513 citations · 1k across the 21 of their papers we have counts for
21 papers
Potential quantum advantage for simulation of fluid dynamics
Xiangyu Li, Xiaolong Yin, Nathan Wiebe +4
Numerical simulation of turbulent fluid dynamics needs to either parameterize turbulence-which introduces large uncertainties-or explicitly resolve the smallest scales-which is pro…
Graph identification of proteins in tomograms (GRIP-Tomo)
August George, Doo Nam Kim, Trevor Moser +3
In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, wit…
Forecasting Avalanches in Branched Actomyosin Networks with Network Science and Machine Learning
Chengxuan Li, James Liman, Yossi Eliaz +1
We explored the dynamical and structural effects of actin-related proteins 2/3 (Arp2/3) on actomyosin networks using mechanochemical simulations of active matter networks. At a nan…
CTRAMER: An open source software package for correlating interfacial charge transfer rate constants with donor acceptor geometries in organic photovoltaic materials
Jacob Tinnin, Huseyin Aksu, Zhengqing Tong +5
In this paper we present CTRAMER (Charge Transfer RAtes from Molecular dynamics, Electronic structure, and Rate theory), an open source software package for calculating interfacial…
Understanding Protein-Complex Assembly through Grand Canonical Maximum Entropy Modeling
Andrei G. Gasic, Atrayee Sarkar, Margaret S. Cheung
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putativ…
Determining the atomic charge of calcium ion requires the information of its coordination geometry in an EF-hand motif
Pengzhi Zhang, Jaebeom Han, Piotr Cieplak +1
It is challenging to parameterize the force field for calcium ions (Ca2+) in calcium-binding proteins because of their unique coordination chemistry that involves the surrounding a…