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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.

Actomyosin-based cortical contractility is a common feature of eukaryotic cells but the capability to produce rhythmic contractions is found in only a few types such as cardiomyocytes. Mechanisms responsible for the acquisition of this capability remain largely unknown. Rhythmic contractility can be induced in non-muscle cells by microtubule depolymerization. Spreading epithelial cells and fibroblasts in which microtubules were depolymerized with nocodazole or colcemid underwent rhythmic oscillations of the body that lasted for several hours before the cells acquired a stable, flattened shape. By contrast, control cells spread and flattened into discoid shapes in a smooth and regular manner. Quantitative analysis of the oscillations showed that they have a period of about 50 seconds. The kinase inhibitors, HA 1077 and H7, and the more specific rho-kinase inhibitor, Y 27632, caused the oscillations to immediately cease and the cells to become flat. Transient increases in cytoplasmic calcium preceded the contractile phase of the oscillations. Wrinkle formation by cells plated on elastic substrata indicated that the contractility of colcemid-treated cells increased in comparison to controls but was drastically decreased after HA 1077 addition. These data suggest that an intact microtubular system normally prevents pulsations by moderating excessive rho-mediated actin myosin contractility. Possible mechanistic interactions between rho-mediated and calcium activated contractile pathways that could produce morphological oscillations are discussed.

It has long been known that accurate electrostatics is a key issue for improving current force fields for large-scale biomolecular simulations. Typically, this calls for an improved and more accurate description of the molecular electrostatic potential, which eliminates the artifacts associated with current point charge-based descriptions. In turn, this involves the partitioning of the extended molecular charge distribution, so that charges and multipole moments can be assigned to different atoms. As an alternate to current approaches, we have investigated a charge partitioning scheme that is based on the maximally localized Wannier functions. This has the advantage of partitioning the charge, and placing it around the molecule in a chemically meaningful manner. Moreover, higher order multipoles may all be calculated without any undue numerical difficulties. Tests on isolated molecules and water dimers, show that the molecular electrostatic potentials generated by such a Wannier-function based approach are in excellent agreement with the density functional-based calculations.

One of the numerous calcium-involving processes in mammalian cells is store-operated calcium entry (SOCE) -- the process in which depletion of calcium stores in the endoplasmic reticulum (ER) induces calcium influx from the extracellular space. Previously supposed to function only in non-excitable cells, SOCE is now known to play a role also in such excitable cells as neurons, muscles and neuroendocrine cells and is found in many different cell types. SOCE participates not only in processes dependent on ER calcium level but also specifically regulates some important processes such as cAMP production, T lymphocyte activation or induction of long-term potentiation. Impairment of SOCE can be an element of numerous disorders such as acute pancreatitis, primary immunodeficiency and, since it can take part in apoptosis or cell cycle regulation, SOCE may also be partially responsible for such serious disorders as Alzheimer disease and many types of cancer. Even disturbances in the 'servant' role of maintaining ER calcium level may cause serious effects because they can lead to ER homeostasis disturbance, influencing gene expression, protein synthesis and processing, and the cell cycle.

Although it has long been known that the classical notions of capacitance need modification at the nanoscale, in order to account for important quantum effects, very few first-principles investigations of these properties exist for any real material systems. Here we present the results of a large-scale ab initio investigation of the capacitance properties of carbon nanotube systems. The simulations are based on a recently developed real-space nonequilibrium Green's-function approach, with special attention being paid to the treatment of the bound states present in the system. In addition, use has been made of a symmetry decomposition scheme for the charge density. This is needed both to speed up the calculations and in order to study the origins of the induced charges. Specific systems investigated include two and three nested nanotube shells, the insertion of a capped nanotube into another, a connected ͑12,0͒/͑6,6͒ nanotube junction, and the properties of a nanotube acting as a probe over a flat aluminum surface. First-principles estimates of the capacitance matrix coefficients for all these systems are provided, along with a discussion of the quantum corrections. For the case of the nanotube junction, the numerical value of the capacitance is sufficiently high, as to be useful for future device applications.