Related papers: Molecular dynamics study of molecular mobility in …
Dynamics of molecular motor dimers, consisting of rigidly bound particles that move along two parallel lattices and interact with underlying molecular tracks, is investigated theoretically by analyzing discrete-state stochastic…
When addressing spatial biological questions using mathematical models, symmetries within the system are often exploited to simplify the problem by reducing its physical dimension. In a reduced-dimension model molecular movement is…
We propose a microscopic simulation for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with the meson exchange potentials between quarks, we construct nucleons and…
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.…
Movements of molecular motors on cytoskeletal filaments are described by directed walks on a line. Detachment from this line is allowed to occur with a small probability. Motion in the surrounding fluid is described by symmetric random…
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…
A simple model of the two-state ratchet type is proposed for molecular chemical engines that convert chemical free energy into mechanical work and vice versa. The engine works by catalyzing a chemical reaction and turning a rotor.…
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…
Molecular motors are macromolecular complexes which use some form of input energy to perform mechanical work. The filamentary tracks, on which these motors move, are made of either proteins (e.g., microtubules) or nucleic acids (DNA or…
We explore electron transport properties for the model of benzene-1, 4-dithiolate (BDT) molecule and for some other geometric models of benzene molecule attached to two semi-infinite one-dimensional metallic electrodes using the Green's…
With the help of a two-dimensional model we study rolling lubrication by circular (2D fullerenes) molecules for a wide range of parameters. The conditions under which microscopic rolling friction may be effective are identified and related…
The stochastic driving force exerted by a single molecular motor (e.g., a kinesin, or myosin) moving on a periodic molecular track (microtubule, actin filament, etc.) is discussed from a general viewpoint open to experimental test. An…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
Intracellular transport along microtubules or actin filaments, powered by molecular motors such as kinesins, dyneins or myosins, has been recently modeled using one-dimensional driven lattice gases. We discuss some generalizations of these…
Extremely fast rotating molecules carrying significantly more energy in their rotation than in any other degree of freedom are known as "super rotors". It has been speculated that super rotors may exhibit a number of unique properties.…
Intracellular transport processes driven by molecular motors can be described by stochastic lattice models of self-driven particles. Here we focus on bidirectional transport models excluding the exchange of particles on the same track. We…
We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental…
The phase behaviour and dynamics of molecular ionic liquids are studied using primitive models and extensive computer simulations. The models account for size disparity between cation and anion, charge location on the cation, and…
Torque is ubiquitous in many molecular systems, including collisions, chemical reactions, vibrations, electronic excitations and especially rotor molecules. We present a straightforward theoretical method based on forces acting on atoms and…
We consider a new class of model systems to study systematically the role of molecular shape in the transport properties of dense liquids. Our model is a liquid binary mixture where both the molecules are non-spherical and characterized by…