A Resource Guide for Consulting with Graduate Students

This resource guide offers undergraduate writing consultants a brief look at some aspects of graduate writing with which they may be unfamiliar. The document is intended to be used in a tutor practicum or in other forms of tutor education

Just don\u27t call it boot camp : Implementing intensive dissertation writing experiences

This roundtable presentation explored intensive writing programs for dissertation writers conducted at two R1 institutions. Evaluations indicated the programs encouraged dissertation progress, provided relational support, and taught skills. The materials here share contextual and curricular information and discuss aspects like group dynamics and timing that can affect program success

Hydrostratigraphic Interpretation of Test-hole and Surface Geophysical Data, Elkhorn and Loup River Basins, Nebraska, 2008 to 2011

The Elkhorn-Loup Model (ELM) was begun in 2006 to understand the effect of various groundwater-management scenarios on surface-water resources. During phase one of the ELM study, a lack of subsurface geological information was identified as a data gap. Test holes drilled to the base of the aquifer in the ELM study area are spaced as much as 25 miles apart, especially in areas of the western Sand Hills. Given the variable character of the hydrostratigraphic units that compose the High Plains aquifer system, substantial variation in aquifer thickness and characteristics can exist between test holes. To improve the hydrogeologic understanding of the ELM study area, the U.S. Geological Survey, in cooperation with the Nebraska Department of Natural Resources, multiple Natural Resources Districts participating in the ELM study, and the University of Nebraska-Lincoln Conservation and Survey Division, described the subsurface lithology at six test holes drilled in 2010 and concurrently collected borehole geophysical data to identify the base of the High Plains aquifer system. A total of 124 time-domain electromagnetic (TDEM) soundings of resistivity were collected at and between selected test-hole locations during 2008-11 as a quick, non-invasive means of identifying the base of the High Plains aquifer system. Test-hole drilling and geophysical logging indicated the base-of-aquifer elevation was less variable in the central ELM area than in previously reported results from the western part of the ELM study area, where deeper paleochannels were eroded into the Brule Formation. In total, more than 435 test holes were examined and compared with the modeled-TDEM soundings. Even where present, individual stratigraphic units could not always be identified in modeled-TDEM sounding results if sufficient resistivity contrast was not evident; however, in general, the base of aquifer [top of the aquifer confining unit (ACU)] is one of the best-resolved results from the TDEM-based models, and estimates of the base-of-aquifer elevation are in good accordance with those from existing test-hole data. Differences between ACU elevations based on modeled-TDEM and test-hole data ranged from 2 to 113 feet (0.6 to 34 meters). The modeled resistivity results reflect the eastward thinning of Miocene-age and older stratigraphic units, and generally allowed confident identification of the accompanying change in the stratigraphic unit forming the ACU. The differences in elevation of the top of the Ogallala, estimated on the basis of the modeled-TDEM resistivity, and the test-hole data ranged from 11 to 251 feet (3.4 to 77 meters), with two-thirds of model results being within 60 feet of the test-hole contact elevation. The modeled-TDEM soundings also provided information regarding the distribution of Plio-Pleistocene gravel deposits, which had an average thickness of 100 feet (30 meters) in the study area; however, in many cases the contact between the Plio-Pleistocene deposits and the overlying Quaternary deposits cannot be reliably distinguished using TDEM soundings alone because of insufficient thickness or resistivity contrast

The SQM/COSMO filter: reliable native pose identification based on the quantum-mechanical description of protein–ligand interactions and implicit COSMO solvation

Current virtual screening tools are fast, but reliable scoring is elusive. Here, we present the "SQM/COSMO filter", a novel scoring function featuring a quantitative semiempirical quantum mechanical (SQM) description of all types of noncovalent interactions coupled with implicit COSMO solvation. We show unequivocally that it outperforms eight widely used scoring functions. The accuracy and chemical generality of the SQM/COSMO filter make it a perfect tool for late stages of virtual screening

An Exploration of the Ozone Dimer Potential Energy Surface

The (O3)2 dimer potential energy surface is thoroughly explored at the ab initio CCSD(T) computational level. Five minima are characterized with binding energies between 0.35 and 2.24 kcal/mol. The most stable may be characterized as slipped parallel, with the two O3 monomers situated in parallel planes. Partitioning of the interaction energy points to dispersion and exchange as the prime contributors to the stability, with varying contributions from electrostatic energy, which is repulsive in one case. Atoms in Molecules analysis of the wavefunction presents specific O⋯O bonding interactions, whose number is related to the overall stability of each dimer. All internal vibrational frequencies are shifted to the red by dimerization, particularly the antisymmetric stretching mode whose shift is as high as 111 cm−1. In addition to the five minima, 11 higher-order stationary points are identified

Photoionization of the fullerene ion C60+

Photoionization cross section of the fullerene ion C60+ has been calculated within a single-electron approximation and also by using a consistent many-body theory accounting for many-electron correlations.Comment: 8 pages, 3 figure

Ab-initio study of model guanine assemblies: The role of pi-pi coupling and band transport

Several assemblies of guanine molecules are investigated by means of first-principle calculations. Such structures include stacked and hydrogen-bonded dimers, as well as vertical columns and planar ribbons, respectively, obtained by periodically replicating the dimers. Our results are in good agreement with experimental data for isolated molecules, isolated dimers, and periodic ribbons. For stacked dimers and columns, the stability is affected by the relative charge distribution of the pi orbitals in adjacent guanine molecules. pi-pi coupling in some stacked columns induces dispersive energy bands, while no dispersion is identified in the planar ribbons along the connections of hydrogen bonds. The implications for different materials comprised of guanine aggregates are discussed. The bandstructure of dispersive configurations may justify a contribution of band transport (Bloch type) in the conduction mechanism of deoxyguanosine fibres, while in DNA-like configurations band transport should be negligible.Comment: 21 pages, 6 figures, 3 tables, to be published in Phys. Rev.

X Linkage of AP3A, a Homolog of the Y-Linked MADS-Box Gene AP3Y in Silene latifolia and S. dioica

Background: The duplication of autosomal genes onto the Y chromosome may be an important element in the evolution of sexual dimorphism.A previous cytological study reported on a putative example of such a duplication event in a dioecious tribe of Silene (Caryophyllaceae): it was inferred that the Y-linked MADS-box gene AP3Y originated from a duplication of the reportedly autosomal orthologAP3A. However, a recent study, also using cytological methods, indicated that AP3A is X-linked in Silenelatifolia. Methodology/Principal Findings: In this study, we hybridized S. latifolia and S. dioicato investigate whether the pattern of X linkage is consistent among distinct populations, occurs in both species, and is robust to genetic methods. We found inheritance patterns indicative of X linkage of AP3A in widely distributed populations of both species. Conclusions/Significance: X linkage ofAP3A and Y linkage of AP3Yin both species indicates that the genes ’ ancestral progenitor resided on the autosomes that gave rise to the sex chromosomesand that neither gene has moved between chromosomes since species divergence.Consequently, our results do not support the contention that inter-chromosomal gene transfer occurred in the evolution of SlAP3Y from SlAP3A

Localized helium excitations in 4He_N-benzene clusters

We compute ground and excited state properties of small helium clusters 4He_N containing a single benzene impurity molecule. Ground-state structures and energies are obtained for N=1,2,3,14 from importance-sampled, rigid-body diffusion Monte Carlo (DMC). Excited state energies due to helium vibrational motion near the molecule surface are evaluated using the projection operator, imaginary time spectral evolution (POITSE) method. We find excitation energies of up to ~23 K above the ground state. These states all possess vibrational character of helium atoms in a highly anisotropic potential due to the aromatic molecule, and can be categorized in terms of localized and collective vibrational modes. These results appear to provide precursors for a transition from localized to collective helium excitations at molecular nanosubstrates of increasing size. We discuss the implications of these results for analysis of anomalous spectral features in recent spectroscopic studies of large aromatic molecules in helium clusters.Comment: 15 pages, 5 figures, submitted to Phys. Rev.