Related papers: Single Molecule Michaelis-Menten Equation beyond Q…
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…
A non--equilibrium occupation distribution relaxes towards the Fermi--Dirac distribution due to electron--electron scattering even in finite Fermi systems. The dynamic evolution of this thermalization process assumed to result from an…
This paper is focused on the transient dynamics of an adiabatic nano-electromechanical system (NEMS), consisting of a nano-mechanical oscillator coupled to a quantum dot. By numerically solving the nonlinear stochastic differential equation…
The small dispersion limit of the focusing nonlinear Schrodinger equation with periodic initial conditions is studied analytically and numerically. First, through a comprehensive set of numerical simulations, it is demonstrated that…
Catalysis, the acceleration of product formation by a substance that is left unchanged, typically results from multiple elementary processes, including diffusion of the reactants toward the catalyst, chemical steps, and release of the…
Achieving dynamic manipulation and control of single molecules at high spatio-temporal resolution is pivotal for advancing atomic-scale computing and nanorobotics. However, this endeavour is critically challenged by complex nature of atomic…
A mode-coupling theory for the slow single-particle dynamics in fluids adsorbed in disordered porous media is derived, which complements previous work on the collective dynamics [V. Krakoviack, Phys. Rev. E 75, 031503 (2007)]. Its…
We present a thermodynamically consistent model describing the dynamics of a multi-component mixture where one enzyme component catalyzes a reaction between other components. We find that the catalytic activity alone can induce phase…
Synthesis of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the…
We prove that for a combined system of classical and quantum particles, it is possible to write a dynamics for the classical particles that incorporates in a natural way the Boltzmann equilibrium population for the quantum subsystem. In…
We study the effects of interatomic interactions on the quantum dynamics of a dense, nanoscale, atomic ensemble driven by a strong electromagnetic field. We use a self-consistent, mean-field technique based on the pseudo-spectral…
The glassy dynamics in confluent epithelial monolayers is crucial for several biological processes, such as wound healing, embryogenesis, cancer progression, etc. Several experiments have indicated that, unlike particulate systems, the…
Switch-like motifs are among the basic building blocks of biochemical networks. A common motif that can serve as an ultrasensitive switch consists of two enzymes acting antagonistically on a substrate, one making and the other removing a…
A single mechanism, endemic to the standard model of physics, is proposed to explain wavefunction collapse, classical motion, dissipation, equilibration, and the transition from pure quantum mechanics through open system decoherence to the…
Nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but much less investigated under non-isothermal conditions. However, once the heat exchange between subsystems is rather slow, the isothermal…
Quantum mechanical equations of motion are strictly linear in state descriptors, such as wavefunctions and density matrices, but equations describing chemical kinetics and hydrodynamics may be non-linear in concentrations. This…
One of the general mechanisms that give rise to the slow cooperative relaxation characteristic of classical glasses is the presence of kinetic constraints in the dynamics. Here we show that dynamical constraints can similarly lead to slow…
Here, steady-state reaction networks are inspected from the viewpoint of individual tagged molecules jumping among their chemical states upon the occurrence of reactive events. Such an agent-based viewpoint is useful for selectively…
Ensemble averaging of molecular states is fundamental for the experimental determination of thermodynamic quantities. A special case occurs for single-molecule investigations under equilibrium conditions, for which free energy, entropy and…
We obtain lower and upper bounds on the skewness and kurtosis associated with the cycle completion time of unicyclic enzymatic reaction schemes. Analogous to a well known lower bound on the randomness parameter, the lower bounds on skewness…