Molecular dynamics simulation of ratchet motion in an asymmetric nanochannel

Ultrahigh-Flux Water Nanopumps Generated by Asymmetric Terahertz Absorption

Controlling active transport of water through membrane channels is essential for advanced nanofluidic devices. Despite advancements in water nanopump design using techniques like short-range invasion and subnanometer-level control, challenges remain facilely and remotely realizing massive waters active transport. Herein, using molecular dynamic simulations, we propose an ultrahigh-flux nanopump, powered by frequency-specific terahertz stimulation, capable of unidirectionally transporting massive water through asymmetric-wettability membrane channels at room temperature without any external pressure. The key physics behind this terahertz-powered water nanopump is revealed to be the energy flow resulting from the asymmetric optical absorption of water.

Experimental study of a nanoscale translocation ratchet

Despite an extensive theoretical and numerical background, the translocation ratchet mechanism, which is fundamental for the transmembrane transport of biomolecules, has never been experimentally reproduced at the nanoscale. Only the Sec61 and bacterial type IV pilus pores were experimentally shown to exhibit a translocation ratchet mechanism. Here we designed a synthetic translocation ratchet and quantified its efficiency as a nanopump. We measured the translocation frequency of DNA molecules through nanoporous membranes and showed that polycations at the trans side accelerated the translocation in a ratchet-like fashion. We investigated the ratchet efficiency according to geometrical and kinetic parameters and observed the ratchet to be only dependent on the size of the DNA molecule with a power law [Formula: see text]. A threshold length of 3 kbp was observed, below which the ratchet did not operate. We interpreted this threshold in a DNA looping model, which quantitatively explained our results.

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.

Ultra-fast vapor generation by a graphene nano-ratchet: a theoretical and simulation study

Vapor generation is of prime importance for a broad range of applications: domestic water heating, desalination and wastewater treatment, etc. However, slow and inefficient evaporation limits its development. In this study, a nano-ratchet, a multilayer graphene with cone-shaped nanopores (MGCN), to accelerate vapor generation has been proposed. By performing molecular dynamics simulation, we found that air molecules were spontaneously transported across MGCN and resulted in a remarkable pressure difference, 21 kPa, between the two sides of MGCN. We studied the dependence of the pressure difference on the ambient temperature and geometry of MGCN in detail. Through further analysis of the diffusive transport, we found that pressure difference depended on the competition between ratchet transport and Knudsen diffusion and it was further found that ratchet transport is dominant. The significant pressure difference could lead to a 15-fold or greater enhancement of vapor generation, which shows the wide applications of this nano-ratchet.

Transport of water molecules through noncylindrical pores in multilayer nanoporous graphene

The permeability inside a multilayer hourglass-shaped pore depends on the length of the flow path of the water molecules.

Autonomous pump against concentration gradient

Using non-equilibrium molecular dynamics and Monte Carlo methods, we have studied the molecular transport in asymmetric nanochannels. The efficiency of the molecular pump depends on the angle and apertures of the asymmetric channel, the environmental temperature and average concentration of the particles. The pumping effect can be explained as the competition between the molecular force field and the thermal disturbance. Our results provide a green approach for pumping fluid particles against the concentration gradient through asymmetric nanoscale thin films without any external forces. It indicates that pumping vacuum can be a spontaneous process.

Ultra-fast single-file transport of a simple liquid beyond the collective behavior zone

Breakdown of the collective single-file behavior leads to ultra-fast transport of a simple liquid.

Wetting Driven by Thermal Fluctuations on Terraced Nanostructures

Theoretical analysis and fully atomistic molecular dynamics simulations reveal a Brownian ratchet mechanism by which thermal fluctuations drive the net displacement of immiscible liquids confined in channels or pores with micro- or nanoscale dimensions. The thermally driven displacement is induced by surface nanostructures with directional asymmetry and can occur against the direction of action of wetting or capillary forces. Mean displacement rates in molecular dynamics simulations are predicted via analytical solution of a Smoluchowski diffusion equation for the position probability density. The proposed physical mechanisms and derived analytical expressions can be applied to engineer surface nanostructures for controlling the dynamics of diverse wetting processes such as capillary filling, wicking, and imbibition in micro- or nanoscale systems.

Asymmetric transport of water molecules through a hydrophobic conical channel

Unlike macroscale systems, symmetry breaking could lead to surprising results for nanoscale systems.

Anomalous diffusion and response in branched systems: a simple analysis

We revisit the diffusion properties and the mean drift induced by an external field of a random walk process in a class of branched structures, as the comb lattice and the linear chains of plaquettes. A simple treatment based on scaling arguments is able to predict the correct anomalous regime for different topologies. In addition, we show that even in the presence of anomalous diffusion, Einstein's relation still holds, implying a proportionality between the mean square displacement of the unperturbed systems and the drift induced by an external forcing.

Effect of the position of constriction on water permeation across a single-walled carbon nanotube

The transportation of water across a cell membrane facilitated by water channel proteins is fundamental to the normal water metabolism in all forms of life. It is understood that the narrow region in a water channel is responsible for gating or selectivity. However, the influence of the position of the narrow region on water transportation is still not thoroughly understood. By choosing a single-walled carbon nanotube (SWNT) as a simplified model and using molecular dynamics simulation, we have found that the water flux through the nanotube would change significantly if the narrow location moves away from the middle region along the tube. Simulation results show that the flux reaches the maximum when the deformation occurs in the middle part of nanotube and decreases as the deformation location moves toward the ends of the nanotube. However, the decrease of water flux is not monotonic and the flux gets the minimum near the ends. These interesting phenomena can be explained in terms of water-water interactions and water-SWNT interactions. It can be concluded that the regulation of water transportation through nanopores depends sensitively on the location of the narrow region, and these findings are helpful in devising high flux nanochannels and nanofiltration as well.

Tunable non-equilibrium gating of flexible DNA nanochannels in response to transport flux

Biological nanochannels made from proteins play a central role in cellular signalling. The rapid emergence of DNA nanotechnology in recent years has opened up the possibility of making similar nanochannels from DNA. Building on previous work on switchable DNA nanocompartment, we have constructed complex DNA nanosystems to investigate the gating behaviour of these nanochannels. Here we show that DNA nanochannels can be gated by stress exerted by permeating solute particles at non-equilibrium states due to the high flexibility of the nanochannels. This novel gating mechanism results in tunable ratchet-like transport of solute particles through the nanochannels. A simple model that couples non-equilibrium channel gating with transport flux can quantitatively explain a number of the phenomena we observe. With only one set of model parameters, we can reproduce diverse gating behaviours, modulated by an inherent gating threshold. This work could lead to the development of new devices based on DNA nanochannels.