Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry

ME Johnson, A Chen, JR Faeder… - Molecular Biology of …, 2021 - Am Soc Cell Biol
Most of the fascinating phenomena studied in cell biology emerge from interactions among
highly organized multimolecular structures embedded into complex and frequently dynamic …

Engineering a Novel Probiotic Toolkit in Escherichia coli Nissle 1917 for Sensing and Mitigating Gut Inflammatory Diseases

N Weibel, M Curcio, A Schreiber, G Arriaga… - ACS Synthetic …, 2024 - ACS Publications
Inflammatory bowel disease (IBD) is characterized by chronic intestinal inflammation with no
cure and limited treatment options that often have systemic side effects. In this study, we …

Turing and Benjamin–Feir instability mechanisms in non-autonomous systems

RA Van Gorder - Proceedings of the Royal Society A, 2020 - royalsocietypublishing.org
The Turing and Benjamin–Feir instabilities are two of the primary instability mechanisms
useful for studying the transition from homogeneous states to heterogeneous spatial or …

Determination of the molecular reach of the protein tyrosine phosphatase SHP-1

L Clemens, M Kutuzov, KV Bayer, J Goyette, J Allard… - Biophysical journal, 2021 - cell.com
Immune receptors signal by recruiting (or tethering) enzymes to their cytoplasmic tails to
catalyze reactions on substrates within reach. This is the case for the phosphatase SHP-1 …

Probing the mechanisms of metal CMP using tribo-electroanalytical measurements: results for a copper/malonate system

S Wei, CA Johnson, D Roy - ECS Journal of Solid State Science …, 2021 - iopscience.iop.org
The experiments reported in this work explore certain fundamental mechanistic aspects of
assessing slurry formulations for chemical mechanical planarization (CMP), an important …

[HTML][HTML] An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology

Y Fu, ON Yogurtcu, R Kothari… - The Journal of …, 2019 - pubs.aip.org
Localization of proteins to a membrane is an essential step in a broad range of biological
processes such as signaling, virion formation, and clathrin-mediated endocytosis. The …

Self-avoiding random walks as a model to study athermal linear polymers under extreme plate confinement

O Parreño, PM Ramos, NC Karayiannis, M Laso - Polymers, 2020 - mdpi.com
Monte Carlo (MC) simulations, built around chain-connectivity-altering moves and a wall-
displacement algorithm, allow us to simulate freely-jointed chains of tangent hard spheres of …

pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems

SNV Arjunan, A Miyauchi, K Iwamoto, K Takahashi - BMC bioinformatics, 2020 - Springer
Background Studies using quantitative experimental methods have shown that intracellular
spatial distribution of molecules plays a central role in many cellular systems. Spatially …

Spatio-temporal patterns of non-autonomous systems on hypergraphs: Turing and Benjamin–Feir mechanisms

W Wang, S Liu - New Journal of Physics, 2023 - iopscience.iop.org
This paper examines the Turing patterns and the spatio-temporal chaos of non-autonomous
systems defined on hypergraphs. The analytical conditions for Turing instability and …

Optical dispersions through intracellular inhomogeneities

M Watabe, Y Hirano, A Iwane, O Matoba… - Physical Review …, 2023 - APS
The transport of intensity equation (TIE) exhibits a noninterferometric correlation between
the intensity and phase variations of intermediate fields (eg, light and electrons) in biological …