Continued study of NAVSTAR/GPS for general aviation

A conceptual approach for examining the full potential of Global Positioning Systems (GPS) for the general aviation community is presented. Aspects of an experimental program to demonstrate these concepts are discussed. The report concludes with the observation that the true potential of GPS can only be exploited by utilization in concert with a data link. The capability afforded by the combination of position location and reporting stimulates the concept of GPS providing the auxiliary functions of collision avoidance, and approach and landing guidance. A series of general recommendations for future NASA and civil community efforts in order to continue to support GPS for general aviation are included

Molecular Electroporation and the Transduction of Oligoarginines

Certain short polycations, such as TAT and polyarginine, rapidly pass through the plasma membranes of mammalian cells by an unknown mechanism called transduction as well as by endocytosis and macropinocytosis. These cell-penetrating peptides (CPPs) promise to be medically useful when fused to biologically active peptides. I offer a simple model in which one or more CPPs and the phosphatidylserines of the inner leaflet form a kind of capacitor with a voltage in excess of 180 mV, high enough to create a molecular electropore. The model is consistent with an empirical upper limit on the cargo peptide of 40--60 amino acids and with experimental data on how the transduction of a polyarginine-fluorophore into mouse C2C12 myoblasts depends on the number of arginines in the CPP and on the CPP concentration. The model makes three testable predictions.Comment: 15 pages, 5 figure

Quiescence: a mechanism for escaping the effects of drug on cell populations

We point out that a simple and generic strategy to lower the risk for extinction consists in the developing a dormant stage in which the organism is unable to multiply but may die. The dormant organism is protected against the poisonous environment. The result is to increase the survival probability of the entire population by introducing a type of zero reproductive fitness. This is possible, because the reservoir of dormant individuals act as a buffer that can cushion fatal fluctuations in the number of births and deaths which without the dormant population would have driven the entire population to extinction.Comment: 18 pages and 9 figure

Preliminary study of NAVSTAR/GPS for general aviation

The activities conducted as a planning effort to focus attention on the applicability of the global positioning system for general aviation are described. The description of GPS, its impact on economic and functional aspects of general aviation avionics, as well as a declaration of potential extensions of the basic concept have been studied in detail

Unifying model of driven polymer translocation

We present a Brownian dynamics model of driven polymer translocation, in which non-equilibrium memory effects arising from tension propagation (TP) along the cis side subchain are incorporated as a time-dependent friction. To solve the effective friction, we develop a finite chain length TP formalism, expanding on the work of Sakaue [Sakaue, PRE 76, 021803 (2007)]. The model, solved numerically, yields results in excellent agreement with molecular dynamics simulations in a wide range of parameters. Our results show that non-equilibrium TP along the cis side subchain dominates the dynamics of driven translocation. In addition, the model explains the different scaling of translocation time w.r.t chain length observed both in experiments and simulations as a combined effect of finite chain length and pore-polymer interactions.Comment: 7 pages, 3 figure

Effect of Salt Concentration on the Electrophoretic Speed of a Polyelectrolyte through a Nanopore

In a previous paper [S. Ghosal, Phys. Rev. E 74, 041901 (2006)] a hydrodynamic model for determining the electrophoretic speed of a polyelectrolyte through an axially symmetric slowly varying nanopore was presented in the limit of a vanishingly small Debye length. Here the case of a finite Debye layer thickness is considered while restricting the pore geometry to that of a cylinder of length much larger than the diameter. Further, the possibility of a uniform surface charge on the walls of the nanopore is taken into account. It is thereby shown that the calculated transit times are consistent with recent measurements in silicon nanopores.Comment: 4 pages, 2 figure

Undulation instability in a bilayer lipid membrane due to electric field interaction with lipid dipoles

Bilayer lipid membranes [BLMs] are an essential component of all biological systems, forming a functional barrier for cells and organelles from the surrounding environment. The lipid molecules that form membranes contain both permanent and induced dipoles, and an electric field can induce the formation of pores when the transverse field is sufficiently strong (electroporation). Here, a phenomenological free energy is constructed to model the response of a BLM to a transverse static electric field. The model contains a continuum description of the membrane dipoles and a coupling between the headgroup dipoles and the membrane tilt. The membrane is found to become unstable through buckling modes, which are weakly coupled to thickness fluctuations in the membrane. The thickness fluctuations, along with the increase in interfacial area produced by membrane buckling, increase the probability of localized membrane breakdown, which may lead to pore formation. The instability is found to depend strongly on the strength of the coupling between the dipolar headgroups and the membrane tilt as well as the degree of dipolar ordering in the membrane.Comment: 29 pages 8 fig

Bubble statistics and positioning in superhelically stressed DNA

We present a general framework to study the thermodynamic denaturation of double-stranded DNA under superhelical stress. We report calculations of position- and size-dependent opening probabilities for bubbles along the sequence. Our results are obtained from transfer-matrix solutions of the Zimm-Bragg model for unconstrained DNA and of a self-consistent linearization of the Benham model for superhelical DNA. The numerical efficiency of our method allows for the analysis of entire genomes and of random sequences of corresponding length ($10^6-10^9$ base pairs). We show that, at physiological conditions, opening in superhelical DNA is strongly cooperative with average bubble sizes of $10^2-10^3$ base pairs (bp), and orders of magnitude higher than in unconstrained DNA. In heterogeneous sequences, the average degree of base-pair opening is self-averaging, while bubble localization and statistics are dominated by sequence disorder. Compared to random sequences with identical GC-content, genomic DNA has a significantly increased probability to open large bubbles under superhelical stress. These bubbles are frequently located directly upstream of transcription start sites.Comment: to be appeared in Physical Review

A Classical Density-Functional Theory for Describing Water Interfaces

We develop a classical density functional for water which combines the White Bear fundamental-measure theory (FMT) functional for the hard sphere fluid with attractive interactions based on the Statistical Associating Fluid Theory (SAFT-VR). This functional reproduces the properties of water at both long and short length scales over a wide range of temperatures, and is computationally efficient, comparable to the cost of FMT itself. We demonstrate our functional by applying it to systems composed of two hard rods, four hard rods arranged in a square and hard spheres in water

Are stress-free membranes really 'tensionless'?

In recent years it has been argued that the tension parameter driving the fluctuations of fluid membranes, differs from the imposed lateral stress, the 'frame tension'. In particular, stress-free membranes were predicted to have a residual fluctuation tension. In the present paper, this argument is reconsidered and shown to be inherently inconsistent -- in the sense that a linearized theory, the Monge model, is used to predict a nonlinear effect. Furthermore, numerical simulations of one-dimensional stiff membranes are presented which clearly demonstrate, first, that the internal 'intrinsic' stress in membranes indeed differs from the frame tension as conjectured, but second, that the fluctuations are nevertheless driven by the frame tension. With this assumption, the predictions of the Monge model agree excellently with the simulation data for stiffness and tension values spanning several orders of magnitude