3,249 research outputs found
Structural, mechanical and thermodynamic properties of a coarse-grained DNA model
We explore in detail the structural, mechanical and thermodynamic properties
of a coarse-grained model of DNA similar to that introduced in Thomas E.
Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101
(2010). Effective interactions are used to represent chain connectivity,
excluded volume, base stacking and hydrogen bonding, naturally reproducing a
range of DNA behaviour. We quantify the relation to experiment of the
thermodynamics of single-stranded stacking, duplex hybridization and hairpin
formation, as well as structural properties such as the persistence length of
single strands and duplexes, and the torsional and stretching stiffness of
double helices. We also explore the model's representation of more complex
motifs involving dangling ends, bulged bases and internal loops, and the effect
of stacking and fraying on the thermodynamics of the duplex formation
transition.Comment: 25 pages, 16 figure
The binary black-hole problem at the third post-Newtonian approximation in the orbital motion: Static part
Post-Newtonian expansions of the Brill-Lindquist and Misner-Lindquist
solutions of the time-symmetric two-black-hole initial value problem are
derived. The static Hamiltonians related to the expanded solutions, after
identifying the bare masses in both solutions, are found to differ from each
other at the third post-Newtonian approximation. By shifting the position
variables of the black holes the post-Newtonian expansions of the three metrics
can be made to coincide up to the fifth post-Newtonian order resulting in
identical static Hamiltonians up the third post-Newtonian approximation. The
calculations shed light on previously performed binary point-mass calculations
at the third post-Newtonian approximation.Comment: LaTeX, 9 pages, to be submitted to Physical Review
Stretching Semiflexible Polymer Chains: Evidence for the Importance of Excluded Volume Effects from Monte Carlo Simulation
Semiflexible macromolecules in dilute solution under very good solvent
conditions are modeled by self-avoiding walks on the simple cubic lattice
( dimensions) and square lattice ( dimensions), varying chain
stiffness by an energy penalty for chain bending. In the absence
of excluded volume interactions, the persistence length of the
polymers would then simply be with , the bond length being the lattice spacing,
and is the thermal energy. Using Monte Carlo simulations applying the
pruned-enriched Rosenbluth method (PERM), both and the chain length
are varied over a wide range ), and
also a stretching force is applied to one chain end (fixing the other end
at the origin). In the absence of this force, in a single crossover from
rod-like behavior (for contour lengths less than ) to swollen coils
occurs, invalidating the Kratky-Porod model, while in a double crossover
occurs, from rods to Gaussian coils (as implied by the Kratky-Porod model) and
then to coils that are swollen due to the excluded volume interaction. If the
stretching force is applied, excluded volume interactions matter for the force
versus extension relation irrespective of chain stiffness in , while
theories based on the Kratky-Porod model are found to work in for stiff
chains in an intermediate regime of chain extensions. While for in
this model a persistence length can be estimated from the initial decay of
bond-orientational correlations, it is argued that this is not possible for
more complex wormlike chains (e.g. bottle-brush polymers). Consequences for the
proper interpretation of experiments are briefly discussed.Comment: 23 pages, 17 figures, 2 tables, to be published in J. Chem. Phys.
(2011
Microscopic formulation of the Zimm-Bragg model for the helix-coil transition
A microscopic spin model is proposed for the phenomenological Zimm-Bragg
model for the helix-coil transition in biopolymers. This model is shown to
provide the same thermophysical properties of the original Zimm-Bragg model and
it allows a very convenient framework to compute statistical quantities.
Physical origins of this spin model are made transparent by an exact mapping
into a one-dimensional Ising model with an external field. However, the
dependence on temperature of the reduced external field turns out to differ
from the standard one-dimensional Ising model and hence it gives rise to
different thermophysical properties, despite the exact mapping connecting them.
We discuss how this point has been frequently overlooked in the recent
literature.Comment: 11 pages, 2 figure
The Effects of Stacking on the Configurations and Elasticity of Single Stranded Nucleic Acids
Stacking interactions in single stranded nucleic acids give rise to
configurations of an annealed rod-coil multiblock copolymer. Theoretical
analysis identifies the resulting signatures for long homopolynucleotides: A
non monotonous dependence of size on temperature, corresponding effects on
cyclization and a plateau in the extension force law. Explicit numerical
results for poly(dA) and poly(rU) are presented.Comment: 4 pages and 2 figures. Accepted in Phys. Rev. E Rapid Com
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Anatomic brain asymmetry in vervet monkeys.
Asymmetry is a prominent feature of human brains with important functional consequences. Many asymmetric traits show population bias, but little is known about the genetic and environmental sources contributing to inter-individual variance. Anatomic asymmetry has been observed in Old World monkeys, but the evidence for the direction and extent of asymmetry is equivocal and only one study has estimated the genetic contributions to inter-individual variance. In this study we characterize a range of qualitative and quantitative asymmetry measures in structural brain MRIs acquired from an extended pedigree of Old World vervet monkeys (n = 357), and implement variance component methods to estimate the proportion of trait variance attributable to genetic and environmental sources. Four of six asymmetry measures show pedigree-level bias and one of the traits has a significant heritability estimate of about 30%. We also found that environmental variables more significantly influence the width of the right compared to the left prefrontal lobe
Cantor type functions in non-integer bases
Cantor's ternary function is generalized to arbitrary base-change functions
in non-integer bases. Some of them share the curious properties of Cantor's
function, while others behave quite differently
A Titanium Nitride Absorber for Controlling Optical Crosstalk in Horn-Coupled Aluminum LEKID Arrays for Millimeter Wavelengths
We discuss the design and measured performance of a titanium nitride (TiN)
mesh absorber we are developing for controlling optical crosstalk in
horn-coupled lumped-element kinetic inductance detector arrays for
millimeter-wavelengths. This absorber was added to the fused silica
anti-reflection coating attached to previously-characterized, 20-element
prototype arrays of LEKIDs fabricated from thin-film aluminum on silicon
substrates. To test the TiN crosstalk absorber, we compared the measured
response and noise properties of LEKID arrays with and without the TiN mesh.
For this test, the LEKIDs were illuminated with an adjustable, incoherent
electronic millimeter-wave source. Our measurements show that the optical
crosstalk in the LEKID array with the TiN absorber is reduced by 66\% on
average, so the approach is effective and a viable candidate for future
kilo-pixel arrays.Comment: 7 pages, 5 figures, accepted for publication in the Journal of Low
Temperature Physic
Horn-Coupled, Commercially-Fabricated Aluminum Lumped-Element Kinetic Inductance Detectors for Millimeter Wavelengths
We discuss the design, fabrication, and testing of prototype horn-coupled,
lumped-element kinetic inductance detectors (LEKIDs) designed for cosmic
microwave background (CMB) studies. The LEKIDs are made from a thin aluminum
film deposited on a silicon wafer and patterned using standard
photolithographic techniques at STAR Cryoelectronics, a commercial device
foundry. We fabricated twenty-element arrays, optimized for a spectral band
centered on 150 GHz, to test the sensitivity and yield of the devices as well
as the multiplexing scheme. We characterized the detectors in two
configurations. First, the detectors were tested in a dark environment with the
horn apertures covered, and second, the horn apertures were pointed towards a
beam-filling cryogenic blackbody load. These tests show that the multiplexing
scheme is robust and scalable, the yield across multiple LEKID arrays is 91%,
and the noise-equivalent temperatures (NET) for a 4 K optical load are in the
range 26\thinspace\pm6 \thinspace \mu \mbox{K} \sqrt{\mbox{s}}
Large Scale Isolation of Expression Vector Cassette by Magnetic Triple Helix Affinity Capture
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