Stochastic approach to molecular interactions and computational theory of metabolic and genetic regulations

Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between transcription factors and the operators of genes and that between ligands and binding sites of allosteric enzymes are typical examples of such molecular interactions. In order to obtain the general mathematical framework of biological regulations, we formulate these interactions as finite Markov processes and establish a computational theory of regulatory activities of macromolecules based mainly on graphical analysis of their state transition diagrams. The contribution is summarized as follows: (1) Stochastic interpretation of Michaelis-Menten equation is given. (2) Notion of \textit{probability flow} is introduced in relation to detailed balance. (3) A stochastic analogy of \textit{Wegscheider condition} is given in relation to loops in the state transition diagram. (4) A simple graphical method of computing the regulatory activity in terms of ligands' concentrations is obtained for Wegscheider cases.Comment: 20 pages, 13 figure

Development of a new two color far infrared laser interferometer for future fusion devices

A new two color far infrared (FIR) laser interferometer under development for future fusion devices will be presented. The laser wavelength is optimized from the consideration of the beam refraction effect due to plasma density gradient and signal-to-noise ratio for an expected phase shift due to plasmas. Laser lines of 57.2 and 47.6 ?m are found to be suitable for the applications to high performance plasmas of Large Helical Device and future fusion devices such as the International Thermonuclear Experimental Reactor. The output power of 57.2 ?m CH_3OD laser is estimated to be ~1.6 W, which is the highest laser power in the FIR wavelength regime. The optical configuration of a new interferometer system using two colors will be proposed. In the system, one detector simultaneously detects the beat signals of the 57.2 and 47.6 ?m laser lines, and each interference signal can be separated electronically (1 MHz for 57.2 ?m and 0.84 MHz expected for 47.6 ?m). Mechanical vibration can be compensated by using the two color interferometer. The present status of the development of the system is also presented

A simulation toolkit for electroluminescence assessment in rare event experiments

A good understanding of electroluminescence is a prerequisite when optimising double-phase noble gas detectors for Dark Matter searches and high-pressure xenon TPCs for neutrinoless double beta decay detection. A simulation toolkit for calculating the emission of light through electron impact on neon, argon, krypton and xenon has been developed using the Magboltz and Garfield programs. Calculated excitation and electroluminescence efficiencies, electroluminescence yield and associated statistical fluctuations are presented as a function of electric field. Good agreement with experiment and with Monte Carlo simulations has been obtained

Analysis of proton-induced fragment production cross sections by the Quantum Molecular Dynamics plus Statistical Decay Model

The production cross sections of various fragments from proton-induced reactions on $^{56}$Fe and $^{27}$Al have been analyzed by the Quantum Molecular Dynamics (QMD) plus Statistical Decay Model (SDM). It was found that the mass and charge distributions calculated with and without the statistical decay have very different shapes. These results also depend strongly on the impact parameter, showing an importance of the dynamical treatment as realized by the QMD approach. The calculated results were compared with experimental data in the energy region from 50 MeV to 5 GeV. The QMD+SDM calculation could reproduce the production cross sections of the light clusters and intermediate-mass to heavy fragments in a good accuracy. The production cross section of $^{7}$Be was, however, underpredicted by approximately 2 orders of magnitude, showing the necessity of another reaction mechanism not taken into account in the present model.Comment: 12 pages, Latex is used, 6 Postscript figures are available by request from [email protected]

Spin current in ferromagnet/insulator/superconductor junctions

A theory of spin polarized tunneling spectroscopy based on a scattering theory is given for tunneling junctions between ferromagnets and d-wave superconductors. The spin filtering effect of an exchange field in the insulator is also treated. We clarify that the properties of the Andreev reflection are largely modified due to a presence of an exchange field in the ferromagnets, and consequently the Andreev reflected quasiparticle shows an evanescent-wave behavior depending on the injection angle of the quasiparticle. Conductance formulas for the spin current as well as the charge current are given as a function of the applied voltage and the spin-polarization in the ferromagnet for arbitrary barrier heights. It is shown that the surface bound states do not contribute to the spin current and that the zero-bias conductance peak expected for a d-wave superconductor splits into two peaks under the influence of the exchange interaction in the insulator.Comment: 14 pages, 11 figure

Spin polarized tunneling in ferromagnet/unconventional superconductor junctions

We study tunneling in ferromagnet/unconventional superconductor (F/S) junctions. We include the effects of spin polarization, interfacial resistance, and Fermi wavevector mismatch (FWM) between the F and S regions. Andreev reflection (AR) at the F/S interface, governing tunneling at low bias voltage, is strongly modified by these parameters. The conductance exhibits a very wide variety of features as a function of applied voltage.Comment: Revision includes new figures with angular averages and correction of minor error

Bulk antiferromagnetism in Na0.82CoO2\bf Na_{0.82}CoO_2 single crystals

Susceptibility, specific heat, and muon spin rotation measurements on high-quality single crystals of $\rm Na_{0.82}CoO_2$ have revealed bulk antiferromagnetism with N\'{e}el temperature $\rm T_N = 19.8 \pm 0.1$ K and an ordered moment perpendicular to the $\rm CoO_2$ layers. The magnetic order encompasses nearly 100% of the crystal volume. The susceptibility exhibits a broad peak around 30 K, characteristic of two-dimensional antiferromagnetic fluctuations. The in-plane resistivity is metallic at high temperatures and exhibits a minimum at $\rm T_N$.Comment: published versio

Synthesis and conformational studies of calixarene analogue chiral [3.3.1]metacyclophanes

Trihydroxy[3.3.1]metacyclophane, which can be regarded as an unsymmetrical or incomplete “homocalix[3]arene”, has been prepared from trimethoxy[3.3.1]metacyclophane by demethylation with trimethylsilyl iodide in MeCN. Di-O-methylation at the lower rim of trihydroxy[3.3.1]metacyclophane in the presence of K₂CO₃ in acetone afforded a novel, inherently chiral calixarene–analogue, namely a macrocyclic [3.3.1]metacyclophane, possessing C₁ symmetry. The inherent chirality of the two conformers was characterized by ¹H NMR spectroscopy by addition of an excess of Pirkle's chiral shift reagent [(S)-(+)-1-(9-anthryl)-2,2,2-trifluoroethanol], which caused a splitting of the OMe group and AB patterns corresponding to the methylene protons

Unconventional Charge Ordering in Na0.70CoO2 below 300 K

We present the results of measurements of the dc-magnetic susceptibility chi(T) and the 23Na-NMR response of Na_{0.70}CoO_{2} at temperatures between 50 and 340 K. The chi(T) data suggest that for T > 75 K, the Co ions adopt an effective configuration of Co^{3.4+}. The 23Na-NMR response reveals pronounced anomalies near 250 and 295 K, but no evidence for magnetic phase transitions is found in chi(T). Our data suggest the onset of a dramatic change in the Co 3d-electron spin dynamics at 295 K. This process is completed at 230 K. Our results maybe interpreted as evidence for either a tendency to electron localization or an unconventional charge-density wave phenomenon within the cobalt oxide layer, CoO_2, 3d electron system near room temperature.Comment: 4 pages, 4 figures, re-submitted to Physical Review Letters. The manuscript has been revised following the recommendations of the referees. The discussion section contains substantial change