Related papers: Single Molecule Michaelis-Menten Equation beyond Q…
Biomolecular condensates provide distinct chemical environments, which control various cellular processes. The diffusive dynamics and chemical kinetics inside phase-separated condensates can be studied experimentally by fluorescently…
General discrete one-dimensional stochastic models to describe the transport of single molecules along coupled parallel lattices with period $N$ are developed. Theoretical analysis that allows to calculate explicitly the steady-state…
For a single enzyme or molecular motor operating in an aqueous solution of non-equilibrated solute concentrations, a thermodynamic description is developed on the level of an individual trajectory of transitions between states. The concept…
A semilinear parabolic equation with constraint modeling the dynamics of a microelectromechanical system (MEMS) is studied. In contrast to the commonly used MEMS model, the well-known pull-in phenomenon occurring above a critical potential…
A molecular dynamics simulation is performed for a supercooled liquid of rigid diatomic molecules. The time-dependent self and collective density correlators of the molecular centers of mass are determined and compared with the predictions…
Micro-Electro Mechanical Systems (MEMS) are defined as very small structures that combine electrical and mechanical components on a common substrate. Here, the electrostatic-elastic case is considered, where an elastic membrane is allowed…
A minimal design for a molecular swimmer is proposed that is a based on a mechanochemical propulsion mechanism. Conformational changes are induced by electrostatic actuation when specific parts of the molecule temporarily acquire net…
Recent experiments indicate that electromagnetic hysteresis behavior can be exhibited at the molecular level.A MD simulation using 2-body potentials and switches to form and break bonds is implemented to determine whether chemical reaction…
Using molecular dynamics simulations we study the slow dynamics of a hard sphere fluid confined in a disordered porous matrix. The presence of both discontinuous and continuous glass transitions as well as the complex interplay between…
Despite linear regression being the most popular statistical modelling technique, in real-life we often need to deal with situations where the true relationship between the response and the covariates is nonlinear in parameters. In such…
The first passage times for enzymatic turnovers in non-equilibrium steady state display a statistical symmetry property related to non-equilibrium fluctuation theorems, that makes it possible to extract the chemical driving force from…
Single molecule time trajectories of biomolecules provide glimpses into complex folding landscapes that are difficult to visualize using conventional ensemble measurements. Recent experiments and theoretical analyses have highlighted…
As well known, the generalized Langevin equation with a memory kernel decreasing at large times as an inverse power law of time describes the motion of an anomalously diffusing particle. Here, we focus attention on some new aspects of the…
The interactions between diffusing molecules and membrane-bound receptors drive numerous cellular processes. In this work, we develop a spatial model of molecular interactions with membrane receptors by homogenizing the cell membrane and…
The statistics of steps and dwell times in reversible molecular motors differ from those of cycle completion in enzyme kinetics. The reason is that a step is only one of several transitions in the mechanochemical cycle. As a result,…
Atherosclerosis is a chronic inflammatory disease occurs due to plaque accumulation in the inner artery wall. In atherosclerotic plaque formation monocytes and macrophages play a significant role in controlling the disease dynamics. In the…
A theory is formulated for time dependent fluctuations of the spectrum of a single molecule in a dynamic environment. In particular, we investigate the photon counting statistics of a single molecule undergoing a spectral diffusion process.…
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual…
We examine the stochastic dynamics of two enzymes that are mechanically coupled to each other, e.g., through an elastic substrate or a fluid medium. The enzymes undergo conformational changes during their catalytic cycle, which itself is…
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…