Related papers: Manipulating single enzymes by an external harmoni…
Mechanochemical coupling was studied for two different types of myosin motors in cells: myosin V, which carries cargo over long distances by as a single molecule; and myosin II, which generates a contracting force in cooperation with other…
Enzyme-mediated reactions may proceed through multiple intermediate conformational states before creating a final product molecule, and one often wishes to identify such intermediate structures from observations of the product creation. In…
Reactions with enzymes are critical in biochemistry, where the enzymes act as catalysis in the process. One of the most used mechanisms for modeling enzyme-catalyzed reactions is the Michaelis-Menten (MM) kinetic. In the ODE level, i.e.…
Spatiotemporal pattern formation in a product-activated enzymic reaction at high enzyme concentrations is investigated. Stochastic simulations show that catalytic turnover cycles of individual enzymes can become coherent and that complex…
We consider the application of Kramers theory to the microscopic calculation of rates of conformational transitions of macromolecules. The main difficulty in such an approach is to locate the transition state in a huge configuration space.…
The rates of activated processes, such as escape from a metastable state and nucleation, are exponentially sensitive to an externally applied field. We describe how this applies to modulation by high-frequency fields and illustrate it with…
In this study, through phenomenological comparison of the velocity-force data of processive motor proteins, including conventional kinesin, cytoplasmic dynein and myosin V, we found that, the ratio between motor velocities of two different…
One of the most intriguing results of single molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active…
We study the ensemble velocity of non-processive motor proteins, described with multiple chemical states. In particular, we discuss the velocity as a function of ATP concentration. Even a simple model which neglects the strain-dependence of…
The century-long Michaelis-Menten rate law and its modifications in the modeling of biochemical rate processes stand on the assumption that the concentration of the complex of interacting molecules, at each moment, rapidly approaches an…
Since molecular energy transformations are responsible for chemical reaction rates at the most fundamental level, chemical kinetics should provide some information about molecular energies. This is the premise and objective of this note. We…
The time-dependent transport through single-molecule magnets coupled to magnetic or non-magnetic electrodes is studied in the framework of the generalized master equation method. We investigate the transient regime induced by the periodic…
Magnetic hysteresis has become a crucial aspect for characterizing single-molecule magnets, but the comprehension of the coercivity mechanism is still a challenge. By using analytical derivation and quantum dynamical simulations, we reveal…
Autocatalytic reaction system with a small number of molecules is studied numerically by stochastic particle simulations. A novel state due to fluctuation and discreteness in molecular numbers is found, characterized as extinction of…
We demonstrate that the Michaelis-Menten reaction mechanism can be accurately approximated by a linear system when the initial substrate concentration is low. This leads to pseudo-first-order kinetics, simplifying mathematical calculations…
Complex biochemical pathways or regulatory enzyme kinetics can be reduced to chains of elementary reactions, which can be described in terms of chemical kinetics. This discipline provides a set of tools for quantifying and understanding the…
We study the statistical properties of a simple genetic regulatory network that provides heterogeneity within a population of cells. This network consists of a binary genetic switch in which stochastic flipping between the two switch states…
We show that an ensemble of $^2\Sigma$ molecules in the rotationally ground state trapped on an optical lattice exhibits collective spin excitations that can be controlled by applying superimposed electric and magnetic fields. In…
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…
Michaelis-Menten equation is a basic equation of enzyme kinetics and gives an acceptable approximation of real chemical reaction processes. Analyzing the derivation of this equation yields the fact that its good performance of approximating…