Related papers: How flexibility can enhance catalysis
The minimal 3-state scheme of kinetic cooperativity of monomeric enzymes is subjected to detailed analysis. The rigorous criteria of positive cooperativity and its sigmoidal version are established in terms of the system parameters (rate…
Transcription factor binding sites vary in their specificity, both within and between species. Binding specificity has a strong impact on the evolution of gene expression, because it determines how easily regulatory interactions are gained…
Enhanced diffusion and anti-chemotaxis of enzymes have been reported in several experiments in the last decade, opening up entirely new avenues of research in the bio-nanosciences both at the applied and fundamental level. Here, we…
Stable matching is a fundamental area with many practical applications, such as centralised clearinghouses for school choice or job markets. Recent work has introduced the paradigm of near-feasibility in capacitated matching settings, where…
Structural Causal Models (SCMs) provide a popular causal modeling framework. In this work, we show that SCMs are not flexible enough to give a complete causal representation of dynamical systems at equilibrium. Instead, we propose a…
In this paper we present a new method for determining optimal designs for enzyme inhibition kinetic models, which are used to model the influence of the concentration of a substrate and an inhibition on the velocity of a reaction. The…
In the context of epigenetic transformations in cancer metastasis, a puzzling effect was recently discovered, in which the elimination (knock-out) of an activating regulatory element leads to increased (rather than decreased) activity of…
Background: Autocatalytic sets are often considered a necessary (but not sufficient) condition for the origin and early evolution of life. Although the idea of autocatalytic sets was already conceived of many years ago, only recently have…
We introduce a kinetically constrained spin model with a local softness parameter, such that spin flips can violate the kinetic constraint with an (annealed) site-dependent rate. We show that adding MC swap moves to this model can…
It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…
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…
Biological locomotion in nature is often achieved by the interaction between a flexible body and its surrounding medium. The interaction of a flexible body with granular media is less understood compared with viscous fluids partially due to…
Systems of PDEs comprised of a combination of constraints and evolution equations are ubiquitous in physics. For both theoretical and practical reasons, such as numerical integration, it is desirable to have a systematic understanding of…
The laws of thermodynamics are usually formulated under the assumption of infinitely large environments. While this idealization facilitates theoretical treatments, real physical systems are always finite and their interaction range is…
Many biological materials consist of sparse networks of disordered fibres, embedded in a soft elastic matrix. The interplay between rigid and soft elements in such composite networks leads to mechanical properties that can go far beyond the…
Enzyme-enriched condensates can organize the spatial distribution of their substrates by catalyzing non-equilibrium reactions. Conversely, an inhomogeneous substrate distribution induces enzyme fluxes through substrate-enzyme interactions.…
Enzyme-substrate kinetics form the basis of many biomolecular processes. The interplay between substrate binding and substrate geometry can give rise to long-range interactions between enzyme binding events. Here, we study a general model…
The network approach became a widely used tool to understand the behaviour of complex systems in the last decade. We start from a short description of structural rigidity theory. A detailed account on the combinatorial rigidity analysis of…
Catalysis plays a key role in many scientific areas, most notably in chemistry and biology. Here we present a catalytic process in a paradigmatic quantum optics setup, namely the Jaynes-Cummings model, where an atom interacts with an…
Competitive inhibitors can, paradoxically, stimulate an enzymatic reaction at low to moderate doses. Competitive inhibition of an enzyme occurs when an inhibitor binds to the enzyme's binding site and blocks the enzyme's target molecule…