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DNA Renaturation at the Water-Phenol Interface
We study DNA adsorption and renaturation in a water-phenol two-phase system,
with or without shaking. In very dilute solutions, single-stranded DNA is
adsorbed at the interface in a salt-dependent manner. At high salt
concentrations the adsorption is irreversible. The adsorption of the
single-stranded DNA is specific to phenol and relies on stacking and hydrogen
bonding. We establish the interfacial nature of a DNA renaturation at a high
salt concentration. In the absence of shaking, this reaction involves an
efficient surface diffusion of the single-stranded DNA chains. In the presence
of a vigorous shaking, the bimolecular rate of the reaction exceeds the
Smoluchowski limit for a three-dimensional diffusion-controlled reaction. DNA
renaturation in these conditions is known as the Phenol Emulsion Reassociation
Technique or PERT. Our results establish the interfacial nature of PERT. A
comparison of this interfacial reaction with other approaches shows that PERT
is the most efficient technique and reveals similarities between PERT and the
renaturation performed by single-stranded nucleic acid binding proteins. Our
results lead to a better understanding of the partitioning of nucleic acids in
two-phase systems, and should help design improved extraction procedures for
damaged nucleic acids. We present arguments in favor of a role of phenol and
water-phenol interface in prebiotic chemistry. The most efficient renaturation
reactions (in the presence of condensing agents or with PERT) occur in
heterogeneous systems. This reveals the limitations of homogeneous approaches
to the biochemistry of nucleic acids. We propose a heterogeneous approach to
overcome the limitations of the homogeneous viewpoint
Electronic structure of the incommensurate compound
We extracted, from strongly-correlated ab-initio calculations, a complete
model for the chain subsystem of the
incommensurate compound. A second neighbor model has been determined as
a function of the fourth crystallographic parameter , for both low and
room temperature crystallographic structures. The analysis of the obtained
model shows the crucial importance of the structural modulations on the
electronic structure through the on-site energies and the magnetic
interactions. The structural distortions are characterized by their long range
effect on the cited parameters that hinder the reliability of analyses such as
BVS. One of the most striking results is the existence of antiferromagnetic
nearest-neighbor interactions for metal-ligand-metal angles of . A
detailed analysis of the electron localization and spin arrangement is
presented as a function of the chain to ladder hole transfer and of the
temperature. The obtained spin arrangement is in agreement with
antiferromagnetic correlations in the chain direction at low temperature
: a complete model for the chain sub-system
A second neighbor model for the chain subsystem of the
has been extracted from ab-initio calculations. This
model does not use periodic approximation but describes the entire chain
through the use of the four-dimensional crystallographic description. Second
neighbors interactions are found to be of same order than the first neighbors
ones. The computed values of the second neighbors magnetic interaction are
coherent with experimental estimations of the intra-dimer magnetic
interactions, even if slightly smaller. The reasons of this underestimation are
detailed. The computed model allowed us to understand the origin of the chain
dimerisation and predicts correctly the relative occurrence of dimers and free
spins. The orbitals respectively supporting the magnetic electrons and the
holes have been found to be essentially supported by the copper 3d orbitals
(spins) and the surrounding oxygen orbitals (holes), thus giving a strong
footing to the existence of Zhang-Rice singlets
Bragg spectroscopy of discrete axial quasiparticle modes in a cigar-shaped degenerate Bose gas
We propose an experiment in which long wavelength discrete axial
quasiparticle modes can be imprinted in a 3D cigar-shaped Bose-Einstein
condensate by using two-photon Bragg scattering experiments, similar to the
experiment at the Weizmann Institute [J. Steinhauer {\em et al.}, Phys. Rev.
Lett. {\bf 90}, 060404 (2003)] where short wavelength axial phonons with
different number of radial modes have been observed. We provide values of the
momentum, energy and time duration of the two-photon Bragg pulse and also the
two-body interaction strength which are needed in the Bragg scattering
experiments in order to observe the long wavelength discrete axial modes. These
discrete axial modes can be observed when the system is dilute and the time
duration of the Bragg pulse is long enough.Comment: 5 pages, 3 figures, title, abstract, results changed, references
added. to appear in The European Physical Journal
Strong Coulomb effects in hole-doped Heisenberg chains
Substances such as the ``telephone number compound''
Sr14Cu24O41 are intrinsically hole-doped. The involved interplay of spin and
charge dynamics is a challenge for theory. In this article we propose to
describe hole-doped Heisenberg spin rings by means of complete numerical
diagonalization of a Heisenberg Hamiltonian that depends parametrically on hole
positions and includes the screened Coulomb interaction among the holes. It is
demonstrated that key observables like magnetic susceptibility, specific heat,
and inelastic neutron scattering cross section depend sensitively on the
dielectric constant of the screened Coulomb potential.Comment: 5 pages, 6 figures, to be published in Eur. Phys. J.
The Construction of Gauge-Links in Arbitrary Hard Processes
Transverse momentum dependent parton distribution and fragmentation functions
are described by hadronic matrix elements of bilocal products of field
operators off the light-cone. These bilocal products contain gauge-links, as
required by gauge-invariance. The gauge-links are path-ordered exponentials
connecting the field operators along a certain integration path. This
integration path is process-dependent, depending specifically on the
short-distance partonic subprocess. In this paper we present the technical
details needed in the calculation of the gauge-links and a calculational scheme
is provided to obtain the gauge-invariant distribution and fragmentation
correlators corresponding to a given partonic subprocess
Time evolution of the classical and quantum mechanical versions of diffusive anharmonic oscillator: an example of Lie algebraic techniques
We present the general solutions for the classical and quantum dynamics of
the anharmonic oscillator coupled to a purely diffusive environment. In both
cases, these solutions are obtained by the application of the
Baker-Campbell-Hausdorff (BCH) formulas to expand the evolution operator in an
ordered product of exponentials. Moreover, we obtain an expression for the
Wigner function in the quantum version of the problem. We observe that the role
played by diffusion is to reduce or to attenuate the the characteristic quantum
effects yielded by the nonlinearity, as the appearance of coherent
superpositions of quantum states (Schr\"{o}dinger cat states) and revivals.Comment: 21 pages, 6 figures, 2 table
Circular 77
A comparative yield trial with 45 named varieties and numbered selections of
potatoes was conducted during the 1989 growing season at the University of Alaska
Fairbanks, Agricultural and Forestry Experiment Station's (AFES) Palmer Research
Center, Matanuska Research Farm, located six miles west of Palmer on Trunk Road.
Nonirrigated trials have been conducted annually since 1982 and irrigated trials
were begun in 1985. Results of previous trials are recorded in AFES Circulars 49, 54, 58,
65 and 71. These circulars are available at the Agricultural and Forestry Experiment
Station offices in Fairbanks and Palmer.
Also included in this report are the results of abbreviated versions of the AFES
potato yield trial that were conducted by cooperating individuals and agencies at six
locations in Alaska.
Varieties with a history of commercial production in the Matanuska Valley
(including Alaska 114, Bake-King, Green Mountain and Superior) are included and
serve as a comparative base for newly developed varieties, numbered selections or
older varieties that have not been tested at this location. Varieties that compare favorably
with the above listed standards may warrant consideration by commercial growers.Introduction -- Matanuska Farm Yield Trials: Cultural Practices and Environmental Conditions, Results and Discussion -- Trials at Other Locations in Alaska: General Procedures, Specific Site Information: Delta Junction, Fairbanks, Homer, Kenai - Soldotna, Kodiak, Kotzebue -- List of Table
EFRC Bulletin 77
EFRC's regular newletter covering policy, agricutlural research, policy and advisory wor
Solvent and thermal stability, and pH kinetics, of proline-specific dipeptidyl peptidase IV-like enzyme from bovine serum
Proline-specific dipeptidyl peptidase-like (DPP IV; EC 3.4.14.5) activity in bovine serum has attracted little attention despite its ready availability
and the paucity of useful proline-cleaving enzymes. Bovine serum DPP IV-like peptidase is very tolerant of organic solvents, particularly acetonitrile: upon incubation for 1 h at room temperature in 70% acetonitrile, 47% dimethylformamide, 54% DMSO and 33% tetrahydrofuran (v/v
concentrations) followed by dilution into the standard assay mixture, the enzyme retained half of its aqueous activity. As for thermal performance in aqueous buffer, its relative activity increased up to 50 ◦C. Upon thermoinactivation at 71 ◦C, pH 8.0 (samples removed periodically, cooled on ice, then assayed under optimal conditions), residual activities over short times fit a first-order decay with a k-value of 0.071±0.0034 min−1. Over
longer times, residual activities fit to a double exponential decay with k1 and k2 values of 0.218±0.025 min−1 (46±4% of overall decay) and 0.040±0.002 min−1 (54±4% of overall decay), respectively. The enzyme’s solvent and thermal tolerances suggest that it may have potential for use as a biocatalyst in industry. Kinetic analysis with the
fluorogenic substrate Gly-Pro-7-aminomethylcoumarin over a range of pH values indicated two pK values at 6.18±0.07 and at 9.70±0.50. We ascribe the lower value to the active site histidine; the higher may be due to the active site serine or to a free amino group in the substrate
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