Related papers: Reaction rate theory for supramolecular kinetics: …
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
The protein folding is regarded as a quantum transition between torsion states on polypeptide chain. The deduction of the folding rate formula in our previous studies is reviewed. The rate formula is generalized to the case of frequency…
We present a mathematical study for the development of Multiple Sclerosis in which a spatio-temporal kinetic { theory} model describes, at the mesoscopic level, the dynamics of a high number of interacting agents. We consider both…
There is increasing evidence that numerous membrane proteins can assemble into aggregates that modulate their function and affect many cellular processes such as signal transduction and endocytosis. Here, we present a theoretical…
Processes involving multi-input multi-step reaction cascades are used in developing novel biosensing, biocomputing, and decision making systems. In various applications different changes in responses of the constituent processing steps…
Molecular modeling of thermally activated chemistry in condensed phases is essential to understand polymerization, depolymerization, and other processing steps of molecular materials. Current methods typically combine molecular dynamics…
We propose a methodology for fully automated calculation of thermal rate coefficients of gas phase chemical reactions, which is based on combining the ring polymer molecular dynamics (RPMD) with the machine-learning interatomic potentials…
The climate crisis demands a rapid shift to sustainable energy technologies and higher efficiency in existing energy systems. Adsorption-based thermochemical energy storage is a promising alternative due to its high energy density and…
Umbrella sampling is an efficient method for the calculation of free energy changes of a system along well-defined reaction coordinates. However, when multiple parallel channels along the reaction coordinate or hidden barriers in directions…
This paper is concerned with classes of models of stochastic reaction dynamics with time-scales separation. We demonstrate that the existence of the time-scale separation naturally leads to the application of the averaging principle and…
The thermal activation process by which a system passes from one local energy minimum to another is a recurring motif in physics, chemistry, and biology. For instance, biopolymer chains are typically modeled in terms of energy landscapes,…
We investigate the effect of macromolecular crowding on protein folding, using purely repulsive crowding particles and a self-organizing polymer model of protein folding. We find that the thermodynamics of folding for typical alpha-, beta-…
Photothermal reactions, involving both photochemical and thermal reaction-steps, are the most abundant sequences in photochemistry. The derivation of their rate-laws is standardized, but the integration of these rate-laws has not yet been…
We describe a model for photon absorption by superconducting tunnel junctions in which the full energy dependence of all the quasiparticle dynamic processes is included. The model supersedes the well-known Rothwarf-Taylor approach, which…
The quantitative description of model protein folding kinetics using a diffusive collective reaction coordinate is examined. Direct folding kinetics, diffusional coefficients and free energy profiles are determined from Monte Carlo…
Simulations with an adaptive time-dependent bias, such as metadynamics, enable an efficient exploration of the conformational space of a system. However, the dynamic information of the system is altered by the bias. With infrequent…
We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…
We examine the phase transition of polymer adsorption as well as the underlying kinetics of polymer binding from dilute solutions on a structureless solid surface. The emphasis is put on the properties of regular multiblock copolymers,…
Proteins can be regarded as thermal nanosensors in an intra-body network. Upon being stimulated by Terahertz (THz) frequencies that match their vibrational modes, protein molecules experience resonant absorption and dissipate their energy…
Chemical reactions at ultracold temperature provide an ideal platform to study chemical reactivity at the fundamental level, and to understand how chemical reactions are governed by quantum mechanics. Recent years have witnessed the…