Related papers: Dynamic Phase Transitions in Coupled Motor Protein…
An extension of the Kinetic Ising model with nonuniform coupling constants on a one-dimensional lattice with boundaries is investigated, and the relaxation of such a system towards its equilibrium is studied. Using a transfer matrix method,…
The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…
We experimentally examine the dynamics of two-particle collisions occuring on a surface. We find that in two-particle collisions a standard coefficient of restitution model may not capture crucial dynamics of this system. Instead, for a…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…
We comprehensively study external forcing-driven dynamical structure formation in a binary dusty plasma mixture. Using two-dimensional driven-dissipative molecular dynamics simulations, we demonstrate phase segregation into bands and lanes…
It was recently argued that one-dimensional systems of several strongly interacting fermions of different mass undergo critical transitions between different spatial orderings when the external confinement adiabatically changes its shape.…
A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the…
Brownian particles interacting sequentially with distinct temperatures and driving forces at each stroke have been tackled as a reliable alternative for the construction of engine setups. However they can behave very inefficiently depending…
Biofilament-motor protein complexes are ubiquitous in biology and drive the transport of cargo vital for many fundamental cellular processes. As they move, motor proteins exert compressive forces on the filaments to which they are attached,…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
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…
This work addresses non-classically damped coupled oscillators with closely spaced modes focusing on the physics of modal interactions. Considering the simplest representative example in the form of an impulsively excited…
While modern structural biology has provided us with a rich and diverse picture of membrane proteins, the biological function of membrane proteins is often influenced by the mechanical properties of the surrounding lipid bilayer. Here we…
The Glauber model on a one-dimensional lattice with boundaries (for the ferromagnetic- and anti-ferromagnetic case) is considered. The large-time behaviour of the one-point function is studied. It is shown that, for any positive…
We present computer simulations of a simple bead-spring model for polymer melts with intramolecular barriers. By systematically tuning the strength of the barriers, we investigate their role on the glass transition. Dynamic observables are…
The motility-induced phase separation exhibited by active particles with repulsive interactions is well known. We show that the interaction softness of active particles destabilizes the highly ordered dense phase, leading to the formation…
Understanding how interparticle interactions govern phase behavior is central to controlling self-organization in multicomponent soft-matter systems. In particular, the role of cross-interactions between unlike components remains…
The dynamics of colloidal particles in potential energy landscapes have mainly been investigated theoretically. In contrast, here we discuss the experimental realization of potential energy landscapes with the help of light fields and the…
The dynamics of molecular motors which occasionally detach from a heterogeneous track like DNA or RNA is considered. Motivated by recent single molecule experiments, we study a simple model for a motor moving along a disordered track using…