Related papers: Single-substrate Enzyme Kinetics: The Quasi-steady…
Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations are widely used in enzyme simulation. Over ten convergence studies of QM/MM methods have revealed over the past several years that key energetic and structural properties…
In the setting of stochastic dynamical systems that eventually go extinct, the quasi-stationary distributions are useful to understand the long-term behavior of a system before evanescence. For a broad class of applicable continuous-time…
A relationship between the preexponent of the rate constant and the distribution over activation barrier energies for enzymatic/protein reactions is revealed. We consider an enzyme solution as an ensemble of individual molecules with…
Model-based prediction of stochastic noise in biomolecular reactions often resorts to approximation with unknown precision. As a result, unexpected stochastic fluctuation causes a headache for the designers of biomolecular circuits. This…
Reliability of kinetic parameters are crucial in understanding enzyme kinetics within cellular system. The present study suggests a few cautions that need introspection for estimation of parameters like K(M), V(max) and K(I) using…
We develop a hierarchy of approximations to the master equation for systems that exhibit translational invariance and finite-range spatial correlation. Each approximation within the hierarchy is a set of ordinary differential equations that…
In this paper, we develop a method for obtaining the approximate solution for the evolution of single-step transformations under non-isothermal conditions. We have applied it to many reaction models and obtained very simple analytical…
The usual semiclassical approximation for atom-field dynamics consists in substituting the field operators by complex numbers related to the (supposedly large enough) intensity of the field. We show that a semiclassical evolution for…
The field of single atom catalysis (SAC) has expanded greatly in recent years. While there has been much success developing new synthesis methods, a fundamental disconnect exists between most experiments and the theoretical computations…
In a conformational nonequilibrium steady state (cNESS), enzyme turnover is modulated by the underlying conformational dynamics. Based on a discrete kinetic network model, we use the integrated probability flux balance method to derive the…
A combination of classical density-functional theory and thermodynamic perturbation theory is applied to a survey of finite-temperature trends in the relative stabilities of one-component crystals and quasicrystals interacting via effective…
In this work, the Quasi-Random Lattice (QRL) model is summarized and critically discussed, in order to outline its potentialities and limitations, in perspective of future developments. QRL primarily focuses on the mean activity coefficient…
The rigorous quantum mechanical description of the collective interaction of many molecules with the radiation field is usually considered numerically intractable, and approximation schemes must be employed. Standard spectroscopy usually…
Understanding the fundamental mechanisms of single-atom catalysis (SAC) is important to design systems with improved performance and stability. This is problematic, however, because single-atom active sites are extremely difficult to…
We introduce a reaction-path statistical mechanics formalism based on the principle of large deviations to quantify the kinetics of single-molecule enzymatic reaction processes under the Michaelis-Menten mechanism, which exemplifies an…
Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to…
We study kinetic models of reversible enzyme reactions and compare two techniques for analytic approximate solutions of the model. Analytic approximate solutions of non-linear reaction equations for reversible enzyme reactions are…
We investigate the stability properties of two different classes of metabolic cycles using a combination of analytical and computational methods. Using principles from structural kinetic modeling (SKM), we show that the stability of…
The Michaelis-Menten mechanism is probably the best known model for an enzyme-catalyzed reaction. For spatially homogeneous concentrations, QSS reductions are well known, but this is not the case when chemical species are allowed to…
$\textit{In situ}$ 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…