Related papers: Optimization of collective enzyme activity via spa…
The stochastic nature of chemical reactions involving randomly fluctuating population sizes has lead to a growing research interest in discrete-state stochastic models and their analysis. A widely-used approach is the description of the…
Diffusion in a one dimensional random force field leads to interesting localisation effects, which we study using the equivalence with a directed walk model with traps. We show that although the average dispersion of positions $\bar{< x^2 >…
Most biochemical reactions in living cells rely on diffusive search for target molecules or regions in a heterogeneous overcrowded cytoplasmic medium. Rapid re-arrangements of the medium constantly change the effective diffusivity felt…
Assembly theory predicts that a distinguishing signature of life is its ability to produce complex molecules in abundance, opening new possibilities for life detection. Experimental validation of this approach has so far relied on abiotic…
Increasing the enzyme concentration generally speeds up enzymatic reactions. However, in this Letter, we show that increasing the enzyme concentration can also slow down the enzymatic reaction. We consider a simple allosteric protein with…
Diffusion-mediated surface phenomena are crucial for human life and industry, with examples ranging from oxygen capture by lung alveolar surface to heterogeneous catalysis, gene regulation, membrane permeation and filtration processes.…
This study presents an integrated approach to understanding epidemic dynamics through a stochastic spatio-temporal simulation model on a multiplex network, blending physical and informational layers. The physical layer maps the geographic…
Understanding how species persist under interacting stressors is a central challenge in ecology. We develop a spatially explicit reaction-diffusion framework to investigate competing species in landscapes shaped by climate variability,…
Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations are widely used in enzyme simulation. Over ten convergence studies of QM/MM methods have revealed over the past several years that key energetic and structural properties…
A living cell senses its environment and responds to external signals. In this work, we study theoretically, the precision at which cells can determine the position of a spatially localized transient extracellular signal. To this end, we…
Local kinetic constraints in quantum many-body systems can generate slow dynamics or complete many-body localisation. Here we focus on a modification of the quantum East model: Inspired by random matrix theory, we randomise the connectivity…
This chapter discusses the way in which dimensionality reduction algorithms such as diffusion maps and sketch-map can be used to analyze molecular dynamics trajectories. The first part discusses how these various algorithms function, as…
The reversible reactions like A+B <-> C in the many-component diffusive system affect the diffusive properties of the constituents. The effective conjugation of irreversible processes of different dimensionality takes place due to the…
We study a model for a protein searching for a target, using facilitated diffusion, on a DNA molecule confined in a finite volume. The model includes three distinct pathways for facilitated diffusion: (a) sliding - in which the protein…
We present a new modeling approach for G protein coupled receptors signaling systems, that take into account the compartmentalization of receptors and their effectors, both at plasma membrane and in dynamic intra-cellular vesicles called…
In this paper, we present a study on how to develop an efficient multiscale simulation strategy for the dynamics of chemically active systems on low-dimensional supports. Such reactions are encountered in a wide variety of situations,…
The formation of dynamical clusters of proteins is ubiquitous in cellular membranes and is in part regulated by the recycling of membrane components. Mean-field models of out-of-equilibrium cluster formation with recycling predict a broad…
We consider biochemical reaction chains and investigate how random external fluctuations, as characterized by variance and coefficient of variation, propagate down the chains. We perform such a study under the assumption that the number of…
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.…
Biochemical signalling cascades transduce extracellular stimuli into cellular responses through sequences of discrete, node-to-node activations. While signal fidelity depends critically on local interaction kinetics, the mechanisms…