Related papers: Phoresis and Enhanced Diffusion Compete in Enzyme …
Enzymes are nano-scale machines that have evolved to drive chemical reactions out of equilibrium in the right place at the right time. Given the complexity and specificity of enzymatic function, bottom-up design of enzymes presents a…
Enzymes within biochemical pathways are often colocalized, yet the consequences of specific spatial enzyme arrangements remain poorly understood. We study the impact of enzyme arrangement on reaction efficiency within a reaction-diffusion…
The more we learn about the cytoplasm of cells, the more we realise that the cytoplasm is not uniform but instead is highly inhomogeneous. In any inhomogeneous solution, there are concentration gradients, and particles move either up or…
Flows enabled by phoretic mechanisms are of significant interest in several biological and biomedical processes, such as bacterial motion and targeted drug delivery. Here, we develop a homogenization-based macroscopic boundary condition…
Chemotaxis, the directional locomotion of cells towards a source of a chemical gradient, is an integral part of many biological processes - for example, bacteria motion, single-cell or multicellular organisms development, immune response,…
Biomolecular condensates help organize the cell cytoplasm and nucleoplasm into spatial compartments with different chemical compositions. A key feature of such compositional patterning is the local enrichment of enzymatically active…
The high accuracy exhibited by biological information transcription processes is due to kinetic proofreading, i.e., by a mechanism which reduces the error rate of the information-handling process by driving it out of equilibrium. We provide…
Aerotaxis is the particular form of chemotaxis in which oxygen plays the role of both the attractant and the repellent. Aerotaxis occurs without methylation adaptation, and it leads to fast and complete aggregation toward the most favorable…
Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
Key enzymatic processes in biology use the nonequilibrium error correction mechanism called kinetic proofreading to enhance their specificity. Kinetic proofreading typically requires several dedicated structural features in the enzyme, such…
We consider the lateral diffusion of a protein interacting with the curvature of the membrane. The interaction energy is minimized if the particle is at a membrane position with a certain curvature that agrees with the spontaneous curvature…
We (Riedel et al. Nature 2015), as well as others, have showed that some enzymes exhibit enhanced diffusion when active. In a recent PRL, (Golestanian, PRL 2015, arXiv:1508.03219) R.Golestanian theoretically examines a number of possible…
Microscopic dynamical aspects of the propulsion of nanomotors by self-phoretic mechanisms are considered. Propulsion by self-diffusiophoresis relies on the mechanochemical coupling between the fluid velocity field and the concentration…
We suppose that a rigid spherical particle is put into a binary fluid mixture with the critical composition in the homogeneous phase near the demixing critical point. A short-range interaction is assumed between each component and the…
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…
We discuss the shear viscosity of a Newtonian solution of catalytic enzymes and substrate molecules. The enzyme is modeled as a two-state dimer consisting of two spherical domains connected with an elastic spring. The enzymatic…
A protein undergoes conformational dynamics with multiple time scales, which results in fluctuating enzyme activities. Recent studies in single molecule enzymology have observe this "age-old" dynamic disorder phenomenon directly. However,…
Biological nanomachines are nanometer-size macromolecular complexes that catalyze chemical reactions in the presence of substrate molecules. The catalytic functions carried out by such nanomachines in the cytoplasm, and biological membranes…
Physics of self-propelled objects at the nanoscale is a rapidly developing research field where recent experiments focused on motion of individual catalytic enzymes. Contrary to the experimental advancements, theoretical understanding of…
This paper introduces a reaction-diffusion-chemotaxis model for bacterial aggregation patterns on the surface of thin agar plates. It is based on the non-linear degenerate cross diffusion model proposed by Kawasaki et al. (J. of Theor.…