Adversarial uncertainty quantification in physics-informed neural networks

Y Yang, P Perdikaris - Journal of Computational Physics, 2019 - Elsevier
We present a deep learning framework for quantifying and propagating uncertainty in
systems governed by non-linear differential equations using physics-informed neural …

Mesoscopic simulations at the physics-chemistry-biology interface

M Bernaschi, S Melchionna, S Succi - Reviews of Modern Physics, 2019 - APS
This review discusses the lattice Boltzmann–particle dynamics (LBPD) multiscale paradigm
for the simulation of complex states of flowing matter at the interface between physics …

OpenRBC: A fast simulator of red blood cells at protein resolution

YH Tang, L Lu, H Li, C Evangelinos, L Grinberg… - Biophysical journal, 2017 - cell.com
We present OpenRBC, a coarse-grained molecular dynamics code, which is capable of
performing an unprecedented in silico experiment—simulating an entire mammal red blood …

Bridging the computational gap between mesoscopic and continuum modeling of red blood cells for fully resolved blood flow

C Kotsalos, J Latt, B Chopard - Journal of Computational Physics, 2019 - Elsevier
We present a computational framework for the simulation of blood flow with fully resolved
red blood cells (RBCs) using a modular approach that consists of a lattice Boltzmann solver …

GPU-accelerated red blood cells simulations with transport dissipative particle dynamics

AL Blumers, YH Tang, Z Li, X Li… - Computer physics …, 2017 - Elsevier
Mesoscopic numerical simulations provide a unique approach for the quantification of the
chemical influences on red blood cell functionalities. The transport Dissipative Particle …

[PDF][PDF] 耗散粒子动力学方法在生物学领域的应用与研究进展: 从蛋白质结构到细胞力学

唐梓涵, **学进, **德昌 - 科学通报, 2023 - researchgate.net
摘要耗散粒子动力学(dissipative particle dynamics, DPD) 是**年发展起来的一种介观尺度的
数值模拟方法, 是研究软物质和复杂流体动力学行为的一种重要手段. 这种新型介观模拟方法 …

A parallel fluid–solid coupling model using LAMMPS and Palabos based on the immersed boundary method

J Tan, TR Sinno, SL Diamond - Journal of computational science, 2018 - Elsevier
The study of viscous fluid flow coupled with rigid or deformable solids has many applications
in biological and engineering problems, eg, blood cell transport, drug delivery, and …

Probing eukaryotic cell mechanics via mesoscopic simulations

K Lykov, Y Nematbakhsh, M Shang… - PLoS computational …, 2017 - journals.plos.org
Cell mechanics has proven to be important in many biological processes. Although there is
a number of experimental techniques which allow us to study mechanical properties of cell …

Intelligent dissipative particle dynamics: Bridging mesoscopic models from microscopic simulations via deep neural networks

T Ye, B **g, D Pan - Journal of Computational Physics, 2023 - Elsevier
We develop a bottom-up coarse graining framework to construct mesoscopic force fields
directly from microscopic dynamics by a machine learning technique. This scheme, called …

Digital blood in massively parallel CPU/GPU systems for the study of platelet transport

C Kotsalos, J Latt, J Beny, B Chopard - Interface Focus, 2021 - royalsocietypublishing.org
We propose a highly versatile computational framework for the simulation of cellular blood
flow focusing on extreme performance without compromising accuracy or complexity. The …