Crystallization of Escherichia coli Catabolite Gene Activator Protein with its DNA Binding Site: The use of Modular DNA

To obtain crystals of the Escherichia coli catabolite gene activator protein (CAP) complexed with its DNA-binding site, we have searched for crystallization conditions with 26 different DNA segments ≥28 base-pairs in length that explore a variety of nucleotide sequences, lengths, and extended 5′ or 3′ termini. In addition to utilizing uninterrupted asymmetric lac site sequences, we devised a novel approach of synthesizing half-sites that allowed us to efficiently generate symmetric DNA segments with a wide variety of extended termini and lengths in the large size range (≥28 bp) required by this protein. We report three crystal forms that are suitable for X-ray analysis, one of which (crystal form III) gives measurable diffraction amplitudes to 3 Å resolution. Additives such as calcium, n-octyl-β-d-glucopyranoside and spermine produce modest improvements in the quality of diffraction from crystal form III. Adequate stabilization of crystal form III is unexpectedly complex, requiring a greater than tenfold reduction in the salt concentration followed by addition of 2-methyl-2,4-pentanediol and then an increase in the concentration of polyethylene glycol.

Numerical Computation of a Certain Dirichlet Series Attached to Siegel Modular Forms of Degree Two

The Rankin convolution type Dirichlet series D-F,D-G(s) of Siegel modular forms F and G of degree two, which was introduced by Kohnen and the second author, is computed numerically for various F and G. In particular, we prove that the series D-F,D-G(s), which shares the same functional equation and analytic behavior with the spinor L-functions of eigenforms of the same weight are not linear combinations of those. In order to conduct these experiments a numerical method to compute the Petersson scalar products of Jacobi Forms is developed and discussed in detail.

Computations of Vector-Valued Siegel Modular Forms

We carry out some computations of vector-valued Siegel modular forms of degree two, weight (k, 2) and level one, and highlight three experimental results: (1) we identify a rational eigenform in a three-dimensional space of cusp forms; (2) we observe that non-cuspidal eigenforms of level one are not always rational; (3) we verify a number of cases of conjectures about congruences between classical modular forms and Siegel modular forms. Our approach is based on Satoh's description of the module of vector-valued Siegel modular forms of weight (k, 2) and an explicit description of the Hecke action on Fourier expansions. (C) 2013 Elsevier Inc. All rights reserved.

The Design of XML-Based Model and Experiment Description Languages for Network Simulation

The Simulation Automation Framework for Experiments (SAFE) is a project created to raise the level of abstraction in network simulation tools and thereby address issues that undermine credibility. SAFE incorporates best practices in network simulationto automate the experimental process and to guide users in the development of sound scientific studies using the popular ns-3 network simulator. My contributions to the SAFE project: the design of two XML-based languages called NEDL (ns-3 Experiment Description Language) and NSTL (ns-3 Script Templating Language), which facilitate the description of experiments and network simulationmodels, respectively. The languages provide a foundation for the construction of better interfaces between the user and the ns-3 simulator. They also provide input to a mechanism which automates the execution of network simulation experiments. Additionally,this thesis demonstrates that one can develop tools to generate ns-3 scripts in Python or C++ automatically from NSTL model descriptions.

Verifying Harder's Conjecture for Classical and Siegel Modular Forms

A conjecture by Harder shows a surprising congruence between the coefficients of “classical” modular forms and the Hecke eigenvalues of corresponding Siegel modular forms, contigent upon “large primes” dividing the critical values of the given classical modular form. Harder’s Conjecture has already been verified for one-dimensional spaces of classical and Siegel modular forms (along with some two-dimensional cases), and for primes p 37. We verify the conjecture for higher-dimensional spaces, and up to a comparable prime p.

Zeros of Weakly Holomorphic Modular Forms of Levels 2 and 3

Let M-k(#)(N) be the space of weakly holomorphic modular forms for Gamma(0)(N) that are holomorphic at all cusps except possibly at infinity. We study a canonical basis for M-k(#)(2) and M-k(#)(3) and prove that almost all modular forms in this basis have the property that the majority of their zeros in a fundamental domain lie on a lower boundary arc of the fundamental domain.