Related papers: Manipulating single enzymes by an external harmoni…
A different view of Henri-Michaelis-Menten (HMM) enzyme kinetics is presented. In the first part of the paper, a simplified but useful description that stresses the cyclic nature of the catalytic process is introduced. The time-dependence…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
Biomolecular condensates in cells are often rich in catalytically-active enzymes. This is particularly true in the case of the large enzymatic complexes known as metabolons, which contain different enzymes that participate in the same…
In an experimental study of single enzyme reactions, it has been proposed that the rate constants of the enzymatic reactions fluctuate randomly, according to a given distribution. To quantify the uncertainty arising from random rate…
Chemical reaction rates must increasingly be determined in systems that evolve under the control of external stimuli. In these systems, when a reactant population is induced to cross an energy barrier through forcing from a temporally…
Reaction constants in traditional Michaelis-Menten type enzyme kinetics are most often determined through a linear Lineweaver-Burk plot. While such a graphical plot is sometimes good to achieve the end, it is always better to go for a few…
Chemical reaction network theory is a powerful framework to describe and analyze chemical systems. While much about the concentration profile in an equilibrium state can be determined in terms of the graph structure, the overall reaction's…
Population transfer between two identical, communicating defects in a one-dimensional tight-binding lattice can be systematically controlled by external time-periodic forcing. Employing a force with slowly changing amplitude, the time it…
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…
We present a theoretical study of atom - molecule collisions in superimposed electric and magnetic fields and show that dynamics of electronic spin relaxation in molecules at temperatures below 0.5 K can be manipulated by varying the…
We present analytical expressions and numerical results for the rates of energy exchange between oscillators and with the environment in a heterogeneous ensemble of globally coupled mechanical phase oscillators. The system is in stationary…
Single-enzyme catalysis offers a promising approach for unravelling the dynamic behaviour of individual enzymes as they undergo a reaction, revealing the complex heterogeneity that is lost in the averaged ensembles. Here we demonstrate…
The study of biochemical pathways usually focuses on a small section of a protein interactions network. Two distinct sources contribute to the noise in such a system: intrinsic noise, inherent in the studied reactions, and extrinsic noise…
Enzymes show two distinct transport behaviors in the presence of their substrates in solution. First, their diffusivity enhances with increasing substrate concentration. In addition, enzymes perform directional motion toward regions with…
Energy transfer plays a vital role in many natural and technological processes. In this work, we study the effects of mechanical motion on the excitation transfer through a chain of interacting molecules with application to biological…
Single enzyme chemotaxis is a phenomenon by which a non-equilibrium spatial distribution of an enzyme is created and maintained by concentration gradients of the substrate and product of the catalyzed reaction. These gradients can arise…
Formation of a magnetic hysteresis loop with respect to a bias voltage is investigated theoretically in a spin-valve device based on a single magnetic molecule. We consider a device consisting of two ferromagnetic electrodes bridged by a…
Switching of the direction of flagella rotations is the key control mechanism governing the chemotactic activity of E. coli and many other bacteria. Power-law distributions of switching times are most peculiar because their emergence cannot…
We investigate a stochastic version of a simple enzymatic reaction which follows the generic Michaelis-Menten kinetics. At sufficiently high concentrations of reacting species, the molecular fluctuations can be approximated as a realization…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…