The nanocaterpillar's random walk: diffusion with ligand–receptor contacts

S Marbach, JA Zheng, M Holmes-Cerfon - Soft Matter, 2022 - pubs.rsc.org
Particles with ligand–receptor contacts bind and unbind fluctuating “legs” to surfaces, whose
fluctuations cause the particle to diffuse. Quantifying the diffusion of such “nanoscale …

Stochastic switching of delayed feedback suppresses oscillations in genetic regulatory systems

BR Karamched, CE Miles - Journal of The Royal Society …, 2023 - royalsocietypublishing.org
Delays and stochasticity have both served as crucially valuable ingredients in mathematical
descriptions of control, physical and biological systems. In this work, we investigate how …

Coarse-grained dynamics of transiently bound fast linkers

S Marbach, CE Miles - The Journal of Chemical Physics, 2023 - pubs.aip.org
Transient bonds between fast linkers and slower particles are widespread in physical and
biological systems. Despite their diverse structure and function, a commonality is that the …

Competition between physical search and a weak-to-strong transition rate-limits kinesin binding times

T Nguyen, BRJ Narayanareddy… - PLoS Computational …, 2024 - journals.plos.org
The self-organization of cells relies on the profound complexity of protein-protein
interactions. Challenges in directly observing these events have hindered progress toward …

Thermodynamic uncertainty for run-and-tumble–type processes

M Shreshtha, RJ Harris - Europhysics Letters, 2019 - iopscience.iop.org
Thermodynamic uncertainty relations have emerged as universal bounds on current
fluctuations in non-equilibrium systems. Here we derive a new bound for a particular class of …

Simulating rolling paths and reorientation behavior of ball-rolling dung beetles

Z Yin, L Zinn-Björkman - Journal of Theoretical Biology, 2020 - Elsevier
Ball-rolling dung beetles show a remarkable ability to maintain a straight path while rolling
dung balls away from a dung pile. Rolling in a straight line is beneficial, as it enables beetles …

Bidirectional, unlike unidirectional transport, allows transporting axonal cargos against their concentration gradient

IA Kuznetsov, AV Kuznetsov - Journal of Theoretical Biology, 2022 - Elsevier
Even though most axonal cargos are synthesized in the soma, the concentration of many of
these cargos is larger at the presynaptic terminal than in the soma. This requires transport of …

A Semi-Markov Approach to Study a Group of Kinesin Motors

L Han, J Fricks - Bulletin of mathematical biology, 2024 - Springer
We propose a general mathematical and computational approach to study cellular transport
driven by a group of kinesin motors. It is a framework for multi-scale modeling that integrates …

Renewal reward perspective on linear switching diffusion systems in models of intracellular transport

MV Ciocanel, J Fricks, PR Kramer… - Bulletin of mathematical …, 2020 - Springer
In many biological systems, the movement of individual agents is characterized having
multiple qualitatively distinct behaviors that arise from a variety of biophysical states. For …

Effective behavior of cooperative and nonidentical molecular motors

JJ Klobusicky, J Fricks, PR Kramer - Research in the mathematical …, 2020 - Springer
Analytical formulas for effective drift, diffusivity, run times, and run lengths are derived for an
intracellular transport system consisting of a cargo attached to two cooperative but not …