Related papers: Enzyme kinetics at the molecular level
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…
In Biology, all motor enzymes operate on the same principle: they trap favourable brownian fluctuations in order to generate directed forces and to move. Whether it is possible or not to copy one such strategy to play the market was the…
Information transmission in cells occurs quite accurately even when concentration changes are "read" by individual target molecules. In this Letter we study molecule number fluctuations when molecules diffuse and react. We show that, for…
Why reaction rate constants for enzymatic reactions are typically inversely proportional to fractional power exponents of solvent viscosity remains to be already a thirty years old puzzle. Available interpretations of the phenomenon invoke…
This paper deals with temporal enzyme distribution in the activation of biochemical pathways. Pathway activation arises when production of a certain biomolecule is required due to changing environmental conditions. Under the premise that…
Systems composed of large numbers of interacting agents often admit an effective coarse-grained description in terms of a multidimensional stochastic dynamical system, driven by small-amplitude intrinsic noise. In applications to…
Chemically active colloids or enzymes cluster into dense droplets driven by their phoretic response to collectively generated chemical gradients. Employing Brownian dynamics simulation techniques, our study of the dynamics of such a…
Living cells exhibit an important out-of-equilibrium mechanical activity, mainly due to the forces generated by molecular motors. These motor proteins, acting individually or collectively on the cytoskeleton, contribute to the violation of…
The classical approaches to the derivation of the (generalized) Mass Action Law (MAL) assume that the intermediate transition state (i) has short life time and (ii) is in partial equilibrium with the initial reagents of the elementary…
This is the first report, to our knowledge, on a systematic method for constructing a large scale kinetic metabolic model with incomplete information on kinetic parametersr, and its initial application to the modeling of central metabolism…
To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…
Biochemical reaction networks in living cells usually involve reversible covalent modification of signaling molecules, such as protein phosphorylation. Under conditions of small molecule numbers, as is frequently the case in living cells,…
In chemistry, a catalyst is a substance which enables a chemical reaction or increases its rate, while remaining unchanged in the process. Instead of chemical reactions, quantum catalysis enhances our ability to convert quantum states into…
Drastic change in dynamics and statistics in a chemical reaction system, induced by smallness in the molecule number, is reported. Through stochastic simulations for random catalytic reaction networks, transition to a novel state is…
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose…
Many eukaryotic and prokaryotic cells can exhibit remarkable sensing ability under small gradient of chemical compound. In this study, we approach this phenomenon by considering the contribution of multiple ligands to the chemical kinetics…
The long-term behavior of a supercritical branching random walk can be described and analyzed with the help of Biggins' martingales, parametrized by real or complex numbers. The study of these martingales with complex parameters is a rather…
Motor enzymes catalyze chemical reactions, like the hydrolysis of ATP, and in the process they also perform work. Recent studies indicate that motor enzymes perform work with specific intermediate steps in their catalyzed reactions,…
Epithelial-Mesenchymal Transition (EMT), and the corresponding reverse process, Mesenchymal-Epithelial Transition (MET), are dynamic and reversible cellular programs orchestrated by many changes at biochemical and morphological levels. A…
Naively, one expects the information communicated by an enzyme downstream within a signaling network, in which the enzyme is embedded, to grow monotonically with the enzyme's rate of product formation. However, here we observe that this…