It is derived…

Soft Condensed Matter · Physics 2015-06-17 Shuanhu Qi , Hans Behringer , Friederike Schmid

Recent probabilistic methods for 3D triangular meshes capture diverse shapes by differentiable mesh connectivity, but face high computational costs with increased shape details. We introduce a new differentiable mesh processing method that…

Computer Vision and Pattern Recognition · Computer Science 2025-07-08 Sanghyun Son , Matheus Gadelha , Yang Zhou , Matthew Fisher , Zexiang Xu , Yi-Ling Qiao , Ming C. Lin , Yi Zhou

The alternating direction method of multipliers (ADMM) is a popular approach for solving optimization problems that are potentially non-smooth and with hard constraints. It has been applied to various computer graphics applications,…

Graphics · Computer Science 2019-09-04 Juyong Zhang , Yue Peng , Wenqing Ouyang , Bailin Deng

Physics-informed neural networks (PINNs) have emerged as new data-driven PDE solvers for both forward and inverse problems. While promising, the expensive computational costs to obtain solutions often restrict their broader applicability.…

Machine Learning · Computer Science 2023-11-06 Junwoo Cho , Seungtae Nam , Hyunmo Yang , Seok-Bae Yun , Youngjoon Hong , Eunbyung Park

The alternating direction multiplier method (ADMM) is widely used in computer graphics for solving optimization problems that can be nonsmooth and nonconvex. It converges quickly to an approximate solution, but can take a long time to…

Optimization and Control · Mathematics 2020-06-29 Wenqing Ouyang , Yue Peng , Yuxin Yao , Juyong Zhang , Bailin Deng

Differentiable physics simulation provides an avenue to tackle previously intractable challenges through gradient-based optimization, thereby greatly improving the efficiency of solving robotics-related problems. To apply differentiable…

Robotics · Computer Science 2025-04-08 Min Liu , Gang Yang , Siyuan Luo , Lin Shao

We propose a new computational framework that combines the recently developed time-parallel (TP) and the compound wavelet matrix (CWM) methods. The framework, termed tpCWM, offers significant computational acceleration by making…

Computational Physics · Physics 2009-09-29 George Frantziskonis , Krishna Muralidharan , Pierre Deymier , Srdjan Simunovic , Sreekanth Pannala

We present a novel reduced-order fluid simulation technique leveraging Dynamic Mode Decomposition (DMD) to achieve fast, memory-efficient, and user-controllable subspace simulation. We demonstrate that our approach combines the strengths of…

Automatic differentiation (AD) has driven recent advances in machine learning, including deep neural networks and Hamiltonian Markov Chain Monte Carlo methods. Partially observed nonlinear stochastic dynamical systems have proved resistant…

Methodology · Statistics 2024-07-04 Kevin Tan , Giles Hooker , Edward L. Ionides

Joint ptycho-tomography is a powerful computational imaging framework to recover the refractive properties of a 3D object while relaxing the requirements for probe overlap that is common in conventional phase retrieval. We use an augmented…

Image and Video Processing · Electrical Eng. & Systems 2021-08-30 Selin Aslan , Zhengchun Liu , Viktor Nikitin , Tekin Bicer , Sven Leyffer , Doga Gursoy

The parallel alternating direction method of multipliers (ADMM) algorithms have gained popularity in statistics and machine learning due to their efficient handling of large sample data problems. However, the parallel structure of these…

Statistics Theory · Mathematics 2024-04-11 Xiaofei Wu , Jiancheng Jiang , Zhimin Zhang

An adjoint formulation leveraging a physics-informed neural network (PINN) is employed to advance the density moment of a runaway electron (RE) distribution forward in time. A distinguishing feature of this approach is that once the adjoint…

Plasma Physics · Physics 2024-12-18 Christopher J. McDevitt , Jonathan Arnaud , Xian-Zhu Tang
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