Related papers: Enzyme kinetics at the molecular level
The rate equation for an arbitrary mth order growth or decay reaction can be expressed in terms of the q-exponential function, with q equal to m. The analysis suggests that a wide variety of reaction rate (kinetic) processes and models, in…
We develop a rigorous theory of hard-sphere dynamics in the kinetic regime, away from thermal equilibrium. In the low density limit, the empirical density obeys a law of large numbers and the dynamics is governed by the Boltzmann equation.…
Bacterial growth depends crucially on metabolic fluxes, which are limited by the cell's capacity to maintain metabolic enzymes. The necessary enzyme amount per unit flux is a major determinant of metabolic strategies both in evolution and…
Enzyme reactions are highly dependent on reaction conditions. To ensure reproducibility of enzyme reaction parameters, experiments need to be carefully designed and kinetic modelling meticulously executed. Furthermore, to enable the…
The progress of the successive rounds of catalytic conversion of substrates into product(s) by a single enzyme is characterized by the distribution of turnover times. Establishing the most general form of dependence of this distribution on…
The lattice Boltzmann model is a simplified kinetic method based on the particle distribution function. We use this method to simulate problems in MEMS, in which the velocity slip near the wall plays an important role. It is demonstrated…
The paper deals with relationships between the individual transmembrane fluxes of binary electrolyte solution components and the experimentally measurable quantities describing rates of transfer processes, namely, the electric current, the…
In living cells, motor proteins, such as kinesin and dynein can move processively along microtubule (MT), and also detach from or attach to MT stochastically. Experiments have found that, the traffic of motor might be jammed, and various…
For Markov processes over discrete configurations, an asymptotic bound on the uncertainty of stochastic fluxes is derived in terms of the harmonic mean of decay rates with respect to the stationary distribution. This bound is necessarily…
Stochastic modeling of transcription is a classic yet long-standing problem in theoretical biophysics. The lack of unified results and a computationally efficient approach for a general, fine-grained transcription model has confined…
Chemotaxis in bacteria such as \textit{E.\ coli} is controlled by the slow methylation of chemoreceptors. As a consequence, intrinsic time and length scales of tens of seconds and hundreds of micrometers emerge, making the Keller--Segel…
Enzyme-substrate kinetics form the basis of many biomolecular processes. The interplay between substrate binding and substrate geometry can give rise to long-range interactions between enzyme binding events. Here, we study a general model…
Theoretical analysis, which maps single molecule time trajectories of a molecular motor onto unicyclic Markov processes, allows us to evaluate the heat dissipated from the motor and to elucidate its dependence on the mean velocity and…
The purpose of the dynamics of moving systems is to search for the mathematical model that describes the link between the resultant applied force, that is the cause, and the speed of system that is the effect. This mathematical link…
Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and environmentally friendly. While several aspects of this…
Synthesis of biopolymers such as DNA, RNA, and proteins are biophysical processes aided by enzymes. Performance of these enzymes is usually characterized in terms of their average error rate and speed. However, because of thermal…
We analyse the mechanism of enzyme-substrate catalysis from the perspective of minimizing the load on the enzymes through sequestration, whilst maintaining at least a minimum reaction flux. In particular, we ask: which binding free energies…
The spatial organization of enzymes often plays a crucial role in the functionality and efficiency of enzymatic pathways. To fully understand the design and operation of enzymatic pathways, it is therefore crucial to understand how the…
Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries, reaction fluxes (rate laws), and…
Enzymes have been recently found to exhibit enhanced diffusion due to their catalytic activities. A recent experiment [C. Riedel et al., Nature 517, 227 (2015)] has found evidence that suggests this phenomenon might be controlled by the…