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 $N_f=2+1$ lattice QCD using domain wall quarks on fine lattices, to attain a new level of precision in systematic and statistical errors. Our calculations use $32^3 \times 64$ 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 $Q^2 \approx$ 1.05 GeV$^2$. 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 $r_1^v$, Pauli radius $r_2^v$ and anomalous magnetic moment $\kappa_v$. 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