Related papers: A Generic Rate Equation for modeling Enzymatic Rea…
A complete derivation, from first principles, of the reaction-rate formula for a generic process taking place in a heat bath of finite volume is given. It is shown that the formula involves no finite-volume correction. Through perturbative…
Chemical reactions often proceed through the formation and the consumption of intermediate species. An example is the creation and subsequent degradation of the substrate-enzyme complexes in an enzymatic reaction. In this paper we provide a…
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…
We present a microscopic approach to quantum dissipation and sketch the derivation of the kinetic equation describing the evolution of a simple quantum system in interaction with a complex quantum system. A typical quantum complex system is…
We analyze the standard model of enzyme-catalyzed reactions at various substrate-enzyme ratios to identify the regions of validity of the quasi-steady-state approximation. Certain prevalent conditions are checked and compared against the…
For some centuries, first order chemical rate constants were determined mainly by a linear logarithmic plot of reagent concentration terms against time where the initial concentration was required, which is experimentally often a…
We propose a whole-body model of the metabolism in man as well as a generalized approach for modeling metabolic networks. Using this approach, we are able to write a large metabolic network in a systematic and compact way. We demonstrate…
In chemical reaction network theory, ordinary differential equations are used to model the temporal change of chemical species concentration. As the functional form of these ordinary differential equations systems is derived from an…
The study of chemical reactions in environments under nonequilibrium conditions has been of interest recently in a variety of contexts, including current-induced reactions in molecular junctions and scanning tunneling microscopy…
Simulating transition dynamics between metastable states is a fundamental challenge in dynamical systems and stochastic processes with wide real-world applications in understanding protein folding, chemical reactions and neural activities.…
Given the evolution of an arbitrary open quantum system, we formulate a general and unambiguous method to separate the internal energy change of the system into an entropy-related contribution and a part causing no entropy change,…
Our ability to calculate rates of biochemical processes using molecular dynamics simulations is severely limited by the fact that the time scales for reactions, or changes in conformational state, scale exponentially with the relevant…
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…
Any organism is embedded in an environment that changes over time. The timescale for and statistics of environmental change, the precision with which the organism can detect its environment, and the costs and benefits of particular protein…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
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…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
As metabolomics datasets are becoming larger and more complex, there is an increasing need for model-based data integration and analysis to optimally leverage these data. Dynamical models of metabolism allow for the integration of…
We propose a nonparametric method for estimating the conditional quantile function that admits a generalized additive specification with an unknown link function. This model nests single-index, additive, and multiplicative quantile…
In the past one hundred years, deterministic rate equations have been successfully used to infer enzyme-catalysed reaction mechanisms and to estimate rate constants from reaction kinetics experiments conducted in vitro. In recent years,…