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Most computer simulations of molecular dynamics take place under equilibrium conditions--in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are…
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator.…
Dynamics of molecular motors that move along linear lattices and interact with them via reversible destruction of specific lattice bonds is investigated theoretically by analyzing exactly solvable discrete-state ``burnt-bridge'' models.…
Dynamic properties of molecular motors whose motion is powered by interactions with specific lattice bonds are studied theoretically with the help of discrete-state stochastic "burnt-bridge" models. Molecular motors are depicted as random…
The generation of unidirectional motion has been a long-standing challenge in engineering of molecular motors and, more generally, machines. A molecular motor is characterized by a set of low energy states that differ in their…
Molecular machines described in this paper are meant to be such molecular systems that make use of conformational mobility (i.e. hindered rotation around chemical bonds and molecular construction deformations with formation and breakage of…
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…
Many types of molecular motors have been proposed and synthesized in recent years, displaying different kinds of motion, and fueled by different driving forces such as light, heat, or chemical reactions. We propose a new type of molecular…
As engineering advances toward the nanoscale, understanding design principles for molecular motors becomes increasingly valuable. Many molecular motors consist of coupled components transducing one free-energy source into another. Here, we…
We propose a simple theoretical model for a molecular chemical engine that catalyzes a chemical reaction and converts the free energy released by the reaction into mechanical work. Binding and unbinding processes of reactant and product…
Molecular spintronics is made possible by the coupling between electronic configuration and magnetic po- larization of the molecules. For control and application of the individual molecular states it is necessary to both read and write…
Systems with two species of active molecular motors moving on (cytoskeletal) filaments into opposite directions are studied theoretically using driven lattice gas models. The motors can unbind from and rebind to the filaments. Two motors…
Routinely navigating through an ever-changing and unsteady environment, and utilizing chemical energy, molecular motors transport the cell's crucial components, such as neurotransmitters and organelles. They generate force and pull cargo,…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
The effect of sequence heterogeneity on the dynamics of molecular motors is reviewed and analyzed using a set of recently introduced lattice models. First, we review results for the influence of heterogenous tracks such as a single-strand…
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…
Inside cells, various cargos are transported by teams of molecular motors. Intriguingly, the motors involved generally have opposite pulling directions, and the resulting cargo dynamics is a biased stochastic motion. It is an open question…
In living cells, molecular motors convert chemical energy into mechanical work. Its thermodynamic energy efficiency, i.e. the ratio of output mechanical work to input chemical energy, is usually high. However, using two-state models, we…
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…
The miniaturization of gears towards the nanoscale is a formidable task posing a variety of challenges to current fabrication technologies. In context, the understanding, via computer simulations, of the mechanisms mediating the transfer of…