Related papers: Modeling of solvent flow effects in enzyme catalys…
New advances in nano sciences open the door for scientists to study biological processes on a microscopic molecule-by-molecule basis. Recent single-molecule biophysical experiments on enzyme systems, in particular, reveal that enzyme…
Enzyme-catalysed reactions involve two distinct timescales. There is a short timescale on which enzymes bind to substrate molecules to produce bound complexes, and a comparatively long timescale on which the complex is transformed into a…
We examine the stochastic dynamics of two enzymes that are mechanically coupled to each other, e.g., through an elastic substrate or a fluid medium. The enzymes undergo conformational changes during their catalytic cycle, which itself is…
A growing amount of evidence points to the fact that many enzymes exhibit fluctuations in their catalytic activity, which are associated with conformational changes on a broad range of timescales. The experimental study of this phenomenon,…
The purpose of this work is to use active particles to study the effect of facilitation on supercooled liquids. To this end we investigate the behavior of a model supercooled liquid doped with intermittently active and intermittently slowed…
We study the enzymatic degradation of an elastic fiber under tension using an an isotropic random-walk model, coupled with binding-unbinding reactions that weaken the fiber. The fiber is represented by a chain of elastic springs in series,…
We present a set of molecular dynamics (MD) simulations of strongly charged, flexible polyelectrolyte chains under poor solvent conditions in a salt free solution. Structural properties of the chains and of the solutions are reported. By…
Mechanochemically active enzymes change their shapes within every turnover cycle. Therefore, they induce circulating flows in the solvent around them and behave as oscillating hydrodynamic force dipoles. Because of non-equilibrium…
Discrete particle simulation, a combined approach of computational fluid dynamics and discrete methods such as DEM (Discrete Element Method), DSMC (Direct Simulation Monte Carlo), SPH (Smoothed Particle Hydrodynamics), PIC…
Electrokinetic transport phenomena can strongly influence the behaviour of macromolecules and colloidal particles in solution, with applications in, e.g., DNA translocation through nanopores, electro-osmotic flow in nanocapillaries, and…
We study the collision dynamics of surfactant-laden droplets and compare it with that of pure water droplets, with a focus on the bridge growth rate, energy balance, and disk dynamics, distinguishing the cases of head-on and off-centre…
Several different enzymes display an apparent diffusion coefficient that increases with the concentration of their substrate. Moreover, their motion becomes directed in substrate gradients. Currently, there are several competing models for…
A four-way coupling scheme for the direct numerical simulation of particle-laden flows is developed and analyzed. It employs a novel adaptive multi-relaxation time lattice Boltzmann method to simulate the fluid phase efficiently. The…
The modelling of electrokinetic flows is a critical aspect spanning many industrial applications and research fields. This has introduced great demand in flexible numerical solvers to describe these flows. The underlying phenomena are…
The cellular milieu is teeming with biochemical nano-machines whose activity is a strong source of correlated non-thermal fluctuations termed active noise. Essential elements of this circuitry are enzymes, catalysts that speed up the rate…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
Why reaction rate constants for enzymatic reactions are typically inversely proportional to fractional power exponents of solvent viscosity remains to be already a thirty years old puzzle. Available interpretations of the phenomenon invoke…
Every mathematical model describing physical phenomena is an approximation to model reality, hence has its limitations. Depending on characteristic values of the variables in the model, different aspects of the model and, e.g.,…
Accurate predictions of charge excitation energies of molecules in the disordered condensed phase are central to the chemical reactivity, stability, and optoelectronic properties of molecules and critically depend on the specific…
We study a fluid-fluid phase transition of the explicit solvent model represented as a mixture of the restricted primitive model (RPM) of ionic fluid and neutral hard spherocylinders (HSC). To this end, we combine two theoretical…