Xavier University of Louisiana , located in the Gert Town section of New Orleans, Louisiana, in the United States, is a private, coeducational, liberal arts college with the distinction of being the only historically black Roman Catholic institution of higher education in the United States. Wikipedia.
Rivas E.,Howard Hughes Medical Institute |
Lang R.,Xavier University of Louisiana |
Eddy S.R.,Howard Hughes Medical Institute
RNA | Year: 2012
The standard approach for single-sequence RNA secondary structure prediction uses a nearest-neighbor thermodynamic model with several thousand experimentally determined energy parameters. An attractive alternative is to use statistical approaches with parameters estimated from growing databases of structural RNAs. Good results have been reported for discriminative statistical methods using complex nearest-neighbor models, including CONTRAfold, Simfold, and ContextFold. Little work has been reported on generative probabilistic models (stochastic context-free grammars [SCFGs]) of comparable complexity, although probabilistic models are generally easier to train and to use. To explore a range of probabilistic models of increasing complexity, and to directly compare probabilistic, thermodynamic, and discriminative approaches, we created TORNADO, a computational tool that can parse a wide spectrum of RNA grammar architectures (including the standard nearest-neighbor model and more) using a generalized super-grammar that can be parameterized with probabilities, energies, or arbitrary scores. By using TORNADO, we find that probabilistic nearest-neighbor models perform comparably to (but not significantly better than) discriminative methods. We find that complex statistical models are prone to overfitting RNA structure and that evaluations should use structurally nonhomologous training and test data sets. Overfitting has affected at least one published method (ContextFold). The most important barrier to improving statistical approaches for RNA secondary structure prediction is the lack of diversity of well-curated single-sequence RNA secondary structures in current RNA databases. Copyright © 2012 RNA Society.
Riley K.E.,Xavier University of Louisiana |
Hobza P.,Czech Institute of Organic Chemistry And Biochemistry
Physical Chemistry Chemical Physics | Year: 2013
In this work we highlight recent work aimed at the characterization of halogen bonds. Here we discuss the origins of the σ-hole, the modulation of halogen bond strength by changing of neighboring chemical groups (i.e. halogen bond tuning), the performance of various computational methods in treating halogen bonds, and the strength and character of the halogen bond, the dihalogen bond, and two hydrogen bonds in bromomethanol dimers (which serve as model complexes) are compared. Symmetry adapted perturbation theory analysis of halogen bonding complexes indicates that halogen bonds strongly depend on both dispersion and electrostatics. The electrostatic interaction that occurs between the halogen σ-hole and the electronegative halogen bond donor is responsible for the high degree of directionality exhibited by halogen bonds. Because these noncovalent interactions have a strong dispersion component, it is important that the computational method used to treat a halogen bonding system be chosen very carefully, with correlated methods (such as CCSD(T)) being optimal. It is also noted here that most forcefield-based molecular mechanics methods do not describe the halogen σ-hole, and thus are not suitable for treating systems with halogen bonds. Recent attempts to improve the molecular mechanics description of halogen bonds are also discussed. © 2013 the Owner Societies.
Delaney K.J.,Xavier University of Louisiana
Plant Science | Year: 2012
Variable indirect photosynthetic rate (Pn) responses occur on injured leaves after insect herbivory. It is important to understand factors that influence indirect Pn reductions after injury. The current study examines the relationship between gas exchange and chlorophyll a fluorescence parameters with injury intensity (% single leaf tissue removal) from clipping or Spodoptera eridania Stoll (Noctuidae) herbivory on Nerium oleander L. (Apocynaceae). Two experiments showed intercellular [CO2] increases but Pn and stomatal conductance reductions with increasing injury intensity, suggesting non-stomatal Pn limitation. Also, Pn recovery was incomplete at 3d post-injury. This is the first report of a negative exponential Pn impairment function with leaf injury intensity to suggest high N. oleander leaf sensitivity to indirect Pn impairment. Negative linear functions occurred between most other gas exchange and chlorophyll a fluorescence parameters with injury intensity. The degree of light harvesting impairment increased with injury intensity via lower (1) photochemical efficiency indicated lower energy transfer efficiency from reaction centers to PSII, (2) photochemical quenching indicated reaction center closure, and (3) electron transport rates indicated less energy traveling through PSII. Future studies can examine additional mechanisms (mesophyll conductance, carbon fixation, and cardenolide induction) to cause N. oleander indirect leaf Pn reductions after injury. © 2011.
Agency: NSF | Branch: Standard Grant | Program: | Phase: HIST BLACK COLLEGES AND UNIV | Award Amount: 197.34K | Year: 2015
The Historically Black Colleges and Universities-Undergraduate Program (HBCU-UP) Research Initiation Awards (RIAs) provide support to STEM junior faculty at HBCUs who are starting to build a research program, as well as for mid-career faculty who may have returned to the faculty ranks after holding an administrative post or who needs to redirect and rebuild a research program. Faculty members may pursue research at their home institution, at an NSF-funded Center, at a research intensive institution or at a national laboratory. The RIA projects are expected to help further the faculty members research capability and effectiveness, to improve research and teaching at his or her home institution, and to involve undergraduate students in research experiences. With support from the National Science Foundation, Xavier University will conduct research in computational chemistry. This research will aid in enhancing Xaviers research capabilities and the educational experiences of undergraduates. This project may increase the retention and graduation rates of undergraduate students at Xavier University, a primarily undergraduate institution, by providing students with cutting-edge skills and research opportunities that can increase their success in STEM fields. The research and educational efforts are expected to expand the participation of groups underrepresented in computational chemistry and support the nations efforts in building a robust STEM workforce.
The aim of this Research Initiation Award proposal is to involve undergraduate students at Xavier University in computational chemistry research. This study will investigate the nature of R-X...pi interactions, a newly discovered type of noncovalent interaction whose properties have not yet been characterized systematically. R-X...pi interactions have been identified as being important in protein-ligand complexes and have begun to be used to compose new materials, strongly indicating the efficacy of this interaction motif as a building block in the design of novel chemical structures. The proposed research aims to elucidate the properties of R-X...pi interactions and compare these properties to those of more common noncovalent interaction types. This research will offer students the opportunity to learn generally about the scientific method, analysis of scientific data, and presentation of scientific results and, more specifically, to learn about the operation of computers (unix environment), molecular electronic methods, and noncovalent interactions. This research experience will offer the students a chance to explore scientific research as a career path.
Agency: NSF | Branch: Standard Grant | Program: | Phase: Chem Struct,Dynmcs&Mechansms B | Award Amount: 200.00K | Year: 2014
In this project funded by the Chemical Structure, Dynamic & Mechanism B Program of the Chemistry Division, Professor Kathleen Morgan of the Department of Chemistry at Xavier University of Louisiana will study the chemical energy content of simple sugars and related compounds. These data are of significance in helping advance our understanding of how biomass, a renewable and carbon-neutral source of energy and chemical feedstock, degrades into useful fuels or chemical building blocks. Xavier University of Louisiana is both a primarily undergraduate institution and a Historically Black College with hundreds of science majors. This project will help train undergraduates with the laboratory and presentation skills needed for future Ph.D. studies or other science-oriented careers. Outreach activities involving K-8 students are also part of the funded project, with a focus on public schools in New Orleans.
Carbohydrates are ubiquitous in nature, yet there are still major gaps in our knowledge of sugar thermochemistry. In this study, heats of formation will be determined for simple monosaccharides having 2-4 carbons; remarkably, these values are unknown. A combination of reaction calorimetry, vaporization measurements, and high-level calculations will be used to obtain the heats of formation for sugars and related compounds such as 1,2-diols. Although high-level calculations can often be used to obtain high quality thermochemical data, the compounds of interest have a large number of important conformations, making accurate calculations far from routine. The heats of formation determined in this study will be used in conjunction with bond energies determined by collaborators, which afford the heats of formation of radicals that are involved in the degradation of biomass. Together these data will help move forward our understanding of the mechanism of biomass degradation.