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

Moments of generalized parton distributions and quark angular momentum of the nucleon

The internal structure of hadrons is important for a variety of topics, including the hadron form factors, proton spin and spin asymmetry in polarized proton scattering. For a systematic study generalized parton distributions (GPDs) encode important information on hadron structure in the entire impact parameter space. We report on a computation of nucleon GPDs based on simulations with two dynamical non-perturbatively improved Wilson quarks with pion masses down to 350MeV. We present results for the total angular momentum of quarks with chiral extrapolation based on covariant baryon chiral perturbation theory.Comment: Presented at 25th International Symposium on Lattice Field Theory, Regensburg, Germany, 30 Jul - 4 Aug 200

Structural and Contextual Patterns in Family Health History Knowledge among African American Adults: A Mixed-Methods Social Network Analysis Study*

Background: Family health history is a strong risk factor for many chronic diseases. Ethnic minorities have been found to have a low awareness of their family health history (FHH), which may pose a contributing factor to health disparities. Purpose: The purpose of this mixed-methods social network analysis study was to identify structural and contextual patterns in African American adults’ FHH knowledge based on interpersonal communication exchanges with their family members. Methods: African American adults completed individually administered family network interviews. Participants’ 3-generation family pedigree served as a visual aid to guide their interview. Our primary outcome of interest for this analysis was whether a family member was reported as someone who talks to the participant about their own (i.e., the family member’s) health, which we refer to as a “personal health informant.” To contextualize quantitative findings, participants were asked to describe how they learned about the health history of the relatives they identified during their interview. Results: Participants (n=37) reported an average family network size of 29.4 relatives (SD = 15.5; Range = 10-67). Each participant, on average, named 17% of their familial network as personal health informants. Multivariate regression results showed that participants were more likely to name an alter as a personal health informant if the alter was female (OR = 2.14, p = 0.0519), from the maternal side of the participant’s family (OR = 1.12, p = 0.0006), had one or more chronic health conditions (OR = 2.41, p = 0.0041), was someone who has discussions with the participant about the participant’s health (OR = 16.28, p < 0.0001), was a source of family health information (OR = 3.46, p = 0.0072), and was someone whose health the participant helps to monitor or track (OR = 5.93, p = 0.0002). Complementary qualitative findings indicate that FHH knowledge is facilitated by open, direct communication among relatives. Personal health informants were described as disclosing information for the purposes of informing others for preventive purposes and for gaining social support. Participants also learned about FHH via other methods, including direct observation, during caretaking, and following a relative’s death. Conclusions: Communication and disclosure practices is an important determinant of African Americans’ FHH knowledge. More culturally and contextually meaningful public health efforts are needed to promote family health history sharing, especially regarding paternal family health history, siblings, and extended relatives

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

Vector meson electromagnetic form factors

The charge, magnetic and quadrupole form factors of vector mesons and the charge form factor of pseudo-scalar mesons are calculated in quenched lattice QCD. The charge radii and magnetic moments are derived. The quark sector contributions to the form factors are calculated separately and we highlight the environmental sensitivity of the light-quark contribution to charge radii.QCDSF Collaboration: M. Gürtler, D. Brömmel, M. Göckeler, Ph. Hägler, R. Horsley, Y. Nakamura, D. Pleiter, P.E.L. Rakow, A. Schäfer, G. Schierholz, H. Stüben and J.M. Zanott

Ab-initio calculation of the electronic and optical excitations in polythiophene: effects of intra- and interchain screening

We present an calculation of the electronic and optical excitations of an isolated polythiophene chain as well as of bulk polythiophene. We use the GW approximation for the electronic self-energy and include excitonic effects by solving the electron-hole Bethe-Salpeter equation. The inclusion of interchain screening in the case of bulk polythiophene drastically reduces both the quasi-particle band gap and the exciton binding energies, but the optical gap is hardly affected. This finding is relevant for conjugated polymers in general.Comment: 4 pages, 1 figur

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

Ab-initio prediction of the electronic and optical excitations in polythiophene: isolated chains versus bulk polymer

We calculate the electronic and optical excitations of polythiophene using the GW approximation for the electronic self-energy, and include excitonic effects by solving the electron-hole Bethe-Salpeter equation. Two different situations are studied: excitations on isolated chains and excitations on chains in crystalline polythiophene. The dielectric tensor for the crystalline situation is obtained by modeling the polymer chains as polarizable line objects, with a long-wavelength polarizability tensor obtained from the ab-initio polarizability function of the isolated chain. With this model dielectric tensor we construct a screened interaction for the crystalline case, including both intra- and interchain screening. In the crystalline situation both the quasi-particle band gap and the exciton binding energies are drastically reduced in comparison with the isolated chain. However, the optical gap is hardly affected. We expect this result to be relevant for conjugated polymers in general.Comment: 15 pages including 4 figures; to appear in Phys. Rev. B, 6/15/200

Quark Soup al dente: Applied Superstring Theory

We discuss the application of the AdS/CFT correspondence to possibly gain new physical insights for the strongly coupled quark-gluon plasma. This article provides an informal summary of a talk given by RCM at the 18th International Conference on General Relativity and Gravitation in July 2007.Comment: This article provides an informal summary of a talk given by RCM at the 18th International Conference on General Relativity and Gravitation in July 200