354 research outputs found
Long term frequency stability analysis of the GPS NAVSTAR 6 Cesium clock
Time domain measurements, taken between the NAVSTAR 6 Spacecraft Vehicle (SV) and the Vandenberg Global Positioning System (GPS) Monitor Site, by a pseudo random noise receiver, were collected over an extended period of time and analyzed to estimate the long term frequency stability of the NAVSTAR 6 onboard frequency standard, referenced to the Vandenberg MS frequency standard. The technique employed separates the clock offset from the composite signal by first applying corrections for equipment delays, ionospheric delay, tropospheric delay, Earth rotation and the relativistic effect. The data are edited and smoothed using the predicted SV ephemeris to calculate the geometric delay. Then all available passes from each of the four GPS monitor stations, are collected at 1-week intervals and used to calculate the NAVSTAR orbital elements. The procedure is then completed by subtracting the corrections and the geometric delay, using the final orbital elements, from the composite signal, thus leaving the clock offset and random error
Submicrosecond comparisons of time standards via the Navigation Technology Satellites (NTS)
An interim demonstration was performed of the time transfer capability of the NAVSTAR GPS system using a single NTS satellite. Measurements of time difference (pseudo-range) are made from the NTS tracking network and at the participating observatories. The NTS network measurements are used to compute the NTS orbit trajectory. The central NTS tracking station has a time link to the Naval Observatory UTC (USNO,MC1) master clock. Measurements are used with the NTS receiver at the remote observatory, the time transfer value UTC (USNO,MC1)-UTC (REMOTE, VIA NTS) is calculated. Intercomparisons were computed using predicted values of satellite clock offset and ephemeus
Submicrosecond comparison of international clock synchronization by VLBI and the NTS satellite
The intercontinental clock synchronization capabilities of Very Long Baseline Interferometry (VLBI) and the Navigation Technology Satellite (NTS) were compared using both methods to synchronize the Cesium clocks at the NASA Deep Space Net complexes at Madrid, Spain and Goldstone, California. Verification of the accuracy of both systems was examined. The VLBI experiments used the Wideband VLBI Data Acquisition System developed at the NASA Jet Propulsion Laboratory. The NTS Satellites were designed and built by the Naval Research Laboratory used with NTS Timing Receivers developed by the Goddard Space Flight Center. The two methods agreed at about the one-half microsecond level
Translocation of structured polynucleotides through nanopores
We investigate theoretically the translocation of structured RNA/DNA
molecules through narrow pores which allow single but not double strands to
pass. The unzipping of basepaired regions within the molecules presents
significant kinetic barriers for the translocation process. We show that this
circumstance may be exploited to determine the full basepairing pattern of
polynucleotides, including RNA pseudoknots. The crucial requirement is that the
translocation dynamics (i.e., the length of the translocated molecular segment)
needs to be recorded as a function of time with a spatial resolution of a few
nucleotides. This could be achieved, for instance, by applying a mechanical
driving force for translocation and recording force-extension curves (FEC's)
with a device such as an atomic force microscope or optical tweezers. Our
analysis suggests that with this added spatial resolution, nanopores could be
transformed into a powerful experimental tool to study the folding of nucleic
acids.Comment: 9 pages, 5 figure
RNA secondary structure formation: a solvable model of heteropolymer folding
The statistical mechanics of heteropolymer structure formation is studied in
the context of RNA secondary structures. A designed RNA sequence biased
energetically towards a particular native structure (a hairpin) is used to
study the transition between the native and molten phase of the RNA as a
function of temperature. The transition is driven by a competition between the
energy gained from the polymer's overlap with the native structure and the
entropic gain of forming random contacts. A simplified Go-like model is
proposed and solved exactly. The predicted critical behavior is verified via
exact numerical enumeration of a large ensemble of similarly designed
sequences.Comment: 4 pages including 2 figure
Finite-size scaling of the error threshold transition in finite population
The error threshold transition in a stochastic (i.e. finite population)
version of the quasispecies model of molecular evolution is studied using
finite-size scaling. For the single-sharp-peak replication landscape, the
deterministic model exhibits a first-order transition at , where is the probability of exact replication of a molecule of length , and is the selective advantage of the master string. For
sufficiently large population size, , we show that in the critical region
the characteristic time for the vanishing of the master strings from the
population is described very well by the scaling assumption \tau = N^{1/2} f_a
\left [ \left (Q - Q_c) N^{1/2} \right ] , where is an -dependent
scaling function.Comment: 8 pages, 3 ps figures. submitted to J. Phys.
Anderson Localization, Non-linearity and Stable Genetic Diversity
In many models of genotypic evolution, the vector of genotype populations
satisfies a system of linear ordinary differential equations. This system of
equations models a competition between differential replication rates (fitness)
and mutation. Mutation operates as a generalized diffusion process on genotype
space. In the large time asymptotics, the replication term tends to produce a
single dominant quasispecies, unless the mutation rate is too high, in which
case the populations of different genotypes becomes de-localized. We introduce
a more macroscopic picture of genotypic evolution wherein a random replication
term in the linear model displays features analogous to Anderson localization.
When coupled with non-linearities that limit the population of any given
genotype, we obtain a model whose large time asymptotics display stable
genotypic diversityComment: 25 pages, 8 Figure
Guest charges in an electrolyte: renormalized charge, long- and short-distance behavior of the electric potential and density profile
We complement a recent exact study by L. Samaj on the properties of a guest
charge immersed in a two-dimensional electrolyte with charges . In
particular, we are interested in the behavior of the density profiles and
electric potential created by the charge and the electrolyte, and in the
determination of the renormalized charge which is obtained from the
long-distance asymptotics of the electric potential. In Samaj's previous work,
exact results for arbitrary coulombic coupling were obtained for a
system where all the charges are points, provided and .
Here, we first focus on the mean field situation which we believe describes
correctly the limit but large. In this limit we can
study the case when the guest charge is a hard disk and its charge is above the
collapse value . We compare our results for the renormalized charge
with the exact predictions and we test on a solid ground some conjectures of
the previous study. Our study shows that the exact formulas obtained by Samaj
for the renormalized charge are not valid for , contrary to a
hypothesis put forward by Samaj. We also determine the short-distance
asymptotics of the density profiles of the coions and counterions near the
guest charge, for arbitrary coulombic coupling. We show that the coion density
profile exhibit a change of behavior if the guest charge becomes large enough
(). This is interpreted as a first step of the counterion
condensation (for large coulombic coupling), the second step taking place at
the usual Manning--Oosawa threshold
Error threshold in finite populations
A simple analytical framework to study the molecular quasispecies evolution
of finite populations is proposed, in which the population is assumed to be a
random combination of the constiyuent molecules in each generation,i.e.,
linkage disequilibrium at the population level is neglected. In particular, for
the single-sharp-peak replication landscape we investigate the dependence of
the error threshold on the population size and find that the replication
accuracy at threshold increases linearly with the reciprocal of the population
size for sufficiently large populations. Furthermore, in the deterministic
limit our formulation yields the exact steady-state of the quasispecies model,
indicating then the population composition is a random combination of the
molecules.Comment: 14 pages and 4 figure
Statistical mechanics of RNA folding: importance of alphabet size
We construct a minimalist model of RNA secondary-structure formation and use
it to study the mapping from sequence to structure. There are strong,
qualitative differences between two-letter and four or six-letter alphabets.
With only two kinds of bases, there are many alternate folding configurations,
yielding thermodynamically stable ground-states only for a small set of
structures of high designability, i.e., total number of associated sequences.
In contrast, sequences made from four bases, as found in nature, or six bases
have far fewer competing folding configurations, resulting in a much greater
average stability of the ground state.Comment: 7 figures; uses revtex
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