2.6k citations · 3.1k across the 14 of their papers we have counts for
14 papers
An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries
Christopher T. Lee, Justin G. Laughlin, John B. Moody +4
Advances in imaging methods such as electron microscopy, tomography and other modalities are enabling high-resolution reconstructions of cellular and organelle geometries. Such adv…
Variational implicit-solvent predictions of the dry-wet transition pathways for ligand-receptor binding and unbinding kinetics
Shenggao Zhou, R. Gregor Weiß, Li-Tien Cheng +3
Ligand-receptor binding and unbinding are fundamental biomolecular processes and particularly essential to drug efficacy. Environmental water fluctuations, however, impact the corr…
3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries
Christopher T. Lee, Justin G. Laughlin, Nils Angliviel de La Beaumelle +5
Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the abil…
The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation
C. T. Lee, J. B. Moody, R. E. Amaro +2
We introduce CASC: a new, modern, and header-only C++ library which provides a data structure to represent arbitrary dimension abstract simplicial complexes (ASC) with user-defined…
RPYFMM: Parallel Adaptive Fast Multipole Method for Rotne-Prager-Yamakawa Tensor in Biomolecular Hydrodynamics Simulations
W. Guan, X. Cheng, J. Huang +4
RPYFMM is a software package for the efficient evaluation of the potential field governed by the Rotne-Prager-Yamakawa (RPY) tensor interactions in biomolecular hydrodynamics simul…
Hierarchical Orthogonal Matrix Generation and Matrix-Vector Multiplications in Rigid Body Simulations
Fuhui Fang, Jingfang Huang, Gary Huber +2
In this paper, we apply the hierarchical modeling technique and study some numerical linear algebra problems arising from the Brownian dynamics simulations of biomolecular systems…