Related papers: Reaction rate theory for supramolecular kinetics: …
A method is formulated, based on combining self-consistent field theory with dynamically corrected transition state theory, for estimating the rates of adsorption and desorption of end-constrained chains (e.g. by crosslinks or…
The folding vs. adsorption behaviour of a coarse-grained off-lattice protein model near an attractive surface is presented within the frame of a Multicanonical Monte Carlo simulations. In the polymer-surface model, the Lennard-Jones…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
To describe vibrationally mediated configuration changes of adsorbates on surfaces we have developed a new theory to calculate both reaction rates and pathways. The method uses the T-matrix to describe excitations of vibrational states by…
Enzyme-catalysed reactions involve two distinct timescales. There is a short timescale on which enzymes bind to substrate molecules to produce bound complexes, and a comparatively long timescale on which the complex is transformed into a…
Among the numerous questions that arise concerning the exploitation of petroleum from unconventional reservoirs, lie the questions of the composition of hydrocarbons present in deep seated HP-HT reservoirs or produced during in-situ…
Decomposition of biomolecular reaction networks into pathways is a powerful approach to the analysis of metabolic and signalling networks. Current approaches based on analysis of the stoichiometric matrix reveal information about…
The high energy emission of microquasars is thought to originate from high energy particles. Depending on the spectral state, the distribution of these particles can be thermal with a high temperature (typically 100 keV) or non-thermal and…
We present a readily computable semi-analytic Layer Response Theory (LRT) for analysis of cohesive energetics involving two-dimensional layers such as BN or graphene. The theory approximates the Random Phase Approximation (RPA) correlation…
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…
Modern potential energy surfaces have shifted attention to molecular simulations of chemical reactions. While various methods can estimate rate constants for conformational transitions in molecular dynamics simulations, their applicability…
A theoretical framework is proposed for an energy decomposition scheme along the reaction coordinate, in which the ensemble average of the potential energy weighted with reactive flux intensity is decomposed into energy components at the…
Understanding protein motion within the cell is crucial for predicting reaction rates and macromolecular transport in the cytoplasm. A key question is how crowded environments affect protein dynamics through hydrodynamic and direct…
We propose an adiabatic reweighting algorithm for computing the free energy along an external parameter from adaptive molecular dynamics simulations. The adaptive bias is estimated using Bayes identity and information from all the sampled…
Self-assembly of proteins is a biological phenomenon which gives rise to spontaneous formation of amyloid fibrils or polymers. The starting point of this phase, called nucleation exhibits an important variability among replicated…
The kinetic compensation effect (KCE), observed in many fields of science, is the systematic variation in the apparent magnitudes of the Arrhenius parameters $E_a$, the energy of activation, and $\nu$, the preexponential factor, as a…
Rate-equation models are a widely-used and inexpensive tool for the simulation of interstellar chemistry under a range of physical conditions. However, their application to grain-surface chemical systems necessitates a number of simplifying…
Most of the current understanding of structure-property relations at the molecular and the supramolecular scales can be formulated in terms of the stability of and the interactions between a limited number of recurring structural motifs…
It is important to extract reaction coordinates or order parameters from protein simulations in order to investigate the local minimum-energy states and the transitions between them. The most popular method to obtain such data is principal…
The study of protein interactions has generated great interest in the food industry. Therefore, research on new supramolecular structures shows promise. Supramolecular structures of the whey proteins {\alpha}-lactalbumin and…