Related papers: Molecular dynamics study of molecular mobility in …
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…
Manipulating and coupling molecule gears is the first step towards realizing molecular-scale mechanical machines. Here, we theoretically investigate the behavior of such gears using molecular dynamics simulations. Within a nearly rigid-body…
Simulations can help unravel the complicated ways in which molecular structure determines function. Here, we use molecular simulations to show how slight alterations of a molecular motor's structure can cause the motor's typical dynamical…
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.…
Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous…
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…
A deformable body can rotate even with no angular momentum, simply by changing its shape. A good example is a falling cat, how it maneuvers in air to land on its feet. Here a first principles molecular level example of the phenomenon is…
We explore quantization of the response of a molecular motor to periodic modulation of control parameters. We formulate the Pumping-Quantization Theorem (PQT) that identifies the conditions for robust integer quantized behavior of a…
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…
While molecular machines play an increasingly significant role in nanoscience research and applications, there remains a shortage of investigations and understanding of the molecular gear (cogwheel), which is an indispensable and…
We study a model of synthetic molecular motor - a [3]-catenane consisting of two small macrocycles mechanically interlocked with a bigger one - subjected to a time-dependent driving using stochastic thermodynamics. The model presents…
Processive molecular motors which drive the traffic of organelles in cells move in a directed way along cytoskeletal filaments. On large time scales, they perform motor walks, i.e., peculiar random walks which arise from the repeated…
Cats use the connection governing parallel transport in the space of shapes to land safely on their feet. Here we argue that this connection also explains the impressive performance of molecular motors by enabling molecules to evade…
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…
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…
Molecular motors perform active movements along cytoskeletal filaments and drive the traffic of organelles and other cargo particles in cells. In contrast to the macroscopic traffic of cars, however, the traffic of molecular motors is…
The dynamics of molecular motors which occasionally detach from a heterogeneous track like DNA or RNA is considered. Motivated by recent single molecule experiments, we study a simple model for a motor moving along a disordered track using…
Molecular dynamics computer simulations are used to investigate thedynamics of a binary mixture of charged (Yukawa) particles with a size-ratio of 1:5. We find that the system undergoes a phase transition where the large particles…
We examine the dependence of the physical quantities of the rotatory molecular motor, such as the rotation velocity and the proton translocation rate, on the chemical reaction rate using the model based only on diffusion process. A peculiar…