Related papers: Physically Valid Biomolecular Interaction Modeling…
In this paper we consider the numerical approximation of the two-phase membrane (obstacle) problem by finite difference method. First, we introduce the notion of viscosity solution for the problem and construct certain discrete nonlinear…
Differentiable particle-based simulation can produce physically plausible motion, but target-driven volumetric shape morphing remains underconstrained: physics-only mass matching captures coarse global structure yet struggles with fine…
1. Inferring ecological interactions is hard because we often lack suitable parametric representations to portray them. Neural ordinary differential equations (NODEs) provide a way of estimating interactions nonparametrically from time…
Denoising diffusion models hold great promise for generating diverse and realistic human motions. However, existing motion diffusion models largely disregard the laws of physics in the diffusion process and often generate…
Accurate interaction potentials between microscopic components such as colloidal particles or cells are crucial to understanding a range of processes, including colloidal crystallization, bacterial colony formation, and cancer metastasis.…
The modern description of elementary particles, as formulated in the Standard Model of particle physics, is built on gauge theories. Gauge theories implement fundamental laws of physics by local symmetry constraints. For example, in quantum…
In micromagnetic simulations, the constant magnitude of the magnetization can be derived from the continuity equation. Since the time evolution of the magnetization in the continuity equation is perpendicular to the plane determined by the…
Proposals to determine biomolecular structures from diffraction experiments using femtosecond X-ray free-electron laser (XFEL) pulses involve a conflict between the incident brightness required to achieve diffraction-limited atomic…
Structural biology relies on accurate three-dimensional biomolecular structures to advance our understanding of biological functions, disease mechanisms, and therapeutics. While recent advances in deep learning have enabled the development…
The effect on the convergence of warm starting the projected Gauss-Seidel solver for nonsmooth discrete element simulation of granular matter are investigated. It is found that the computational performance can be increased by a factor 2 to…
We investigate effective interactions between a colloidal particle, immersed in a binary mixture of smaller spheres, and a semipermeable membrane. The colloid is modeled as a big hard sphere and the membrane is represented as an infinitely…
Fluid-Structure Interaction (FSI) can be investigated by means of non-linear Finite Element Models (FEM), suitable to capture large deflections of structural parts interacting with fluids, and Computational Fluid Dynamics (CFD). High…
Quality molecular representations are key to foundation model development in bio-medical research. Previous efforts have typically focused on a single representation or molecular view, which may have strengths or weaknesses on a given task.…
A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and…
Friction modeling has always been a challenging problem due to the complexity of real physical systems. Although a few state-of-the-art structured data-driven methods show their efficiency in nonlinear system modeling, deterministic…
The hydrodynamic interactions among bacterial cell bodies, flagella, and surrounding boundaries are essential for understanding bacterial motility in complex environments. In this study, we demonstrate that each slender flagellum can be…
Bidimensional spiking models currently gather a lot of attention for their simplicity and their ability to reproduce various spiking patterns of cortical neurons, and are particularly used for large network simulations. These models…
We propose an energy-stable parametric finite element method (ES-PFEM) for simulating solid-state dewetting of thin films in two dimensions via a sharp-interface model, which is governed by surface diffusion and contact line (point)…
In this paper, we introduce a novel parallel contact algorithm designed to run efficiently in High-Performance Computing based supercomputers. Particular emphasis is put on its computational implementation in a multiphysics finite element…
Interactive segmentation is a promising strategy for building robust, generalisable algorithms for volumetric medical image segmentation. However, inconsistent and clinically unrealistic evaluation hinders fair comparison and misrepresents…