Related papers: Manipulating single enzymes by an external harmoni…
The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…
To study the dynamics of chemical processes, we often adopt rate equations to observe the change in chemical concentrations. However, when the number of the molecules is small, the fluctuations cannot be neglected. We often study the…
The metabolic state of a cell, comprising fluxes, metabolite concentrations and enzyme levels, is shaped by a compromise between metabolic benefit and enzyme cost. This hypothesis and its consequences can be studied by computational models…
We investigate the mutiphoton process between different Bloch states in an amplitude modulated optical lattice. In the experiment, we perform the modulation with more than one frequency components, which includes a high degree of freedom…
We discuss the force-velocity relations obtained in a two-state crossbridge model for molecular motors. They can be calculated analytically in two limiting cases: for a large number and for one pair of motors. The effect of the…
The paper proposes the method to analyze the internal dynamics of nanoscopic systems by periodic modulation of the electrochemical potentials of the attached leads and measuring the time-averaged current. The idea is presented using the…
A non-equilibrium steady state is characterized by a non-zero steady dissipation rate. Chemical reaction systems under suitable conditions may generate such states. We propose here a method that is able to distinguish states with identical…
Shrinking spintronic devices to the nanoscale ultimately requires localized control of individual atomic magnetic moments. At these length scales, the exchange interaction plays important roles, such as in the stabilization of…
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…
Biomolecular machines transduce between different forms of energy. These machines make directed progress and increase their speed by consuming free energy, typically in the form of nonequilibrium chemical concentrations. Machine dynamics…
We examine a mechanism of locomotion of active particles whose surface is uniformly coated with mobile enzymes. The enzymes catalyze a reaction that drives phoretic flows but their homogeneous distribution forbids locomotion by symmetry. We…
Different graphical plots involving the catalytic rate with the (initial) substrate concentration exist in the enzyme kinetics literature to estimate the reaction constants. But, none of these standard plots can unambiguously distinguish…
Many biological molecular motors and machines are driven by chemical reactions that occur in specific catalytic sites. We study whether the arrival of molecules to such an active site can be accelerated by the presence of a nearby inactive…
The classical theory of enzymatic inhibition aims to quantitatively describe the effect of certain molecules -- called inhibitors -- on the progression of enzymatic reactions, but growing signs indicate that it must be revised to keep pace…
We study the dynamics of simple reactions where the chemical species are confined on a general, time-modulated surface, and subjected to externally-imposed stirring. The study of these inhomogeneous effects requires a model based on a…
We predict and study the quantum-electrodynamical effect of parametric self-induced excitation of a molecule moving above the dielectric or conducting medium with periodic grating. In this case the radiation reaction force modulates the…
Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
We show that oscillations are excited in a complex system under the influence of the external force, if the parameters of the system experience rapid change due to the changes in its internal structure. This excitation is collision-like and…
By monitoring the sampling of states with different magnetizations in transition matrix procedures a family of accurate and easily implemented techniques are constructed that automatically control the variation of the temperature or energy…
Through the analysis of density of states (DOS), we study two different kinds of cyclic molecules, a sodium atomic circle and a Polycyclic Aromatic Hydrocarbons (PAH) molecule respectively under an external magnetic field. The results of…