Super-Arrhenius diffusion in a binary colloidal mixture at low volume fraction: an effect of depletion interaction due to an asymmetric barrier.

We report results from the molecular dynamics simulations of a binary colloidal mixture subjected to an external potential barrier along one of the spatial directions at low volume fraction, ϕ = 0.2. The variations in the asymmetry of the external potential barrier do not change the dynamics of the smaller particles, showing Arrhenius diffusion. However, the dynamics of the larger particles shows a crossover from sub-Arrhenius to super-Arrhenius diffusion with the asymmetry in the external potential at the low temperatures and low volume fraction. Super-Arrhenius diffusion is generally observed in the high density systems where the transient cages are present due to dense packing, e.g., supercooled liquids, jammed systems, diffusion through porous membranes, dynamics within the cellular environment, etc. This model can be applied to study the molecular transport across cell membranes, nano-, and micro-channels which are characterized by spatially asymmetric potentials.

A stochastic model for dynamics of FtsZ filaments and the formation of Z -ring.

Understanding the mechanisms responsible for the formation and growth of FtsZ polymers and their subsequent formation of the Z -ring is important for gaining insight into the cell division in prokaryotic cells. In this work, we present a minimal stochastic model that qualitatively reproduces in vitro observations of polymerization, formation of dynamic contractile ring that is stable for a long time and depolymerization shown by FtsZ polymer filaments. In this stochastic model, we explore different mechanisms for ring breaking and hydrolysis. In addition to hydrolysis, which is known to regulate the dynamics of other tubulin polymers like microtubules, we find that the presence of the ring allows for an additional mechanism for regulating the dynamics of FtsZ polymers. Ring breaking dynamics in the presence of hydrolysis naturally induce rescue and catastrophe events in this model irrespective of the mechanism of hydrolysis.

Anomalous dynamics of binary colloidal mixtures over a potential barrier: effect of depletion interaction.

The dynamics of a binary colloidal mixture under the influence of an external potential barrier has been studied by molecular dynamics simulations. The attractive depletion interaction between the barrier and larger particles fastens the dynamics of the larger particles over the potential barrier. At low temperatures, depletion interactions cause the larger particles to diffuse faster than smaller particles, which is counterintuitive. The repulsive barrier leads the small particles to undergo an anomalous diffusion which resembles the dynamics of systems undergoing a glass transition, while the larger particles undergo normal diffusion even at very low temperature.

Separation of mixtures at nano length scales: blow torch and levitation effect.

A new conceptual basis for the separation of multicomponent molecular mixtures is proposed. A separation method where different components of the mixtures are driven in opposite directions is realized by a judicious combination of two effects, viz., levitation and blow torch effects. Monte Carlo simulations of two Lennard-Jones binary mixtures with different-sized components are shown to be separated well if at least one of the components lies in the anomalous regime and the others lie in the linear regime. A separation factor of 10(8) is obtained on nano length scales as compared to 10(3), obtainable through conventional methods of separation on macrolength scales.

Source of reaction-diffusion coupling in confined systems due to temperature inhomogeneities.

Diffusion is often accompanied by a reaction or sorption which can induce temperature inhomogeneities. Monte Carlo simulations of Lennard-Jones atoms in zeolite NaCaA are reported with a hot zone presumed to be created by a reaction. Our simulations show that localized hot regions can alter both the kinetic and transport properties. Further, enhancement of the diffusion constant is greater for larger barrier height, a surprising result of considerable significance to many chemical and biological processes. We find an unanticipated coupling between reaction and diffusion due to the presence of hot zone in addition to that which normally exists via concentration.

Rotational motion of methane within the confines of zeolite NaCa A: molecular dynamics and ab initio calculations.

Molecular dynamics simulation of a five-site model of methane within zeolite NaCaA and ab initio calculations have been reported. Methane shows a preferential orientation during its passage through the eight-ring window. Partial freezing of certain rotational degrees of freedom is observed during the passage of methane through the eight-ring window, which acts as a bottleneck for diffusion of methane. Both the orientation and the rotational motion of methane and its experimental verification can indicate the accuracy of the intermolecular potential between methane and zeolite employed in this study. Intracage motion of methane shows that methane performs a rolling motion rather than a sliding motion within the supercage.

Rotational dynamics of propane in Na-Y zeolite: a molecular dynamics and quasielastic neutron-scattering study.

We report results from molecular dynamics (MD) simulations and quasielastic neutron-scattering (QENS) measurements on the rotational dynamics of propane in Na-Y zeolite at room temperature with a loading of four molecules per alpha cage. Rotational part of the intermediate scattering function F(Q,t) obtained from the MD simulation suggests that rotational motion is faster relative to the translational motion. Various rotational models fitted to the MD data suggest that rotation is isotropic. It is found that the hydrogen atoms lie, on the average, on a sphere of radius 1.88+/-0.05 A, which is also the average distance of the hydrogen atoms from the center of mass of the propane molecule. Results from QENS measurements are in excellent agreement with those obtained from MD, suggesting that the intermolecular potential employed in the MD simulation provides a realistic description of propane motion within faujasite. The rotational diffusion constant D(R) is 1.05+/-0.09 x 10(12) sec(-1) from the QENS data, which may be compared with that obtained from the MD data (0.82+/-0.05 x 10(12) sec(-1)).