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

Helicity Dependent and Independent Generalized Parton Distributions of the Nucleon in Lattice QCD

A complete description of the nucleon structure in terms of generalized parton distributions (GPDs) at twist 2 level requires the measurement/computation of the eight functions H, E, \tilde H, \tilde E, H_T, E_T, \tilde H_T and \tilde E_T, all depending on the three variables x, \xi and t. In this talk, we present and discuss our first steps in the framework of lattice QCD towards this enormous task. Dynamical lattice QCD results for the lowest three Mellin moments of the helicity dependent and independent GPDs are shown in terms of their corresponding generalized form factors. Implications for the transverse coordinate space structure of the nucleon as well as the orbital angular momentum (OAM) contribution of quarks to the nucleon spin are discussed in some detail.Comment: 5 pages, 5 figures, Talk presented by Ph.H. at Electron-Nucleus Scattering VIII, Elba, Italy, June 21-25, 2004; typos corrected, minor change in wording on p.4&

Teaching Professional Networking: Students Building Contacts Outside the Classroom

This pilot study implemented a method for teaching professional networking to college business communication students. The method introduced students to data on new college graduate unemployment and underemployment, research on methods for filling open positions, and the concept of six degrees of separation. Where most examples of professional networking instruction in prior research took place exclusively in the classroom, this method required students to make and track contacts in their chosen professional fields. Student reactions were captured in reflection papers and an open response survey and analyzed qualitatively using coding and similarity comparison (Boeije, 2010). Responses were not overly surprising as students indicated learning about their career field, the importance of utilizing connections, challenges in networking, and the benefits that can come from networking. The hands-on nature of the instruction and need for networking as a skill among CTE students creates opportunities for future research

Signal processing in local neuronal circuits based on activity-dependent noise and competition

We study the characteristics of weak signal detection by a recurrent neuronal network with plastic synaptic coupling. It is shown that in the presence of an asynchronous component in synaptic transmission, the network acquires selectivity with respect to the frequency of weak periodic stimuli. For non-periodic frequency-modulated stimuli, the response is quantified by the mutual information between input (signal) and output (network's activity), and is optimized by synaptic depression. Introducing correlations in signal structure resulted in the decrease of input-output mutual information. Our results suggest that in neural systems with plastic connectivity, information is not merely carried passively by the signal; rather, the information content of the signal itself might determine the mode of its processing by a local neuronal circuit.Comment: 15 pages, 4 pages, in press for "Chaos

Transverse Structure of Nucleon Parton Distributions from Lattice QCD

This work presents the first calculation in lattice QCD of three moments of spin-averaged and spin-polarized generalized parton distributions in the proton. It is shown that the slope of the associated generalized form factors decreases significantly as the moment increases, indicating that the transverse size of the light-cone quark distribution decreases as the momentum fraction of the struck parton increases.Comment: 4 pages, 1 figur

Calculation of the nucleon axial charge in lattice QCD

Protons and neutrons have a rich structure in terms of their constituents, the quarks and gluons. Understanding this structure requires solving Quantum Chromodynamics (QCD). However QCD is extremely complicated, so we must numerically solve the equations of QCD using a method known as lattice QCD. Here we describe a typical lattice QCD calculation by examining our recent computation of the nucleon axial charge.Comment: Prepared for Scientific Discovery through Advanced Computing (SciDAC 2006), Denver, Colorado, June 25-29 200

Nucleon structure in the chiral regime with domain wall fermions on an improved staggered sea

Moments of unpolarized, helicity, and transversity distributions, electromagnetic form factors, and generalized form factors of the nucleon are presented from a preliminary analysis of lattice results using pion masses down to 359 MeV. The twist two matrix elements are calculated using a mixed action of domain wall valence quarks and asqtad staggered sea quarks and are renormalized perturbatively. Several observables are extrapolated to the physical limit using chiral perturbation theory. Results are compared with experimental moments of quark distributions and electromagnetic form factors and phenomenologically determined generalized form factors, and the implications on the transverse structure and spin content of the nucleon are discussed.Comment: Talks of J.W. Negele and D.B. Renner at Lattice 200

A Method for Distinctly Marking Honey Bees, Apis mellifera, Originating from Multiple Apiary Locations

Inexpensive and non-intrusive marking methods are essential to track natural behavior of insects for biological experiments. An inexpensive, easy to construct, and easy to install bee marking device is described in this paper. The device is mounted at the entrance of a standard honey bee Apis mellifera L. (Hymenoptera: Apidae) hive and is fitted with a removable tube that dispenses a powdered marker. Marking devices were installed on 80 honey bee colonies distributed in nine separate apiaries. Each device held a tube containing one of five colored fluorescent powders, or a combination of a fluorescent powder (either green or magenta) plus one of two protein powders, resulting in nine unique marks. The powdered protein markers included egg albumin from dry chicken egg whites and casein from dry powdered milk. The efficacy of the marking procedure for each of the unique markers was assessed on honey bees exiting each apiary. Each bee was examined, first by visual inspection for the presence of colored fluorescent powder and then by egg albumin and milk casein specific enzyme-linked immunosorbent assays (ELISA). Data indicated that all five of the colored fluorescent powders and both of the protein powders were effective honey bee markers. However, the fluorescent powders consistently yielded more reliable marks than the protein powders. In general, there was less than a 1% chance of obtaining a false positive colored or protein-marked bee, but the chance of obtaining a false negative marked bee was higher for “protein-marked” bees

Generalized Parton Distributions in Full Lattice QCD

We present recent results on generalized parton distributions from dynamical lattice QCD calculations. Our set of twelve different combinations of couplings and quark masses allows for a preliminary study of the pion mass dependence of the transverse nucleon structure.Comment: 8 pages, 5 figures; Talk presented by Ph.H. at Light-Cone 2004, Amsterdam, 16 - 20 Augus