Related papers: Molecular dynamics study of molecular mobility in …
Single molecular rotor is an important component for constructing bot-tom-up molecular mechanical machines and a window for shedding light on complex physical and chemical questions about motions of organic molecules on surfaces. Stability…
The effect on molecular transport due to chemical modification of the metal-molecule interface is investigated, using as an example the prototypical molecular device formed by attaching a p-disubstituted benzene molecule onto two gold…
In condensed matter physics, particularly in perovskite materials, the rotational motion of molecules and ions is associated with important issues such as ion conduction mechanism. Constrained Molecular Dynamics (MD) simulations offer a…
Molecular rotation, vibration, internal rotation, isomerization, tunneling, intermolecular dynamics of weakly and strongly interacting systems, intra-to-inter-molecular energy transfer, hindered rotation and hindered translation over…
In order to increase the efficiency of the computer simulation of biological molecules, it is very common to impose holonomic constraints on the fastest degrees of freedom; normally bond lengths, but also possibly bond angles. However, as…
Understanding of the molecular interaction between asphaltenes and other molecules, which may act as its solvents, provides insights into the nature of its stability in petroleum fluids and its phase transitions. Molecular dynamics…
We introduce some basic concepts for designer molecules with functional units which are driven by entropic rather than energetic forces. This idea profits from the mechanically interlocked nature of topological molecules such as catenanes…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
Ring polymers are prevalent in natural and engineered systems, including circular bacterial DNA, crown ethers for cation chelation, and mechanical nanoswitches. The morphology and dynamics of ring polymers are governed by the chemistry and…
Using an optical centrifuge to control molecular rotation in an extremely broad range of angular momenta, we study coherent rotational dynamics of nitrogen molecules in the presence of collisions. We cover the range of rotational quantum…
The movement of motor particles consisting of one or several molecular motors bound to a cargo particle is studied theoretically. The particles move on patterns of immobilized filaments. Several patterns are described for which the motor…
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…
The pump process of the ratchet model inspired by the $F_o$ rotatory motor of ATP synthase is investigated. In this model there are two kinds of characteristic time. One is dynamical, the relaxation time of the system. Others are chemical,…
Endothelial cells are responsible for the formation of the capillary blood vessel network. We describe a system of endothelial cells by means of two-dimensional molecular dynamics simulations of point-like particles. Cells' motion is…
Molecular dynamics simulation is a prominent way of analyzing the dynamic properties of a system. The molecular dynamics simulation of diffusion, an important transport property, of dilute solution of cysteine in SPCE water at five…
Molecular motors play pivotal roles in organizing the interior of cells. A motor efficient in cargo transport would move along cytoskeletal filaments with a high speed and a minimal error in transport distance (or time) while consuming a…
The realization of molecular-based electronic devices depends to a large extent on the ability to mechanically stabilize the involved molecular bonds, while making use of efficient resonant charge transport through the device. Resonant…
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…
Synthetic nanoscale complexes capable of mechanical movement are often studied theoretically using discrete-state models that involve instantaneous transitions between metastable states. A number of general results have been derived within…
We address a molecular dissociation mechanism that is known to occur when a H 2 molecule approaches a catalyst with its molecular axis parallel to the surface. It is found that molecular dissociation is a form of quantum dynamical phase…