Related papers: Information flow, Gating, and Energetics in dimeri…
Heat engines and information engines have each historically served as motivating examples for the development of thermodynamics. While these two types of systems are typically thought of as two separate kinds of machines, recent empirical…
Reconstituted filamentous actin networks with myosin motor proteins form active gels, in which motor proteins generate forces that drive the network far from equilibrium. This motor activity can also strongly affect the network elasticity;…
Molecular machines are stochastic systems that catalyze the energetic processes keeping living cells alive and structured. Inspired by the examples of F1-ATP synthase and the bacterial flagellum, we present a minimal model of an externally…
We study a one-dimensional hamiltonian chain of masses perturbed by an energy conserving noise. The dynamics is such that, according to its hamiltonian part, particles move freely in cells and interact with their neighbors through…
Kinetic proofreading is an error correction mechanism present in the processes of the central dogma and beyond, and typically requires the free energy of nucleotide hydrolysis for its operation. Though the molecular players of many…
The performance of a molecular motor, characterized by its power output and energy efficiency, is investigated in the motor design space spanned by the stepping rate function and the motor-track interaction potential. Analytic results and…
We present a self-contained engine, which is made of one or more two-level systems, each of which is coupled to a single bath, as well as to a common load composed of a particle on a tilted lattice. We show that the energy and the entropy…
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…
Non-stoquastic drivers are known to improve the performance of quantum annealing by reducing first-order phase transitions into second-order ones in several mean-field-type model systems. Nevertheless, statistical-mechanical analysis shows…
Aspects of the dynamical glass transition are considered within a mean field spin glass model. At the dynamical transition the the system condenses in a state of lower entropy. The difference, the information entropy or complexity, is…
The past few years have seen many advances in our understanding of the dynamics of polymeric fluids. These include improvements on the successful reptation theory; an emerging molecular theory of semiflexible chain dynamics; and an…
Molecular motors perform active movements along cytoskeletal filaments and drive the traffic of organelles and other cargo particles in cells. In contrast to the macroscopic traffic of cars, however, the traffic of molecular motors is…
The interfacial behaviour of water remains a central question to fields as diverse as protein folding, friction and ice formation[1,2]. While the structural and dynamical properties of water at interfaces differ strongly from those in the…
We experimentally showed that biological molecular motor F$_1$-ATPase (F$_1$) implements an optimal rectification mechanism. F$_1$ hardly suppresses adenosine triphosphate (ATP) synthesis, which is the F$_1$'s physiological role while…
Myosin II plays a pivotal role in muscle contraction by generating force through the cooperative action of multiple motors on actin filaments. In this study, we integrate the nonlinear elasticity of the neck linker in individual myosin II…
Dynamics of reaction coordinates during barrier-crossing are key to understand activated processes in complex systems such as proteins. The default assumption from Kramers physical intuition is that of a diffusion process. However, the…
The symmetry breaking of the actin network from radial to longitudinal symmetry has been identified as the major mechanism for keratocytes (fish cells) motility on solid substrate. For strong friction coefficient, the two dimensional actin…
The cell cytoskeleton is a striking example of "active" medium driven out-of-equilibrium by ATP hydrolysis. Such activity has been shown recently to have a spectacular impact on the mechanical and rheological properties of the cellular…
Intracellular transport of large cargoes, such as organelles, vesicles or large proteins, is a complex dynamical process that involves the interplay of ATP-consuming molecular motors, cytoskeleton filaments and the viscoelastic cytoplasm.…
Hysteresis can be found in driven many-body systems such as magnets and superfluids. Rate-dependent hysteresis arises when a system is driven periodically while relaxing towards equilibrium. A two-state paramagnet driven by an oscillating…