Related papers: Field theory of enzyme-substrate systems with rest…
When two or more atoms bind to a solid surface, the substrate can mediate an interaction between them. In this paper, we use density-functional theory to quantify the substrate-mediated pair interaction between two adatoms on a…
Highly specific spatiotemporal interactions between cognate molecular partners essentially sustain all biochemical transactions in the living matter. That such an exquisite level of accuracy may result from encountering forces solely driven…
Recent experiments have revealed that the diffusivity of exothermic and fast enzymes is enhanced when they are catalytically active, and different physical mechanisms have been explored and quantified to account for this observation. We…
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…
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…
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…
New advances in nano sciences open the door for scientists to study biological processes on a microscopic molecule-by-molecule basis. Recent single-molecule biophysical experiments on enzyme systems, in particular, reveal that enzyme…
Within mean-field theory we study wetting of elastic substrates. Our analysis is based on a grand canonical free energy functional of the fluid number density and of the substrate displacement field. The substrate is described in terms of…
We show that the force generated by active enzyme molecules are strong enough to influence the dynamics of their surroundings under artificial crowded environments. We measured the behavior of polymer microparticles in a…
Understanding and modeling enzyme-substrate interactions is crucial for catalytic mechanism research, enzyme engineering, and metabolic engineering. Although a large number of predictive methods have emerged, they do not incorporate prior…
Designing enzymes with substrate-binding pockets is a critical challenge in protein engineering, as catalytic activity depends on the precise interaction between pockets and substrates. Currently, generative models dominate functional…
Key enzymatic processes in biology use the nonequilibrium error correction mechanism called kinetic proofreading to enhance their specificity. Kinetic proofreading typically requires several dedicated structural features in the enzyme, such…
We examined theory for force-induced unbinding on a two-dimensional free energy surface where the internal dynamics of biomolecules is coupled with the rupture process under constant tension f. We show that only if the transition state…
A growing amount of evidence points to the fact that many enzymes exhibit fluctuations in their catalytic activity, which are associated with conformational changes on a broad range of timescales. The experimental study of this phenomenon,…
Enzymes are nano-scale machines that have evolved to drive chemical reactions out of equilibrium in the right place at the right time. Given the complexity and specificity of enzymatic function, bottom-up design of enzymes presents a…
Alignment interactions in active matter are typically modeled as relaxational dynamics toward local consensus. In unbounded systems, this makes alignment effectively decoupled from local density and therefore unable to sustain self-confined…
Experiments show that the movement of eukaryotic cells is regulated by a process of phase separation of two competing enzymes on the cell membrane, that effectively amplifies shallow external gradients of chemical attractant. Notably, the…
Lattice spin models featuring kinetic constraints constitute a paradigmatic setting for the investigation of glassiness and localization phenomena. The intricate dynamical behavior of these systems is a result of the dramatically reduced…
The relaxation time of a classical spin interacting with a large conduction-electron system is computed for a weak magnetic field, which initially drives the spin out of equilibrium. We trace the spin and the conduction-electron dynamics on…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…