Related papers: Free Energy Transduction in a Chemical Motor Model
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
Living systems efficiently use chemical fuel to do work, process information, and assemble patterns despite thermal noise. Whether high efficiency arises from general principles or specific fine-tuning is unknown. Here, applying a recent…
Catalysis-driven synthetic molecular motors operate in a loose mechanochemical coupling regime, one in which a decomposition of a fuel molecule does not reliably produce a forward step. In that regime, stochastic backward steps can…
Synthetic nanomotors powered by chemical reactions have been designed to act as vehicles for active cargo transport, drug delivery as well as a variety of other uses. Collections of such motors, acting in consort, can self-assemble to form…
In this paper we investigate the use of path-integral formalism and the concepts of entropy and traffic in the context of molecular motors. We show that together with time-reversal symmetry breaking arguments one can find bounds on…
Molecular machines consist of either a single protein or a macromolecular complex composed of protein and RNA molecules. Just like their macroscopic counterparts, each of these nano-machines has an engine that "transduces" input energy into…
Chemical gradients provide the primordial energy for biological functions by driving the mechanical movement of microscopic engines. Their thermodynamic properties remain elusive, especially concerning the dynamic change in energy demand in…
Transformers generate valid and diverse chemical structures, but little is known about the mechanisms that enable these models to capture the rules of molecular representation. We present a mechanistic analysis of autoregressive…
Electric circuits manipulate electric charge and magnetic flux via a small set of discrete components to implement useful functionality over continuous time-varying signals represented by currents and voltages. Much of the same…
Biomolecular machines are protein complexes that convert between different forms of free energy. They are utilized in nature to accomplish many cellular tasks. As isothermal nonequilibrium stochastic objects at low Reynolds number, they…
With reference to the experimental observations by T. Yanagida and his co-workers on actomyosin interaction, a Brownian motor of fluctuating ratchet kind is designed with the aim to describe the interaction between a Myosin II head and a…
In many biological systems localized mechanical information is transmitted by mechanically neutral chemical signals. Typical examples include contraction waves in acto-myosin cortex at cellular scale and peristaltic waves at tissue level.…
In recent years, several artificial molecular motors driven and controlled by electric currents have been proposed. Similar to Brownian machines, these systems work by turning random inelastic tunneling events into a directional rotation of…
We discover a new type of nonequilibrium phase transition in a model of chromatin dynamics, which accounts for the coherent motions that have been observed in experiment. The coherent motion is due to the long-range cooperation of molecular…
Kinesin motors have been studied extensively both experimentally and theoretically. However, the microscopic mechanism of the processive movement of kinesin is still an open question. In this paper, we propose a hand-over-hand model for the…
We present a model of an ATP-fueled molecular machine which push a polymer through a pore channel. The machine acts between two levels (working-waiting), and the working one remains active for a fixed time giving a constant force. The…
A comparison is made between conventional Michaelis-Menten kinetics and two models that take into account the duration of the conformational changes that take place at the molecular level during the catalytic cycle of a monomer. The models…
The muscle contraction, operation of ATP synthase, maintaining the shape of a cell are believed to be secured by motor proteins, which can be modelled using the Brownian ratchet mechanism. We consider the randomly flashing ratchet model of…
F1F0 ATP synthase (ATPase) either facilitates the synthesis of ATP in the mitochondrial membranes and bacterial inner membranes in a process driven by the proton moving force (pmf), or uses the energy from ATP hydrolysis to pump protons…
Emergence, optimization and stability of a motor-like motion in a fluctuating environment are analyzed. The emergence of motion is shown to be a general phenomenon. A motor converges to the state with the minimum of effective temperature…