Theory of nonequilibrium free energy transduction by molecular machines

AI Brown, DA Sivak - Chemical reviews, 2019 - ACS Publications
Biomolecular machines are protein complexes that convert between different forms of free
energy. They are utilized in nature to accomplish many cellular tasks. As isothermal …

Thermodynamic uncertainty relations and molecular-scale energy conversion

MW Jack, NJ López-Alamilla, KJ Challis - Physical Review E, 2020 - APS
The thermodynamic uncertainty relation (TUR) is a universal constraint for nonequilibrium
steady states that requires the entropy production rate to be greater than the relative …

Optical chromatography of ultrasmall particles by Brownian motion in a tilted optical potential induced by bound states in the continuum

E Bulgakov, G Shadrina - Journal of the Optical Society of America B, 2025 - opg.optica.org
We investigate sorting Rayleigh optical particles up to several nanometers in size during
Brownian motion in a tilted periodic potential with multiple deep wells. The wells are induced …

Virial-like thermodynamic uncertainty relation in the tight-binding regime

NJ López-Alamilla, RUL Cachi - Chaos: An Interdisciplinary Journal of …, 2022 - pubs.aip.org
We presented a methodology to approximate the entropy production for Brownian motion in
a tilted periodic potential. The approximation stems from the well known thermodynamic …

Reconstructing free-energy landscapes for cyclic molecular motors using full multidimensional or partial one-dimensional dynamic information

NJ López-Alamilla, MW Jack, KJ Challis - Physical Review E, 2019 - APS
Diffusion on a free-energy landscape is a fundamental framework for describing molecular
motors. In the landscape framework, energy conversion between different forms of energy …

A model of minimal entropy generation for cytoskeletal transport systems with multiple interacting motors

NJ López-Alamilla, RUL Cachi - Biophysical Chemistry, 2022 - Elsevier
We study the steady-state rate of entropy generation for multiple interacting particles. The
description used is based on the partially asymmetric exclusion process in a lattice with …

[PDF][PDF] Reconstructing Free-Energy Landscapes for Cyclic Motor Proteins

NJ Lopez Alamilla - 2019 - ourarchive.otago.ac.nz
Cyclic motor proteins are responsible for energy conversion processes inside the cell. Their
dynamical behaviour can be described theoretically in terms of over-damped Brownian …

[CITATION][C] Energy and information flows in strongly coupled rotary machines

E Lathouwers - 2021 - Simon Fraser University