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Ordinary differential equation models have become a standard tool for the mechanistic description of biochemical processes. If parameters are inferred from experimental data, such mechanistic models can provide accurate predictions about…

Quantitative Methods · Quantitative Biology 2018-10-12 Fabian Fröhlich , Carolin Loos , Jan Hasenauer

Many enhanced sampling techniques rely on the identification of a number of collective variables that describe all the slow modes of the system. By constructing a bias potential in this reduced space one is then able to sample efficiently…

Computational Physics · Physics 2019-03-05 Michele Invernizzi , Michele Parrinello

We present a multi-scale computational framework suitable for designing solid lubricant interfaces fully in silico. The approach is based on stochastic thermodynamics founded on the classical thermally activated two-dimensional…

Materials Science · Physics 2022-04-27 Paola C. Torche , Andrea Silva , Denis Kramer , Tomas Polcar , Ondrej Hovorka

It is important to accurately model materials' properties at lower length scales (micro-level) while translating the effects to the components and/or system level (macro-level) can significantly reduce the amount of experimentation required…

Computers and Society · Computer Science 2022-11-08 Kazuma Kobayashi , Shoaib Usman , Carlos Castano , Dinesh Kumar , Syed Alam

In this work, we consider the coupled systems of linear unsteady partial differential equations, which arise in the modeling of poroelasticity processes. Stability estimates of weighted difference schemes for the coupled system of equations…

Numerical Analysis · Computer Science 2013-11-18 A. E. Kolesov , P. N. Vabishchevich , M. V. Vasilyeva

Hierarchical (first-order) structured deformations are studied from the variational point of view. The main contributions of the present research are the first steps, at the theoretical level, to establish a variational framework to…

Optimization and Control · Mathematics 2022-08-26 Ana Cristina Barroso , José Matias , Marco Morandotti , David R. Owen , Elvira Zappale

In many contexts it is extremely costly to perform enough high quality experimental measurements to accurately parameterize a predictive quantitative model. However, it is often much easier to carry out large numbers of experiments that…

Data Analysis, Statistics and Probability · Physics 2017-11-22 Alpha A. Lee , Michael P. Brenner , Lucy J. Colwell

Long simulation times in climate sciences typically require coarse grids due to computational constraints. Nonetheless, unresolved subscale information significantly influences the prognostic variables and can not be neglected for reliable…

Numerical Analysis · Mathematics 2018-02-22 Konrad Simon , Jörn Behrens

Consider the macroscale modelling of microscale spatiotemporal dynamics. Here we develop a new approach to ensure coarse scale discrete models preserve important self-adjoint properties of the fine scale dynamics. The first part explores…

Cellular Automata and Lattice Gases · Physics 2008-11-06 A. J. Roberts

The possibility to simulate the properties of many-body open quantum systems with a large number of degrees of freedom is the premise to the solution of several outstanding problems in quantum science and quantum information. The challenge…

Quantum Physics · Physics 2019-07-03 Alexandra Nagy , Vincenzo Savona

High-dimensional recordings of dynamical processes are often characterized by a much smaller set of effective variables, evolving on low-dimensional manifolds. Identifying these latent dynamics requires solving two intertwined problems:…

Machine Learning · Computer Science 2026-01-21 Manuel Hinz , Maximilian Mauel , Patrick Seifner , David Berghaus , Kostadin Cvejoski , Ramses J. Sanchez

This work investigates variational frameworks for modeling stochastic dynamics in incompressible fluids, focusing on large-scale fluid behavior alongside small-scale stochastic processes. The authors aim to develop a coupled system of…

Fluid Dynamics · Physics 2025-03-21 Arnaud Debussche , Etienne Mémin

Achieving strongly symmetric stress approximations for linear elasticity problems in high-contrast media poses a significant computational challenge. Conventional methods often struggle with prohibitively high computational costs due to…

Numerical Analysis · Mathematics 2025-09-03 Eric T. Chung , Changqing Ye , Xiang Zhong

Plasticity is inherent to many engineering materials such as metals. While it can degrade the load-carrying capacity of structures via material yielding, it can also protect structures through plastic energy dissipation. To fully harness…

Computational Engineering, Finance, and Science · Computer Science 2025-02-05 Yingqi Jia , Xiaojia Shelly Zhang

Variability in multiple independent input parameters makes it difficult to estimate the resultant variability in the system's overall response. The Propagation of Errors and Monte-Carlo techniques are two major methods to predict the…

Other Condensed Matter · Physics 2026-04-28 Seungju Yeoa , Paul Funkenbuscha , Hesam Askari

We discuss certain basic features of the equation-free (EF) approach to modeling and computation for complex/multiscale systems. We focus on links between the equation-free approach and tools from systems and control theory (design of…

Cellular Automata and Lattice Gases · Physics 2007-05-23 C. I. Siettos , R. Rico-Martinez , I. G. kevrekidis

In this paper, we propose a variationally consistent technique for decreasing the maximum eigenfrequencies of structural dynamics related finite element formulations. Our approach is based on adding a symmetric positive-definite term to the…

Numerical Analysis · Mathematics 2022-07-27 Stein K. F. Stoter , Thi-Hoa Nguyen , René R. Hiemstra , Dominik Schillinger

Recent advances in physics-augmented neural networks have enabled thermodynamically consistent data-driven constitutive modeling of complex inelastic materials. Most existing approaches, however, implicitly adopt a specific thermodynamic…

Materials Science · Physics 2026-05-28 Reese E. Jones , Jan N. Fuhg

The large time and length scales and, not least, the vast number of particles involved in industrial-scale simulations inflate the computational costs of the Discrete Element Method (DEM) excessively. Coarse grain models can help to lower…

Computational Physics · Physics 2017-05-11 Daniel Queteschiner , Thomas Lichtenegger , Simon Schneiderbauer , Stefan Pirker

The behavior of materials is influenced by a wide range of phenomena occurring across various time and length scales. To better understand the impact of microstructure on macroscopic response, multiscale modeling strategies are essential.…

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