658 research outputs found
Computer simulation of protein systems
Ligand binding to dihydrofolate reductase (DHFR) is discussed. This is an extremely important enzyme, as it is the target of several drugs (inhibitors) which are used clinically as antibacterials, antiprotozoals and in cancer chemotherapy. DHFR catalyzes the NADPH (reduced nicotinamide adenine dinucleotide phosphate) dependent reduction of dihydrofolate to tetrahydrofolate, which is used in several pathways of purine and pyrimidine iosynthesis, including that of thymidylate. Since DNA synthesis is dependent on a continuing supply of thymidylate, a blockade of DHFR resulting in a depletion of thymidylate can lead to the cessation of growth of a rapidly proliferating cell line. DHFR exhibits a significant species to species variability in its sensitivity to various inhibitors. For example, trimethoprim, an inhibitor of DHFR, binds to bacterial DHFR's 5 orders of magnitude greater than to vertebrate DHFR's. The structural mechanics, dynamics and energetics of a family of dihydrofolate reductases are studied to rationalize the basis for the inhibitor of these enyzmes and to understand the molecular basis of the difference in the binding constants between the species. This involves investigating the conformational changes induced in the protein on binding the ligand, the internal strain imposed by the enzyme on the ligand, the restriction of fluctuations in atom positions due to binding and the consequent change in entropy
Nucleon Electromagnetic Form Factors from Lattice QCD using 2+1 Flavor Domain Wall Fermions on Fine Lattices and Chiral Perturbation Theory
We present a high-statistics calculation of nucleon electromagnetic form
factors in lattice QCD using domain wall quarks on fine lattices, to
attain a new level of precision in systematic and statistical errors. Our
calculations use lattices with lattice spacing a=0.084 fm for
pion masses of 297, 355, and 403 MeV, and we perform an overdetermined analysis
using on the order of 3600 to 7000 measurements to calculate nucleon electric
and magnetic form factors up to 1.05 GeV. Results are shown
to be consistent with those obtained using valence domain wall quarks with
improved staggered sea quarks, and using coarse domain wall lattices. We
determine the isovector Dirac radius , Pauli radius and
anomalous magnetic moment . We also determine connected contributions
to the corresponding isoscalar observables. We extrapolate these observables to
the physical pion mass using two different formulations of two-flavor chiral
effective field theory at one loop: the heavy baryon Small Scale Expansion
(SSE) and covariant baryon chiral perturbation theory. The isovector results
and the connected contributions to the isoscalar results are compared with
experiment, and the need for calculations at smaller pion masses is discussed.Comment: 44 pages, 40 figure
Bacterial community structure in two sediments with different organic matter content of a tropical coastal lagoon (Brazil)
Palavras-chave: bactérias, estrutura da comunidade, sedimento, lagoa tropical, Brazil
Long-lived photoexcited states in polydiacetylenes with different molecular and supramolecular organization
With the aim of determining the importance of the molecular and supramolecular organization on the excited states of polydiacetylenes, we have studied the photoinduced absorption spectra of the red form of poly[1,6-bis(3,6-didodecyl-N-carbazolyl)-2,4-hexadiyne] (polyDCHD-S) and the results compared with those of the blue form of the same polymer. An interpretation of the data is given in terms of both the conjugation length and the interbackbone separation also in relation to the photoinduced absorption spectra of both blue and red forms of poly[1,6-bis(N-carbazolyl)-2,4-hexadiyne] (polyDCHD), which does not carry the alkyl substituents on the carbazolyl side groups. Information on the above properties is derived from the analysis of the absorption and Raman spectra of this class of polydiacetylenes
Phase diagram and optical conductivity of the one-dimensional spinless Holstein model
The effects of quantum lattice fluctuations on the Peierls transition and the
optical conductivity in the one-dimensional Holstein model of spinless fermions
have been studied by developing an analytical approach, based on the unitary
transformation method. We show that when the electron-phonon coupling constant
decreases to a finite critical value the Peierls dimerization is destroyed by
the quantum lattice fluctuations. The dimerization gap is much more reduced by
the quantum lattice fluctuations than the phonon order parameter. The
calculated optical conductivity does not have the inverse-square-root
singularity but have a peak above the gap edge and there exists a significant
tail below the peak. The peak of optical-conductivity spectrum is not directly
corresponding to the dimerized gap. Our results of the phase diagram and the
spectral-weight function agree with those of the density matrix renormalization
group and the exact diagonalization methods.Comment: 9 pages, 4 figures include
Ab initio prediction of Boron compounds arising from Borozene: Structural and electronic properties
Structure and electronic properties of two unusual boron clusters obtained by
fusion of borozene rings has been studied by means of first principles
calculations, based on the generalized-gradient approximation of the density
functional theory, and the semiempirical tight-binding method was used for the
transport calculations. The role of disorder has also been considered with
single vacancies and substitutional atoms. Results show that the pure boron
clusters are topologically planar and characterized by (3c-2e) bonds, which can
explain, together with the aromaticity (estimated by means of NICS), the
remarkable cohesive energy values obtained. Such feature makes these systems
competitive with the most stable boron clusters to date. On the contrary, the
introduction of impurities compromises stability and planarity in both cases.
The energy gap values indicate that these clusters possess a semiconducting
character, while when the larger system is considered, zero-values of the
density of states are found exclusively within the HOMO-LUMO gap. Electron
transport calculations within the Landauer formalism confirm these indications,
showing semiconductor-like low bias differential conductance for these
stuctures. Differences and similarities with Carbon clusters are highlighted in
the discussion.Comment: 10 pages, 2 tables, 5 figure
On the elastic constants of the zeolite chlorosodalite
The use of force-field based molecular modeling to predict the elastic constants of the zeolite chlorosodalite is described. Theoretical predictions of the on-axis and off-axis elastic constants strongly suggest that an error exists in the published elastic constants of the material. When the previous experimental data are corrected by transposing the published directional ultrasound velocities, excellent agreement is observed between the off-axis plots of sodalite produced by experiment and modeling. Further confirmation of the prediction is supplied by considering the Zener ratios of other inorganic materials that possess cubic symmetry. ©2006 American Institute of Physics
Hadron Structure on the Lattice
A few chosen nucleon properties are described from a lattice QCD perspective:
the nucleon sigma term and the scalar strangeness in the nucleon; the vector
form factors in the nucleon, including the vector strangeness contribution, as
well as parity breaking effects like the anapole and electric dipole moment;
and finally the axial and tensor charges of the nucleon. The status of the
lattice calculations is presented and their potential impact on phenomenology
is discussed.Comment: 17 pages, 9 figures; proceedings of the Conclusive Symposium of the
Collaborative Research Center 443 "Many-body structure of strongly
interacting systems", Mainz, February 23-25, 201
Eddy current studies from the undulator-based positron source target wheel prototype
The efficiency of future positron sources for the next generation of high-energy particle colliders (e.g. ILC, CLIC, LHeC) can be improved if the positron-production target is immersed in the magnetic field of adjacent capture optics. If the target is also rotating due to heat deposition considerations then eddy currents may be induced and lead to additional heating and stresses. In this paper we present data from a rotating target wheel prototype for the baseline ILC positron source. The wheel has been operated at revolution rates up to 1800rpm in fields of the order of 1 Tesla. Comparisons are made between torque data obtained from a transducer on the target drive shaft and the results of finite-element simulations. Rotordynamics issues are presented and future experiments on other aspects of the positron source target station are considered
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