Related papers: Physically Valid Biomolecular Interaction Modeling…
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…
This work outlines a new multi-physics-compatible immersed rigid body method for Eulerian finite-volume simulations. To achieve this, rigid bodies are represented as a diffuse scalar field and an interface seeding method is employed to…
A biological pathway represents a set of genes that serves a particular cellular or a physiological function. The genes within the same pathway are expected to function together and hence may interact with each other. It is also known that…
Bimanual manipulation requires policies that can reason about 3D geometry, anticipate how it evolves under action, and generate smooth, coordinated motions. However, existing methods typically rely on 2D features with limited spatial…
Highly accurate biomolecular structure prediction is a key component of developing biomolecular foundation models, and one of the most critical aspects of building foundation models is identifying the recipes for scaling the model. In this…
We present an operator-splitting scheme for fluid-structure interaction (FSI) problems in hemodynamics, where the thickness of the structural wall is comparable to the radius of the cylindrical fluid domain. The equations of linear…
We present an immersed boundary method to simulate the creeping motion of a rigid particle in a fluid described by the Stokes equations discretized thanks to a finite element strategy on unfitted meshes, called Phi-FEM, that uses the…
We develop a unified framework for analyzing cross-modal compatibility in learned representations. The core object is a modality-independent neighborhood site on sample indices, equipped with a cellular sheaf of finite-dimensional real…
We have studied p-shell nuclei using a two-frequency shell-model approach with an effective interaction derived from the Bonn-A nucleon-nucleon potential by means of a G-matrix folded-diagram method. First, we briefly describe our…
Geometric deep learning (GDL) has demonstrated huge power and enormous potential in molecular data analysis. However, a great challenge still remains for highly efficient molecular representations. Currently, covalent-bond-based molecular…
Stochastic differential equation mixed-effects models (SDEMEMs) are flexible hierarchical models that are able to account for random variability inherent in the underlying time-dynamics, as well as the variability between experimental units…
The interaction between thin structures and incompressible Newtonian fluids is ubiquitous both in nature and in industrial applications. In this paper we present an isogeometric formulation of such problems which exploits a boundary…
The simulation of soil-structure interaction problems involving two-phase materials poses significant challenges in geotechnical engineering. These challenges arise due to differences in material stiffnesses, the interaction between…
Computational modeling and simulation of fluid-structure interactions constitute a fundamental cornerstone for advancing aerospace engineering endeavors. This paper addresses the notion and implementation of the immersed boundary method for…
This article presents a novel computational model to study the selective filtering of biological hydrogels due to the surface charge and size of diffusing particles. It is the first model that includes the random 3D fiber orientation and…
This work describes a geometric framework on molecular reaction dynamics based on the variational principle, where the Schr{\"o}dinger equation must be solved to ``see'' how a reaction occurs. First, the mathematical preliminaries are given…
We show that a system of three trapped ultracold and strongly interacting atoms in one-dimension can be emulated using an optical fiber with a graded-index profile and thin metallic slabs. While the wave-nature of single quantum particles…
The goal of this work is to develop a numerical simulation that accurately captures the biomechanical response of bacterial biofilms and their associated extracellular matrix (ECM). In this, the second of a two-part effort, the primary…
Diffusion Transformers (DiTs) have demonstrated strong performance in generative modeling, particularly in image synthesis, making them a compelling choice for molecular conformer generation. However, applying DiTs to molecules introduces…
Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, meaning that the serial limit has already been reached in…