arXiv subjects

Josh E. Baker

Publications and source records attributed to Josh E. Baker.

4 recordsLinked to original sources

arXiv2023

Cells Solved the Gibbs Paradox by Learning to Contain Entropic Forces

As Nature's version of machine learning, evolution has solved many extraordinarily complex problems, none perhaps more remarkable than learning to harness an increase in chemical entropy (disorder) to generate directed chemical forces (order). Using muscle as a model system, here I unpack the basic mechanism by which life creates order from disorder. In short, evolution tuned the physical properties of certain proteins to contain changes in chemical entropy. As it happens, these are the "sensible" properties Gibbs postulated were needed to solve his paradox.

q-bio.BM↗

arXiv2022

Mechanics, Energetics, Entropy and Kinetics of a Binary Mechanical Model System

With the formal construction of a thermodynamic spring, I describe the mechanics, energetics, entropy, and kinetics of a binary mechanical model system. A protein that transitions between two metastable structural states behaves as a molecular switch, and an ensemble of molecular switches that displace compliant elements equilibrated with a system force constitutes a binary mechanical model system. In biological systems, many protein switches equilibrate with cellular forces, yet the statistical mechanical problem relevant to this system has remained unsolved. A binary mechanical model system establishes a limited number of macroscopic parameters into which structural and mechanistic details must be fit. Novel advances include a non-equilibrium kinetic and energetic equivalence; scalable limits on kinetics and energetics; and entropic effects on kinetics and mechanics. The model unifies disparate models of molecular motor mechanochemistry, accounts for the mechanical performance of muscle in both transient and steady states, and provides a new perspective on biomechanics with a focus here on how muscle and molecular motor ensembles work.

physics.bio-ph↗

arXiv2022

Chemical Relaxation of a Binary Mechanical Model System

With potential relevance to biomechanics, an interesting problem in statistical mechanics not previously solved is a binary mechanical model system. Discrete chemical states of proteins are often associated with discrete metastable structural states, such that with a change in state a protein acts as a molecular switch. An ensemble of molecular switches that displace compliant elements equilibrated with an external force, F, constitutes a binary mechanical model system. As one in a series of publications developing this model, here I consider the mechanical performance of this system. Four processes naturally emerge from a transient analysis which are consistent with the four phases observed in a muscle force transient.

cond-mat.stat-mech↗

arXiv2003

Free Energy Transduction in a Chemical Motor Model

Motor enzymes catalyze chemical reactions, like the hydrolysis of ATP, and in the process they also perform work. Recent studies indicate that motor enzymes perform work with specific intermediate steps in their catalyzed reactions, challenging the classic view (in Brownian motor models) that work can only be performed within biochemical states. An alternative class of models (chemical motor models) has emerged in which motors perform work with biochemical transitions, but many of these models lack a solid physicochemical foundation. In this paper, I develop a self consistent framework for chemical motor models. This novel framework accommodates multiple pathways for free energy transfer, predicts rich behaviors from the simplest multi motor systems, and provides important new insights into muscle and motor function.

physics.bio-ph↗