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8. Cross-Jet Transport in Geophysical Turbulence Professor Lee Panetta Department of Atmospheric Sciences

9. Atmospheric Sciences, Panetta Overview The nature of cross-jet transport is of interest to the chemistry of the stratosphere and the biology of the upper extratropical oceans. Here I use a combination of pseudo-spectral and particle tracking methods to investigate the nature of transport across self-organized jets in rapidly rotating stratified flow. Simulations indicate the presence of an anomalous, subdiffusive scaling regime for single particle dispersion which is intermediate between the short-time “ballistic” and long-time “diffusive” regimes. The regime is seen over a range of forcing strengths, but a physically based scaling can be chosen which collapses results to a single dispersion curve.

10. Atmospheric Sciences, Panetta Mathematical Model The two-layer system consists of two horizontal fluid layers, bounded above and below by a rigid horizontal surface, and separated by an immiscible interface. The layers have slightly different densities, with the denser (cold) fluid beneath the lighter (warm) fluid. Key variables in the theory are the layer "potential vorticities" variables Qi, defined in terms of the non-dimensional streamfunction Yi in layer i, by Qi = by + 2 Yi + (-1)i (Y1 - Y2 / 2). The system we integrate numerically governs the evolution of deviations Qi from a specified state with an interface having a spatially uniform structure, a tilt upward to the north. This is effectively a spatially uniform thermal forcing. The evolution equations are D Results shown here use a 512 x 512 grid in each layer.

11. Atmospheric Sciences, Panetta Cross-Jet Transport in Geophysical Turbulence After a spin-up period, the solution settles into a quasi-steady state with a sequence of turbulent jets oriented in the east-west direction. The mean latitude of each jet is surprisingly persistent, even though eddy-to-mean-flow kinetic energy ratios can be well in excess of unity. The figure below shows the evolution in time of the x-averaged eastward component of the wind in the upper layer for in one simulation. There are four steady jets in the north, and alternately one and two in the south. Adjustment of domain width can remove this transience, which is a "quantization" effect due to the presence of a dynamically determined jet scale.

12. Atmospheric Sciences, Panetta Cross-Jet Transport in Geophysical Turbulence Instantaneous fields of potential vorticity show narrowly concentrated regions of tight gradient, corresponding to eastward jets, and compact vortices which arise from waves which form on the jets and break. Both spatial structures play important roles in transport.

13. Atmospheric Sciences, Panetta Cross-Jet Transport in Geophysical Turbulence The figure below shows an instantaneous potential vorticity field for the upper layer, and two groups of tracers whose positions are indicated by asterisks. The tracers were released a short time before on lines of constant latitude halfway between westerly (i.e. eastward) jets, in regions of relatively weak potential vorticity gradient (compare previous figure). Also indicated by arrows on the side are the average positions of the nearest westerly jets.

14. Atmospheric Sciences, Panetta Cross-Jet Transport in Geophysical Turbulence The figure below shows a selection of four tracer trajectories, with initial release points indicated by asterisks. The dotted lines indicate the narrow regions of (time averaged) high gradients of potential vorticity, which are the regions of strong eastward jets. Two of the tracers shown started in these regions, and were cast out, and two started outside these regions. One of the latter (green trajectory) actually crossed a nearby jet. The animation provided below shows how this jet crossing occurs, namely in a wave-breaking event that results in a vortex being formed. The tracer is initially carried along by the vortex. The statistics of such "cross-jet transport" are of our principal interest. To study this, information from repeated releases of groups of tracers of the sort shown in Fig 3 was analyzed.

15. Atmospheric Sciences, Panetta Cross-Jet Transport in Geophysical Turbulence Results on single particle dispersion rates from five different choices of B are summarized in Fig 5 below. Smaller values of B correspond to flows more strongly driven. The sampling strategy was that for each value of B, 10 groups of 1024 tracers were released halfway between mean westerly jet positions. To account for the difference in energy levels in the flows, distances were rescaled by interjet spacing distance.

16. Atmospheric Sciences, Panetta Animation of Results The animation shows a number of features (see the first frame below): • The labels on the side are nondimensional length units in the x (eastward) and y (northward) directions; • Colors indicate potential vorticity, with high values indicated by red and low values by blue. The sharp gradation between yellow and red, and between yellow and blue, correspond to cores of two eastward jets; • The dashed curves are lines of constant streamfunction values. Each jet is seen to be part of a street-like array; eddies of locally high streamfunction values are the south, and locally low values are to the north (see the "H" and "L"); • There are different symbols indicating positions (see arrow) of the three tracers released in the flow at nondimensional time "t=0". As time evolves these tracers quickly become widely separated, and the tracer marked by the asterisk is seen in the animation to actually cross the southern jet in a wave-breaking event.

17. Atmospheric Sciences, Panetta

18. Beef Cattle Genomics and Bioinformatics Professor David L. Adelson Clare A. Gill

19. Bioinformatics, Adelson and Gill Current projects • Our most pressing project at present is our contribution of bovine BAC clones to the Bovine Genome Project. • We have sent 50,000 BACs to Marco Marra’s group for fingerprinting. • We need to end sequence these clones as well (bidirectional).

20. Bioinformatics, Adelson and Gill For this we require laboratory automation Biorobot for DNA isolations High throughput PCR machine 96 capillary DNA Sequencer

21. Bioinformatics, Adelson and Gill Automation consequences • Sample tracking: • Labeling needs to be automated. • Sample sheets need to be automated. • Results need to be collected and entered into a database. • With over 500 sequences collected every day, an analysis pipeline needs to be in place and at least semi-automated. • Database needs to be integrated to manage not only DNA preps and sequences, but phenotypes, genotypes and BLAST results.

22. Bioinformatics, Adelson and Gill Work flow for automated sequencing • Select 384 well plate for growth. • Automatically generate MegaBACE sample sheets (4x96) and transfer over network to MegaBACE. • Inoculate 4x96 well grow boxes and bar code. • Grow clones. • Robotic DNA isolation (bar code DNA plates). • Robotic DNA sequencing reaction set up (bar code). • Cycle sequencing • Robotic sequencing clean up (bar code). • Load sequencer (bar code reader). • Auto file transfer to sequence analysis server.

23. Bioinformatics, Adelson and Gill Sequence data pipeline Trace files (sequencer) phred (LINUX box) HT-BLAST SGI Origin 3800 48 cpu supercomputer Tab delimited parsed output (LINUX box) MySQL table (LINUX box) Web server (LINUX box)

24. Bioinformatics, Adelson and Gill SGI Origion 3800 • High throughput BLAST1,2 requires a multiprocessor machine with large, shared memory for maximum speed of search. • BLAST parallelizes and scales well, allowing the data pipeline to keep up with the new data generated and update search results for previously generated data. 1Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. 2Camp, N., Cofer, H., and Gomperts, R. 1998. High-Throughput BLAST. http://www.sgi.com/industries/sciences/chembio/resources/papers/HTBlast/HT_Whitepaper.html Ref Type: Electronic Citation.

25. Bioinformatics, Adelson and Gill Database structure • Multiple databases at present, not a single integrated database. • Angleton data in one database • Sequence similarity in another db. • Sensory panel data (meat science) in another db.

26. Bioinformatics, Adelson and Gill Family database

27. Bioinformatics, Adelson and Gill Meat sensory data

28. Bioinformatics, Adelson and Gill Sequence similarity db

29. Bioinformatics, Adelson and Gill In silico mapping • We get two kinds of information back from sequence similarity searches • Location of homolog in reference genome. • Functional properties of homolog. • We would like to be able to represent both types of information simultaneously. • For now we can only provide the physical location of the homolog in the reference genome (usually the human genome).

30. Bioinformatics, Adelson and Gill Overall db diagram

31. Laboratory for Molecular Simulation (LMS) Texas A&M University Department of Chemistry Director: Prof. Michael B. Hall Manager: Lisa M. Thomson Contributors: M. B. Hall L. M. Thomson J. D. Hoefelmeyer F. Gabbaï C. E. Webster D. H. Russell H. A. Sawyer G. F. Verbeck http://www.chem.tamu.edu/LMS

32. Computational Chemistry, Hall et al. LMS Resources • HARDWARE - All computationally intensive calculations are carried out on the Texas A&M Supercomputing Facility’s systems: • 32-cpu IBM Regatta p690 • 32-cpu SGI Origin 2000 • 48-cpu SGI Origin 3800 • SOFTWARE - The LMS uses a variety of molecular modeling software. This software includes the following: • AMPAC • Cerius2 • CHARMm • Dalton • Gaussian 98 (G98) • GaussView • Insight II • MacroModel • Materials Studio • Molden • MOLPRO • Q-Chem • Quanta • Spock • TINKER

33. Computational Chemistry, Hall et al. A Theoretical Study of the Primary Oxo Transfer Reaction of a Dioxo Molybdenum(VI) Compound with Imine Thiolate Chelating Ligands: A Molybdenum Oxotransferase Analogue (Thomson and Hall) Molybdenum containing enzymes are a broad class of enzymes that are essential for the metabolism of carbon, nitrogen and sulfur in a wide variety of organisms. In humans, sulfite oxidase is the enzyme responsible for the metabolism of the toxin sulfite to sulfate. Analogue reaction systems have been developed to mimic the activity of the molybdoenzymes. These analogue systems can be used to verify experimental data on the structure and reaction mechanism of the complex enzyme systems. This study focuses on the elucidation of the reaction mechanism of an analogue system. Density functional calculations on MoO2(NHCHCH2SH)2 + P(CH3)3  MoO(NHCHCH2SH)2 + OP(CH3)3 were performed at the B3P86 level of theory as implemented in Gaussian 94/98, using a double- quality basis set for all atoms and the inclusion of a polarization function on the phosphorus. The DFT results indicate that this reaction proceeds through a two step mechanism via an associative intermediate shown in the Figure A. The substrate was found to attack one of the terminal oxo groups to form an unusual 3c-4e- O-P-C bond in the first transition state, TSI. The OP(CH3)3 group then rotates to almost lie in the MoO2 plane to form the intermediate, INT. The second transition state, TSII, involves the weakening of the Mo-OP(CH3)3 bond and the concomitant rearrangement of the ligands. Figure B shows an important anti-bonding interaction the help to eliminate the product, OP(CH3)3. The overall exothermicity of this reaction is 32.7 kcal/mol (-Ho) and Go = -27.1 kcal/mol, a value consistent with the equilibrium lying far to the right. The H‡ for the first step (rate determining) was found to be 9.4 kcal/mol, and the second step had a H‡ = 3.3 kcal/mol. These results are within the uncertainty of the experimental system, for which the rate determining H‡ = 9.6(6).

34. Computational Chemistry, Hall et al. Figure A. The B3P86 results for the reaction of MoO2(NHCHCH2SH)2 + P(CH3)3  MoO(NHCHCH2SH)2 + OP(CH3)3. These results indicate that this reaction proceeds through a two step mechanism via an associative intermediate.

35. Computational Chemistry, Hall et al. Figure B. 0.05 isodensity surface of a) REAC, b) TS1 and c) INT. (b) shows the important anti-bonding interaction the help to eliminate the product, OP(CH3)3

36. Computational Chemistry, Hall et al. An Intramolecular Boron-Boron One-Electron s-Bond (Hoefelmeyer and Gabbaï) Owing to their isoelectronic relationship to neutral methyl radicals, the chemistry of stable boron-centered radical anions R3B•- (R=aryl rings) has been investigated intensely. Although delocalization of the radical over the aryl rings accounts for the stability of such systems, EPR studies show that, in some instances, the unpaired electron is mainly localized at boron. In organodiboranes, one-electron reduction leads to the formation of a one-electron s-bond formed by the overlap of the parallel pz boron orbitals. Interestingly, the isolation of boron radicals in which the unpaired electron occupies a molecular orbital formed by the combination of overlapping colinear atomic orbitals is much more elusive. Motivated by the importance of stable radicals to the field of material science, we have set out to prepare a stable boron radical, of the general form (R3B)2•-, and report on the formation of a radical that features a boron-boron one electron -bond.   A single-crystal X-ray analysis of 1,8-bis(diphenylboryl)-naphthalene revealed the existence of a sterically congested structure with a boron-boron distance of 3.002(2) Å (Figure A). A one-electron reduction of 1 affords the radical anion 2 (Figure A). While it has so far not been possible to obtain single crystals of 2, we have performed a series of DFT calculations on 1 and 2 with the B3LYP functional as implemented in Gaussian 98 ( Basis set: 6-31G on C, and H, and 6-31+G* basis set on B). Examination of the B3LYP orbitals (Figure B) reveals that, in 1, the pz orbitals of the neighboring boron centers overlap substantially and contribute to the Lowest Unoccupied Molecular Orbital (LUMO). The calculated structure for 2 differs from that of 1 in several aspects, but most noteworthy is that the boron-boron distance decreases substantially (3.16 Å in 1 to 2.82 Å in 2) in agreement with the presence of a bonding interaction. Both boron atoms are the dominant contributors to the singly occupied Highest Occupied Molecular Orbital (HOMO), which has a strong boron-boron -bond character (Figure B). This one-electron -bond can be viewed as the occupation of the formerly vacant boron pz-orbitals upon one-electron reduction of 1. The minor contributions of the ring carbon atoms substantiate the importance of the stabilizing effect provided by aryl substituents in stable radicals.

37. Computational Chemistry, Hall et al. An Intramolecular Boron-Boron One-Electrons-Bond (Hoefelmeyer and Gabbaï) Figure A. X-ray crystal structure of 1,8-bis(diphenylboryl)-naphthalene, 1, and B3P86 optimized structure of the reduced species, 2, 1,8-bis(diphenylboryl)-naphthalene anion. Figure B. 0.05 isodensity surface for the Lowest Unoccupied Molecular Orbital (LUMO) of 1, and the Highest Occupied Molecular Orbital (HOMO) for 2, illustrating the overlap of pz orbitals of the neighboring boron centers forming the strong boron-boron -bond character in 2.

38. Computational Chemistry, Hall et al. Theoretical Studies of Carbon-Hydrogen and Carbon-Carbon Bond Activation of Cyclopropane by Cationic Ir(III) (Webster and Hall) The reactions of cyclopropane with the coordinately unsaturated species produced by mild thermal activation of [Cp*Ir(P(CH3)3)CH3]+L (L = Cl2CH2, OSO2CF3-) (shown in the scheme below) have been investigated with density functional calculations (B3LYP). The pathway for the production of endo or exo 3-allyl complexes from the reaction of cyclopropane with the IrIII model complex [CpIr(PH3)CH3]+ proceeds through C-H bond activated IrV intermediates and CH4 elimination, followed by ring opening of the iridium cyclopropyl complexes through an iridium carbene vinyl intermediate to their respective 3-allyl products. This unexpected mechanism breaks two C-C bonds simultaneously and then re-forms one en route from the iridium cyclopropane complex to the iridium allyl products. The interconversion between endo and exo 3-allyl can be assisted by solvent through an 1-allyl intermediate. Thermal rearrangement of the cyclopropyl kinetic product proceeds back through the same s-agostic complex, producing the thermodynamically more stable metallocyclobutane complex.

39. Computational Chemistry, Hall et al. Theoretical Studies of Carbon-Hydrogen and Carbon-Carbon Bond Activation of Cyclopropane by Cationic Ir(III) (Webster and Hall) Schematic representation of the potential energy surface for the reaction of C3H6 with (CpIrPH3CH3)+. Relative energies are in kcal mol-1 and for structures 8 and 8' through 14 and 14' include the energy of CH4. Optimized structures can be found on the following slides.

40. Computational Chemistry, Hall et al. Theoretical Studies of Carbon-Hydrogen and Carbon-Carbon Bond Activation of Cyclopropane by Cationic Ir(III) (Webster and Hall) Optimized structures of the reactant, transition states, intermediates, and products for the reaction of C3H6 with (CpIrPH3CH3)+.

41. Computational Chemistry, Hall et al. Theoretical Studies of Carbon-Hydrogen and Carbon-Carbon Bond Activation of Cyclopropane by Cationic Ir(III) (Webster and Hall) Optimized structures of the reactant, transition states, intermediates, and products for the reaction of C3H6 with (CpIrPH3CH3)+.

42. Computational Chemistry, Hall et al. Theoretical Studies of Carbon-Hydrogen and Carbon-Carbon Bond Activation of Cyclopropane by Cationic Ir(III) (Webster and Hall) Reaction paths for the conversion of endo and exo-allyl

43. Computational Chemistry, Hall et al. Theoretical Studies of Carbon-Hydrogen and Carbon-Carbon Bond Activation of Cyclopropane by Cationic Ir(III) (Webster and Hall) 0.04 isodensity surface of Highest Occupied Molecular Orbital (HOMO) for the interconversion of endo and exo-allyl via “rotating” . The energetic diagram illustrates that this is a high barrier mechanism due to an increase in the energy of the HOMO.

44. Computational Chemistry, Hall et al. Molecular Modeling and Ion Mobility Time-of-Flight Mass Spectroscopy (Russell, Sawyer, Thomson, and Verbeck) Dr. Russell’s group of the Laboratory for Biological Mass Spectrometry uses the Supercomputing Facility in conjunction with the Laboratory for Molecular Simulation (LMS), for predictive modeling of molecular ions drifting through a bath gas, usually He, Ar, and N2. Experimental analysis is carried out using ion mobility time-of-flight mass spectrometry. Our first focus is on the separation of proteins and peptides due to conformational differences in the drift tube (labeled A in the following figure). In order to accurately analyze the peak profiles of the mobility spectra we use molecular mechanics/dynamics to sample the conformational space of the peptides and then calculate the energies of the different conformations using MOPAC calculations at the semi-empirical (AM1) level of theory. Our second focus is on the separation of of small organic molecules with the same mass, but differ by electronic structure (labeled B). High-level ab initio calculations are used to analyze the potential energy surface of small radical cation organic molecules such that we can predict which radical cation reacts longer with the bath gas.

45. Computational Chemistry, Hall et al. Molecular Modeling and Ion Mobility Time-of-Flight Mass Spectroscopy (Russell, Sawyer, Thomson, and Verbeck) A B

46. Computational Studies of Molecular Photoionization Professor Robert R. Lucchese Department of Chemistry Texas A&M University Collaborators: Ping Lin Eric Stratmann Alexandra Natalense Robert Zurales Shaleen Botting Funding: Welch Foundation National Science Foundation Texas A&M Supercomputer Facility

47. Computational Chemistry, Lucchese et al. Molecular Photoionization • When light of sufficient energy interacts with a molecule, a photon can be absorbed leading to the ionization of the molecule: • The probability for ionization is proportional to the square of the dipole matrix element which is an integral over the wave functions that represent the initial state, the final ion state, and the photoelectron:

48. Computational Chemistry, Lucchese et al. Scattering Equations • The initial state, Yi, and the final ion state are, Yf, are described using standard quantum chemistry techniques. • The wave function for the photoelectron, , is the solution of a one-electron integral scattering equation: • This equation is not solved directly, we instead use a variational method to compute the required dipole matrix elements.

49. Computational Chemistry, Lucchese et al. Schwinger Variational Equations • The dipole matrix element can be reduced to an integral over the coordinates of a single electron which in the bracket notation is: • By expanding the wave function in a basis set, the matrix elements can be approximated by the following Schwinger variational matrix expression:

50. Computational Chemistry, Lucchese et al. Single-Center Expansions • All integrals are evaluated using single-center expansions where each function is expanded as Typical values: lmax = 60 for N2 and lmax= 120 for CS2 • With this expansion all three-dimensional integrals become a sum over a set of radial integrals which are computed on a radial grid: R. E. Stratmann et al., J. Chem. Phys. 104, 8989 (1996), and references therein.