Related papers: BioNetFlux: A Python Framework for Reaction--Diffu…
Comprehending the long-timescale dynamics of protein-ligand complexes is very important for drug discovery and structural biology, but it continues to be computationally challenging for large biomolecular systems. We introduce…
Network models facilitate inexpensive simulations, but require careful handling of bifurcation conditions. We here present the graphnics library, which combines FEniCS with NetworkX to facilitate network simulations using the finite element…
Accurate and efficient simulations of physical phenomena governed by partial differential equations (PDEs) are important for scientific and engineering progress. While traditional numerical solvers are powerful, they are often…
This article presents a unified mathematical framework for modeling coupled poro-viscoelastic and thermo-viscoelastic phenomena, formulated as a system of first-order in time partial differential equations. The model describes the evolution…
We present a comprehensive workflow to simulate single-phase flow and transport in fractured porous media using the discrete fracture matrix approach. The workflow has three primary parts: (1) a method for conforming mesh generation of and…
Predicting the effects of perturbations in-silico on cell state can identify drivers of cell behavior at scale and accelerate drug discovery. However, modeling challenges remain due to the inherent heterogeneity of single cell gene…
We present a novel hybridizable discontinuous Galerkin (HDG) method on unfitted meshes for single-phase Darcy flow in a fractured porous media. In particular we apply the HDG methodology to the recently introduced reinterpreted discrete…
We propose a new Neural Galerkin Normalizing Flow framework to approximate the transition probability density function of a diffusion process by solving the corresponding Fokker-Planck equation with an atomic initial distribution,…
Multi-omics data offer unprecedented insights into complex biological systems, yet their high dimensionality, sparsity, and intricate interactions pose significant analytical challenges. Network-based approaches have advanced multi-omics…
We present a new method for simulating incompressible immiscible two-phase flow in porous media. The semi-implicit method decouples the wetting phase pressure and saturation equations. The equations are discretized using a hybridizable…
Autonomous navigation requires a broad spectrum of skills, from static goal-reaching to dynamic social traversal, yet evaluation remains fragmented across disparate protocols. We introduce DynBench, a dynamic navigation benchmark featuring…
We present a topology-based method for mesh-partitioning in three-dimensional discrete fracture network (DFN) simulations that take advantage of the intrinsic multi-level nature of a DFN. DFN models are used to simulate flow and transport…
In this work we review discontinuous Galerkin finite element methods on polytopal grids (PolydG) for the numerical simulation of multiphysics wave propagation phenomena in heterogeneous media. In particular, we address wave phenomena in…
Plasmonic nanostructures significantly improve the performance of photoconductive devices (PCDs) in generating terahertz radiation. However, they are geometrically intricate and result in complicated electromagnetic (EM) field and carrier…
We are interested in exploring interacting particle systems that can be seen as microscopic models for a particular structure of coupled transport flux arising when different populations are jointly evolving. The scenarios we have in mind…
Design of modern nanostructured semiconductor devices often calls for simulation tools capable of modeling arbitrarily-shaped multiscale geometries. In this work, to this end, a discontinuous Galerkin (DG) method-based framework is…
We propose and analyze a seamless extended Discontinuous Galerkin (DG) discretization of advection-diffusion equations on semi-infinite domains. The semi-infinite half line is split into a finite subdomain where the model uses a standard…
13C-based metabolic flux analysis (13C-MFA) is a cornerstone of quantitative systems biology, yet its increasing data complexity and methodological diversity place high demands on simulation software. We introduce 13CFLUX(v3), a…
Mathematical modeling at the level of the full cardiovascular system requires the numerical approximation of solutions to a one-dimensional nonlinear hyperbolic system describing flow in a single vessel. This model is often simulated by…
The quasi-static multiple network poroelastic theory (MPET) model, first introduced in the context of geomechanics, has recently found new applications in medicine. In practice, the parameters in the MPET equations can vary over several…