Related papers: Phoresis and Enhanced Diffusion Compete in Enzyme …

Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have…

Phoretic swimmers are a class of artificial active particles that has received significant attention in recent years. By making use of self-generated gradients (e.g. in temperature, electric potential or some chemical product) phoretic…

Understanding and modeling enzyme-substrate interactions is crucial for catalytic mechanism research, enzyme engineering, and metabolic engineering. Although a large number of predictive methods have emerged, they do not incorporate prior…

Numerous cell-types have shown a remarkable ability to detect and move along gradients in stiffness of an underlying substrate -- a process known as durotaxis. The mechanisms underlying durotaxis are still unresolved, but generally believed…

In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing…

Lubrication theory is broadly applicable to the flow characterization of thin fluid films and the motion of particles near surfaces. We offer an extension to lubrication theory by starting with Stokes equations and considering higher-order…

The enzyme turnover rate is a fundamental parameter in enzyme kinetics, reflecting the catalytic efficiency of enzymes. However, enzyme turnover rates remain scarce across most organisms due to the high cost and complexity of experimental…

The present work was inspired by the recent developments in laboratory experiments made on chip, where culturing of multiple cell species was possible. The model is based on coupled reaction-diffusion-transport equations with chemotaxis,…

Enzymes are biological catalysts that can accelerate chemical reactions compared to uncatalyzed reactions in aqueous environments. Their catalytic efficiency is quantified by the turnover number (kcat), a parameter in enzyme kinetics.…

Cells can use periodic enzyme activities to adapt to periodic environments or existing internal rhythms and to establish metabolic cycles that schedule biochemical processes in time. A periodically changing allocation of the protein budget…

Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…

Despite decades of extensive research, the large-scale analysis of membrane proteins remains a difficult task. This is due to the fact that membrane proteins require a carefully balanced hydrophilic and lipophilic environment, which optimum…

We investigate how an active bath of enzymes influences the liquid-liquid phase separation (LLPS) of a non-interacting condensing protein. The enzyme we choose to use as the active driver is urease, an enzyme that has been shown by several…

In this paper, we apply dimensional analysis to study a diffusive molecular communication system that uses diffusing enzymes in the propagation environment to mitigate intersymbol interference. The enzymes bind to information molecules and…

Chemotaxis is the response of a particle to a gradient in the chemical composition of the environment. While it was originally observed for biological organisms, it is of great interest in the context of synthetic active particles such as…

Most of our understanding of bacterial chemotaxis comes from studies of Escherichia coli. However, recent evidence suggests significant departures from the E. coli paradigm in other bacterial species. This variation may stem from different…

A central question is how the conformational changes of proteins affect their function and the inhibition of this function by drug molecules. Many enzymes change from an open to a closed conformation upon binding of substrate or inhibitor…

We consider the diffusion and spreading of chainlike molecules on solid surfaces. We first show that the steep spherical cap shape density profiles, observed in some submonolayer experiments on spreading polymer films, imply that the…

As an attempt to understand the homochirality of organic molecules in life, a chemical reaction model is proposed where the production of chiral monomers from achiral substrate is catalyzed by the polymers of the same enatiomeric type. This…

The strong fascination exerted by the binary compound of FeSe demands reliable engineering protocols and more effective approaches towards inducing superconductivity in FeSe thin films. Our study addresses the peculiarities in pulsed laser…