Related papers: Enzyme-Substrate Complex Formation Modulates Diffu…
The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of…
Diffusion models generate structure by progressively transforming noise into data, yet the mechanisms underlying this transition remain poorly understood. In this work, we show that pattern formation in trained diffusion models can be…
Patterns in reaction-diffusion systems often contain two spatial scales; a long scale determined by a typical wavelength or domain size, and a short scale pertaining to front structures separating different domains. Such patterns naturally…
Understanding how patterns and travelling waves form in chemical and biological reaction-diffusion models is an area which has been widely researched, yet is still experiencing fast development. Surprisingly enough, we still do not have a…
Multistationarity in biological systems is a mechanism of cellular decision making. In particular, signaling pathways regulated by protein phosphorylation display features that facilitate a variety of responses to different biological…
The function of biomolecules such as proteins depends on their ability to interconvert between a wide range of structures or "conformations." Researchers have endeavored for decades to develop computational methods to predict the…
We examine the dynamics of a two-dimensional stripe, bubble, and crystal forming system interacting with a periodic one-dimensional substrate under an applied drive that is rotated with respect to the substrate periodicity direction $x$. We…
This is the first report, to our knowledge, on a systematic method for constructing a large scale kinetic metabolic model with incomplete information on kinetic parametersr, and its initial application to the modeling of central metabolism…
Chemically fueled supramolecular systems can exhibit complex, time-dependent behaviors reminiscent of living matter when maintained far from equilibrium by continuous energy or fuel consumption. Here, we introduce a minimal…
Cellulases hold great promise for the production of biofuels and biochemicals. However, they are modular enzymes acting on a complex heterogeneous substrate. Because of this complexity, the computational prediction of their catalytic…
The equilibration of enzyme and complex concentrations in deterministic Michaelis-Menten reaction networks underlies the hyperbolic dependence between the input (substrates) and output (products). This relationship was first obtained by…
Due to inter-subunit communication, multisubunit enzymes usually hydrolyze ATP in a concerted fashion. However, so far the principle of this process remains poorly understood. In this study, from the viewpoint of statistical thermodynamics,…
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…
We investigate diffusion-driven instabilities in a FitzHugh-Nagumo reaction-diffusion system with superdiffusive transport, modeled by fractional Laplacian operators with different diffusion orders for the activator and the inhibitor. A…
We investigate the transport of interacting active run-and-tumble particles moving under an external drift force through a periodic array of obstacles for increasing drive amplitudes. For high activity where the system forms a motility…
Crowded environments modify the diffusion of macromolecules, generally slowing their movement and inducing transient anomalous subdiffusion. The presence of obstacles also modifies the kinetics and equilibrium behavior of tracers. While…
Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically…
There are various examples of phenotypic plasticity in ecosystems that serve as the basis for a wide range of inducible defences against predation. These strategies include camouflage, burrowing, mimicry, evasive actions, and even…
Diffusioosmotic flow arises in microfluidic configurations due to solute concentration gradients. In soft microfluidic channels, internal pressure gradients generated by diffusioosmotic flow to conserve mass result in elastic deformation of…
The hyperbolic dependence of catalytic rate on substrate concentration is a classical result in enzyme kinetics, quantified by the celebrated Michaelis-Menten equation. The ubiquity of this relation in diverse chemical and biological…