No abstract

We determine the scaling exponents of polymer translocation ͑PT͒ through a nanopore by extensive computer simulations of various microscopic models for chain lengths extending up to N = 800 in some cases. We focus on the scaling of the average PT time ϳ N ␣ and the mean-square change of the PT coordinate, ͗s 2 ͑t͒͘ ϳ t ␤ . We find ␣ =1+2 and ␤ =2/ ␣ for unbiased PT in two dimensions ͑2D͒ and three dimensions ͑3D͒. The relation ␣␤ = 2 holds for driven PT in 2D, with a crossover from ␣ Ϸ 2 for short chains to ␣ Ϸ 1+ for long chains. This crossover is, however, absent in 3D where ␣ = 1.42Ϯ 0.01 and ␣␤ Ϸ 2.2 for N Ϸ 40− 800.

With a recently developed ab initio nonequilibrium Green's function formalism, we have examined the problem of quantum transport through prototypical, short, semiconducting nanotube devices. Metallic behavior is predicted for very short nanotubes, which crosses over to semiconducting behavior as the tube length is increased. This behavior finds its origins in the evanescent modes that are present in these finite-sized systems, which cannot be ignored. A complex band structure analysis makes the contributions of these modes particularly transparent.The recent advent of molecular electronics systems has opened up a new frontier, whose aim is the ultimate miniaturization of electronic systems. 1 The current-voltage (I-V) characteristics of such atomic and molecular systems hold forth the promise of revolutionary new devices for ultrasensitive probes and detectors, very high-speed and ultralarge density electronic components, and the possibility of novel logic layouts. This field has benefitted considerably from the development of self-organized structures, such as carbon nanotubes, 2 which have acted as an important theoretical 3-5 and experimental laboratory for exploring quantum transport at a nanometer length scale. In particular, semiconducting carbon nanotubes 6 show promise as field-effect transistors with better device properties than Si MOSFETs (metaloxide-semiconductor field-effect transistors). 7,8 In this brief paper, we report on ab initio simulations of the I-V characteristics of short, semiconducting nanotubes, which are shown to display metallic characteristics. This behavior finds its origins in the evanescent modes present in the system. Evanescent modes-in contrast to propagating modes-are modes that decay exponentially away from the leads. Hence, their contributions are usually ignored. Here, we show that they can make a substantial difference to the I-V characteristics of at least some molecular electronic systems. The properties of these evanescent modes are conveniently analyzed in terms of the complex band structure of the system. 9 To calculate the I-V characteristics of the carbon nanotube-based two-probe devices (see Fig. 1), use was made of a recently developed real-space, nonequilibrium Green's function (NEGF) formalism 10,11 combined with density functional theory (DFT) based simulations. This NEGF-DFT computational package has been extensively described elsewhere. 12,13 Its advantages include: (i) a proper treatment of the open boundary conditions as appropriate for a device under a bias voltage V b ; (ii) a fully atomistic treatment of the electrodes; (iii) a self-consistent treatment, within the DFT framework, of the charge density via NEGFs thereby incorporating the effects of both the scattering and bound states of the system. In addition, as the entire code is based on realspace grids, efficient use of parallel supercomputers enables one to treat large-scale systems.Our investigations focused primarily on carbon nanotubes coupled to Al-leads. Typically, a given two-probe device con...

Ion channels catalyze ionic permeation across membranes via water-filled pores. To understand how changes in intracellular magnesium concentration regulate the influx of Mg2+ into cells, we examine early events in the relaxation of Mg2+ channel CorA toward its open state using massively-repeated molecular dynamics simulations conducted either with or without regulatory ions. The pore of CorA contains a 2-nm-long hydrophobic bottleneck which remained dehydrated in most simulations. However, rapid hydration or “wetting” events concurrent with small-amplitude fluctuations in pore diameter occurred spontaneously and reversibly. In the absence of regulatory ions, wetting transitions are more likely and include a wet state that is significantly more stable and more hydrated. The free energy profile for Mg2+ permeation presents a barrier whose magnitude is anticorrelated to pore diameter and the extent of hydrophobic hydration. These findings support an allosteric mechanism whereby wetting of a hydrophobic gate couples changes in intracellular magnesium concentration to the onset of ionic conduction.