Molecular Modeling of Nucleic Acid Structure: Energy and Sampling

An overview of computer simulation techniques as applied to nucleic acid systems is presented. This unit expands an accompanying overview unit (UNIT ) by discussing methods used to treat the energy and sample representative configurations. Emphasis is placed on molecular mechanics and empirical force fields.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143698/1/cpnc0708.pd

Solar Polar Fields During Cycles 21 --- 23: Correlation with Meridional Flows

We have examined polar magnetic fields for the last three solar cycles, {$\it{viz.}$}, cycles 21, 22 and 23 using NSO Kitt Peak synoptic magnetograms. In addition, we have used SoHO/MDI magnetograms to derive the polar fields during cycle 23. Both Kitt Peak and MDI data at high latitudes (78${^{\circ}}$--90${^{\circ}}$) in both solar hemispheres show a significant drop in the absolute value of polar fields from the late declining phase of the solar cycle 22 to the maximum of the solar cycle 23. We find that long term changes in the absolute value of the polar field, in cycle 23, is well correlated with changes in meridional flow speeds that have been reported recently. We discuss the implication of this in influencing the extremely prolonged minimum experienced at the start of the current cycle 24 and in forecasting the behaviour of future solar cycles.Comment: 4 Figures 11 pages; Revised version under review in Solar Physic

Regulated complex assembly safeguards the fidelity of Sleeping Beauty transposition

The functional relevance of the inverted repeat structure (IR/DR) in a subgroup of the Tc1/mariner superfamily of transposons has been enigmatic. In contrast to mariner transposition, where a topological filter suppresses single-ended reactions, the IR/DR orchestrates a regulatory mechanism to enforce synapsis of the transposon ends before cleavage by the transposase occurs. This ordered assembly process shepherds primary transposase binding to the inner 12DRs (where cleavage does not occur), followed by capture of the 12DR of the other transposon end. This extra layer of regulation suppresses aberrant, potentially genotoxic recombination activities, and the mobilization of internally deleted copies in the IR/DR subgroup, including Sleeping Beauty (SB). In contrast, internally deleted sequences (MITEs) are preferred substrates of mariner transposition, and this process is associated with the emergence of Hsmar1-derived miRNA genes in the human genome. Translating IR/DR regulation to in vitro evolution yielded an SB transposon version with optimized substrate recognition (pT4). The ends of SB transposons excised by a K248A excision(+)/integration(-) transposase variant are processed by hairpin resolution, representing a link between phylogenetically, and mechanistically different recombination reactions, such as V(D)J recombination and transposition. Such variants generated by random mutation might stabilize transposon-host interactions or prepare the transposon for a horizontal transfer

Light meson mass dependence of the positive parity heavy-strange mesons

We calculate the masses of the resonances D_{s0}^*(2317) and D_{s1}(2460) as well as their bottom partners as bound states of a kaon and a D^*- and B^*-meson, respectively, in unitarized chiral perturbation theory at next-to-leading order. After fixing the parameters in the D_{s0}^*(2317) channel, the calculated mass for the D_{s1}(2460) is found in excellent agreement with experiment. The masses for the analogous states with a bottom quark are predicted to be M_{B^*_{s0}}=(5696\pm 40) MeV and M_{B_{s1}}=(5742\pm 40) MeV in reasonable agreement with previous analyses. In particular, we predict M_{B_{s1}}-M_{B_{s0}^*}=46\pm 1 MeV. We also explore the dependence of the states on the pion and kaon masses. We argue that the kaon mass dependence of a kaonic bound state should be almost linear with slope about unity. Such a dependence is specific to the assumed molecular nature of the states. We suggest to extract the kaon mass dependence of these states from lattice QCD calculations.Comment: 10 page

Magnetic switching in granular FePt layers promoted by near-field laser enhancement

Light-matter interaction at the nanoscale in magnetic materials is a topic of intense research in view of potential applications in next-generation high-density magnetic recording. Laser-assisted switching provides a pathway for overcoming the material constraints of high-anisotropy and high-packing density media, though much about the dynamics of the switching process remains unexplored. We use ultrafast small-angle x-ray scattering at an x-ray free-electron laser to probe the magnetic switching dynamics of FePt nanoparticles embedded in a carbon matrix following excitation by an optical femtosecond laser pulse. We observe that the combination of laser excitation and applied static magnetic field, one order of magnitude smaller than the coercive field, can overcome the magnetic anisotropy barrier between "up" and "down" magnetization, enabling magnetization switching. This magnetic switching is found to be inhomogeneous throughout the material, with some individual FePt nanoparticles neither switching nor demagnetizing. The origin of this behavior is identified as the near-field modification of the incident laser radiation around FePt nanoparticles. The fraction of not-switching nanoparticles is influenced by the heat flow between FePt and a heat-sink layer

Analytic continuations of de Sitter thick domain wall solutions

We perform some analytic continuations of the de Sitter thick domain wall solutions obtained in our previous paper hep-th/0201130 in the system of gravity and a scalar field with an axion-like potential. The obtained new solutions represent anti-de Sitter thick domain walls and cosmology. The anti-de Sitter domain wall solutions are periodic, and correspondingly the cosmological solutions represent cyclic universes. We parameterize the axion-like scalar field potential and determine the parameter regions of each type of solutions.Comment: Additons in section 5, 8 pages, 7 figures, RevTe

Vacuum creation of quarks at the time scale of QGP thermalization and strangeness enhancement in heavy-ion collisions

The vacuum parton creation in quickly varying external fields is studied at the time scale of order 1 fm/$c$ typical for the quark-gluon plasma formation and thermalization. To describe the pre-equilibrium evolution of the system the transport kinetic equation is employed. It is shown that the dynamics of production process at times comparable with particle inverse masses can deviate considerably from that based on classical Schwinger-like estimates for homogeneous and constant fields. One of the effects caused by non-stationary chromoelectric fields is the enhancement of the yield of $s\bar{s}$ quark pairs. Dependence of this effect on the shape and duration of the field pulse is studied together with the influence of string fusion and reduction of quark masses.Comment: REVTEX, 11pp. incl. 4 figures, to be published in Phys. Lett.

Beam Test Results of the BTeV Silicon Pixel Detector

The results of the BTeV silicon pixel detector beam test carried out at Fermilab in 1999-2000 are reported. The pixel detector spatial resolution has been studied as a function of track inclination, sensor bias, and readout threshold.Comment: 8 pages of text, 8 figures, Proceedings paper of Pixel 2000: International Workshop on Semiconductor Pixel Detectors for Particles and X-Rays, Genova, June 5-8, 200

Non-perturbative effects in a rapidly expanding quark-gluon plasma

Within first-order phase transitions, we investigate the pre-transitional effects due to the nonperturbative, large-amplitude thermal fluctuations which can promote phase mixing before the critical temperature is reached from above. In contrast with the cosmological quark-hadron transition, we find that the rapid cooling typical of the RHIC and LHC experiments and the fact that the quark-gluon plasma is chemically unsaturated suppress the role of non-perturbative effects at current collider energies. Significant supercooling is possible in a (nearly) homogeneous state of quark gluon plasma.Comment: LaTeX, 7 pages with 7 Postscript figures. Figures added, discussions added. Version to appear in Phys. Rev.

Performance of prototype BTeV silicon pixel detectors in a high energy pion beam

The silicon pixel vertex detector is a key element of the BTeV spectrometer. Sensors bump-bonded to prototype front-end devices were tested in a high energy pion beam at Fermilab. The spatial resolution and occupancies as a function of the pion incident angle were measured for various sensor-readout combinations. The data are compared with predictions from our Monte Carlo simulation and very good agreement is found.Comment: 24 pages, 20 figure