Related papers: Kinesin's backsteps under mechanical load
Complex biochemical pathways or regulatory enzyme kinetics can be reduced to chains of elementary reactions, which can be described in terms of chemical kinetics. This discipline provides a set of tools for quantifying and understanding the…
ATP synthase's intrinsic molecular electrostatic potential (MESP) adds constructively to, and hence reinforces, the chemiosmotic voltage. This ATP synthase voltage represents a new free energy term that appears to have been overlooked. This…
In recent literature there has been a lot of interest in the phenomena of noise induced transport in the absence of an average bias occurring in spatially periodic systems far from equilibrium. One of the main motivations in this area is to…
Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorportated nucleotide. The replication fidelity is shown to increase…
We studied the unzipping kinetics of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. PCR analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip…
We examine the interactions between actively rotating proteins moving in a membrane. Experimental evidence suggests that such rotor proteins, like the ATP synthases of the inner mitochondrial membrane, can arrange themselves into lattices.…
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…
We present a study on filamentous actin solutions containing heavy meromyosin subfragments of myosin II motor molecules. We focus on the viscoelastic phase behavior and internal dynamics of such networks during ATP depletion. Upon…
Classical descriptions of enzyme kinetics ignore the physical nature of the intracellular environment. Main implicit assumptions behind such approaches are that reactions occur in compartment volumes which are large enough so that molecular…
A system containing a pre-steady state standard (non-autocatalytic) reaction, with multiple paths, evolves toward a kinetic state with the minimum attainable activation free energy. Displacement of the path frequency distribution in this…
The proton motive force (PMF) across the inner mitochondrial membrane delivers approximately 0.2 eV of energy per proton, powering the FoF1-ATP synthase molecular motor. Here, we provide a detailed accounting of how this energy is utilized:…
Cells move by run and tumble, a kind of dynamics in which the cell alternates runs over straight lines and re-orientations. This erratic motion may be influenced by external factors, like chemicals, nutrients, the extra-cellular matrix, in…
Catalysis lies at the heart of chemical reactivity, yet its foundational principles remain fragmented across the distinct domains of homogeneous, heterogeneous, and enzymatic systems Here, we propose a unifying theoretical model that…
We perform stability analysis of a kinetic bacterial chemotaxis model of bacterial self-organization, assuming that bacteria respond sharply to chemical signals. The resulting discontinuous tumbling kernel represents the key challenge for…
A jump-diffusion process is proposed to describe the displacements performed by single myosin heads along actin filaments during the rising phases. The process consists of the superposition of a Wiener and a jump process, with jumps…
We study a Michaelis-Menten reaction for a single two-state enzyme molecule, whose transition rates between the two conformations are modulated by an harmonically oscillating external force. In particular, we obtain a range of optimal…
Length-regulation of microtubules (MTs) is essential for many cellular processes. Molecular motors like kinesin 8, which move along MTs and also act as depolymerases, are known as key players in MT dynamics. However, the regulatory…
Phase separation is the thermodynamic process that explains how droplets form in multicomponent fluids. These droplets can provide controlled compartments to localize chemical reactions, and reactions can also affect the droplets' dynamics.…
Single kinesin molecular motors can processively move along a microtubule (MT) a few micrometers on average before dissociating. However, cellular length scales over which transport occurs are several hundred microns and more. Why seemingly…
The kinetics of ordering and concurrent ordering and clustering is analyzed with an equation of motion initially developed to account for dissipative processes in quantum systems. A simplified energy eigenstructure, or…