相关论文: Mechanistic rules for de novo design of enzymes

This paper deals with temporal enzyme distribution in the activation of biochemical pathways. Pathway activation arises when production of a certain biomolecule is required due to changing environmental conditions. Under the premise that…

Mobile microscopic bodies, such as motile cells, can be modelled phenomenologically as ``active particles'' which can move against external forces by depleting an internal energy depot. The microscopic mechanisms underlying such ``active''…

The question of characterization of the degree of non-equilibrium activity in active matter systems is studied in the context of a stochastic microswimmer model driven by a chemical cycle. The resulting dynamical properties and entropy…

The rate of a chemical reaction can often be determined by the properties of a rank-1 saddle and the associated transition state separating reactants and products. We have found evidence that such rates can be controlled and even enhanced…

We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical…

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.…

Living systems contain intricate biochemical networks whose structure is closely related to their function and allows them to exhibit robust behavior in the presence of external stimuli. Such networks typically involve catalytic enzymes,…

Biological molecular machines are bifunctional enzymes that catalyze two processes: one donating free energy and the other accepting it. Recent studies show that most protein enzymes have rich stochastic dynamics of transitions between the…

From a purely operational standpoint, the existence of microbes that can grow under extreme conditions, or "extremophiles", leads to the question of how the molecules making up these microbes can maintain both their structure and function.…

The design of a biodegradable, environmentally friendly surfactant is carried out, taking the structure of a known surfactant that lacks these qualities as the starting point, using mesoscopic computer simulations. The newly designed…

An equilibrium reversible cycle with a certain engine to transduce the energy of any chemical reaction into mechanical energy is proposed. The efficiency for chemical energy transduction is also defined so as to be compared with Carnot…

Dynamic cooperativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic…

The kinetics of dislocation reactions, such as dislocation multiplication, controls the plastic deformation in crystals beyond their elastic limit, therefore critical mechanisms in a number of applications in materials science. We present a…

We develop an general formalism of single enzyme kinetics in two dimension where substrates diffuse stochastically on a square lattice in presence of disorder. The dynamics of the model could be decoupled effectively to two stochastic…

Biological molecular motors are high-performance nanomachines that convert chemical energy into mechanical motion via chemomechanical coupling. Their reaction cycles typically comprise a series of intermediate chemical states between the…

Living cells exhibit a complex organization comprising numerous compartments, among which are RNA- and protein-rich membraneless, liquid-like organelles known as biomolecular condensates. Energy-consuming processes regulate their formation…

$\textit{In situ}$ environmental transmission electron microscopy (ETEM) is a powerful tool for observing structural modifications taking place in heterogeneous catalysts under reaction conditions. However, to strengthen the link between…

We present the results of a self-consistent, unified molecular dynamics study of simple model heteropolymers in the continuum with emphasis on folding, sequence design and the determination of the interaction parameters of the effective…

Enzyme kinetics has historically been described by deterministic models, with the Michaelis-Menten (MM) equation serving as a paradigm. However, recent experimental and theoretical advances have made it clear that stochastic fluctuations,…

Chemical reactions involve the movement of charges, and this work presents a mathematical model for describing chemical reactions in electrolytes. The model is developed using an energy variational method that aligns with classical…