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Spatial and temporal pattern formation in reaction-diffusion systems is typically studied with two or more equations, as scalar reaction-diffusion equations confined to convex domains do not admit stable inhomogeneous states in time or…
We studied the step dynamics during crystal sublimation and growth in the limit of fast surface diffusion and slow kinetics of atom attachment-detachment at the steps. For this limit we formulate a model free of the quasi-static…
The practical description of disordered chemical reactions, where reactions involve multiple species at multiple sites, is presently challenge using correlated electronic structure methods. Here we describe the gradient theory of…
The concept of allostery in which macromolecules switch between two different conformations is a central theme in biological processes ranging from gene regulation to cell signaling to enzymology. Allosteric enzymes pervade metabolic…
The study of pattern emergence together with exploration of the exemplar Turing model is enjoying a renaissance both from theoretical and experimental perspective. Here, we implement a stability analysis of spatially dependent reaction…
In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense…
Enzyme design is a critical area in biotechnology, with applications ranging from drug development to synthetic biology. Traditional methods for enzyme function prediction or protein binding pocket design often fall short in capturing the…
Motor enzymes are remarkable molecular machines that use the energy derived from the hydrolysis of a nucleoside triphosphate to generate mechanical movement, achieved through different steps that constitute their kinetic cycle. These…
A relationship between the preexponent of the rate constant and the distribution over activation barrier energies for enzymatic/protein reactions is revealed. We consider an enzyme solution as an ensemble of individual molecules with…
Throughout developmental biology and ecology, transport can be driven by nonlocal interactions. Examples include cells that migrate based on contact with pseudopodia extended from other cells, and animals that move based on their vision of…
Diffusive transport of small molecules within the internal structures of biological and synthetic material systems is complex because the crowded environment presents chemical and physical barriers to mobility. We explored this mobility…
We report the first study of a network of connected enzyme-catalyzed reactions, with added chemical and enzymatic processes that incorporate the recently developed biochemical filtering steps into the functioning of this biocatalytic…
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.…
The theory of patterns formation for a reaction-diffusion system defined on a multiplex is developed by means of a perturbative approach. The intra-layer diffusion constants act as small parameter in the expansion and the unperturbed state…
We consider the development of hyperbolic transport models for the propagation in space of an epidemic phenomenon described by a classical compartmental dynamics. The model is based on a kinetic description at discrete velocities of the…
Inspired by active shape morphing in developing tissues and biomaterials, we investigate two generic mechanochemical models where the deformations of a thin elastic sheet are driven by, and in turn affect, the concentration gradients of a…
The paper addresses the single-file diffusion in the presence of an absorbing boundary. The emphasis is on an interplay between the hard-core interparticle interaction and the absorption process. The resulting dynamics exhibits several…
Predicting enzyme kinetic parameters quantifies how efficiently an enzyme catalyzes a specific substrate under defined biochemical conditions. Canonical parameters such as the turnover number ($k_\text{cat}$), Michaelis constant…
This paper investigates pattern formation in reaction--diffusion systems with both diffusive and nondiffusive components, providing necessary and sufficient conditions for diffusion-driven instability (DDI) and establishing the existence of…
Stochasticity is a defining feature of the pairwise forces governing interactions in biological systems-from molecular motors to cell-cell adhesion-yet its consequences on large-scale dynamics remain poorly understood. Here, we show that…