Related papers: Molecular dynamics study of molecular mobility in …
In applications of mechanics, including quantum mechanics, we often consider complex systems, where complete solutions of the underlying "fundamental" equations is both impractical and unnecessary to describe appropriate observations…
We investigate the dynamics of an active gel of bundled microtubules that is driven by clusters of kinesin molecular motors. Upon the addition of ATP, the coordinated action of thousands of molecular motors drives the gel to a highly…
Recent experiments reveal both passive subdiffusion of various nanoparticles and anomalous active transport of such particles by molecular motors in the molecularly crowded environment of living biological cells. Passive and active…
Advances in controlled polymerization have enabled the synthesis of mechanically interlocked polymers like molecular knots and linear[n]catenane. These aesthetic macromolecules with unique topological constraints in the form of mechanical…
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…
Ultra-precision machining of metals, the breaking of nanowires under tensile stress and fracture of nanoscale materials are examples of technologically important processes which are both extremely difficult and costly to investigate…
One common feature of a vehicle, an ant and a kinesin motor is that they all convert chemical energy, derived from fuel or food, into mechanical energy required for their forward movement; such objects have been modelled in recent years as…
We present a molecular dynamics study of the collective dynamics of a flexible model for the fragile glass-former orthoterphenyl [ S. Mossa, R. Di leonardo, G. Ruocco, and M. Sampoli, Phys. Rev. E 62, 612 (2000)]. We study the behavior of…
A new molecular motor is conceptually constructed from a double-walled carbon nanotube (DWNT) consisting of a long inner single-walled carbon nanotube (SWNT) and a short outer SWNT with different chirality. The interaction between inner and…
Detonation of a three-dimensional reactive non-isotropic molecular crystal is modeled using molecular dynamics simulations. The detonation process is initiated by an impulse, followed by the creation of a stable fast reactive shock wave.…
Thermodynamic uncertainty relations (TURs) relate precision to the dissipation rate, yet the inequalities can be far from saturation. Indeed, in catenane molecular motor simulations, we record precision far below the TUR limit. We further…
An ab initio quantum-classical mixed scheme for the time evolution of electrode-device-electrode systems is introduced to study nuclear dynamics in quantum transport. Two model systems are discussed to illustrate the method. Our results…
The addition of individual quanta of rotational excitation to a molecule has been shown to markedly change its reactivity by significantly modifying the intermolecular interactions. So far, it has only been possible to observe these…
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…
Nonequilibrium dynamics of biomembranes with active inclusions is considered. The inclusions represent protein molecules which perform cyclic internal conformational motions driven by the energy brought with ATP ligands. As protein…
Recent biological experiments have shown that certain types of cells are able to move in structured and confined environment even without the activation of focal adhesion. Focusing on this particular phenomenon and based on previous works,…
Molecular motors are found throughout the cells of the human body, and have many different and important roles. These micro-machines move along filament tracks, and have the ability to convert chemical energy into mechanical work that…
A molecular rotor mechanism is proposed to explain weak magnetic field effects in biology. Despite being nanoscale (1 nm), this rotor exhibits quantum superposition and interference. Analytical modeling shows its quantum dynamics are highly…
For decades astronomers and astrophysicists believed that only positively charged ions were worthy of relevance in drawing the networks for possible chemical reactions in the interstellar medium, as well as in modeling the physical…
In a single molecule assay, the motion of a molecular motor is often inferred from measuring the stochastic trajectory of a large probe particle attached to it. We discuss a simple model for this generic set-up taking into account…