The XENON dark matter experiment aims to detect hypothetical weakly interacting massive particles (WIMPs) scattering off nuclei within its liquid xenon (LXe) target. The trace 85Kr in the xenon target undergoes beta-decay with a 687 keV end point and 10.8 year halflife, which contributes background events and limits the sensitivity of the experiment. In order to achieve the desired sensitivity, the contamination by krypton is reduced to the part per trillion (ppt) level by cryogenic distillation. The conventional methods are not well suited for measuring the krypton contamination at such a low level. In this work, we have developed an atom trap trace analysis (ATTA) device to detect the ultra-low krypton concentration in the xenon target. This project was proposed to the National Science Foundation (NSF) as a Major Research Instrumentation (MRI) development [Aprile and Zelevinsky, 2009] and is funded by NSF and Columbia University. The ATTA method, originally developed at Argonne National Laboratory, uses standard laser cooling and trapping techniques, and counts single trapped atoms. Since the isotopic abundance of 85Kr in nature is 1.5 × 10^-11, the 85Kr/Xe level is expected to be ~10^-23, which is beyond the capability of our method. Thus we detect the most abundant (57%) isotope 84Kr, and infer the 85Kr contamination from their known abundances. To avoid contamination by krypton, the setup is tested and optimized with 40Ar which has a similar cooling wavelength to 84Kr. Two main challenges in this experiment are to obtain a trapping efficiency high enough to detect krypton impurities at the ppt level, and to achieve the resolution to discriminate single atoms. The device is specially designed and adjusted to meet these challenges. After achieving these criteria with argon gas, we precisely characterize the efficiency of the system using Kr-Xe mixtures with known ratios, and find that ~90 minutes are required to trap one 84Kr atom at the 1-ppt Kr/Xe contamination. This thesis describes the design, construction, and experimental results of the ATTA project at Columbia University.

We present the development of the adjoint of a physically based cirrus formation parameterization that computes the sensitivity of formed crystal number concentration to numerous model variables (e.g., updraft velocity, soluble aerosol geometric mean diameter and number concentration, insoluble aerosol geometric mean diameter and number concentration, and ice deposition coefficient). The adjoint is demonstrated in the CESM Community Atmosphere Model Version 5.1, where sensitivity information is computed and used to quantify which variables are most responsible for modeled variability in formed crystal number concentration. The sensitivity of formed crystal number concentration to updraft velocity is positive and largest over the tropics where regions of deep convection are collocated with large sulfate number concentrations. Sensitivity to sulfate number concentration is largest over the tropics where updraft cooling is sufficient and sulfate number concentration is low, pointing to a sulfate limited regime. Outside of the tropics, crystal production is dominated by heterogeneous freezing; unexpectedly, sensitivities to insoluble aerosol number concentration for accumulation and coarse mode dust, black carbon, and organic carbon are negative in sign here. This is a result of infrequent, anomalously high updraft velocity events causing shifts in the dominant modes of freezing which act to bias sensitivity information when annually averaged. Updraft velocity is responsible for ~95% of the variability in formed crystal number concentration in the high latitudes of the Northern Hemisphere. In the tropics, sulfate number concentration controls variability in formed crystal number concentration since crystal production here is sulfate limited. Insoluble aerosol species play a secondary role in influencing the variability of crystal concentrations; coarse mode dust is the largest contributor to crystal number variability at nearly 60%, although the spatial extent of this influence is small and concentrated over highly localized dust events. When globally averaged, nearly 90% of the variability in crystal number concentration can be described by only updraft velocity, sulfate number, temperature, and coarse mode dust number concentration. Although these results depend on parameter assumptions, the robustness of the underlying physics of the cirrus formation parameterization used throughout this work suggests that this approach can be a powerful method for efficiently identifying the origin of microphysical dependencies within large scale atmospheric simulations.

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In this thesis, we present our findings on two major topics, both of which are studies of molecules on metal surfaces by scanning tunneling microscopy (STM). The first topic is on adsorption of a model amine compound, 1,4-benzenediamine (BDA), on the reconstructed Au(111) surface, chosen for its potential application as a molecular electronic device. The molecules were deposited in the gas phase onto the substrate in the vacuum chamber. Five different patterns of BDA molecules on the surface at different coverages, and the preferred adsorption sites of BDA molecules on reconstructed Au(111) surface, were observed. In addition, BDA molecules were susceptible to tip-induced movement, suggesting that BDA molecules on metal surfaces can be a potential candidate in STM molecular manipulations. We also studied graphene nanoislands on Co(0001) in the hope of understanding interaction of expitaxially grown graphene and metal substrates. This topic can shed a light on the potential application of graphene as an electronic device, especially in spintronics. The graphene nanoislands were formed by annealing contorted hexabenzocoronene (HBC) on the Co(0001) surface. In our experiments, we have determined atop registry of graphene atoms with respect to the underlying Co surface. We also investigated the low-energy electronic structures of graphene nanoislands by scanning tunneling spectroscopy. The result was compared with a first-principle calculation using density functional theory (DFT) which suggested strong coupling between graphene pi-bands and cobalt d-electrons. We also observed that the islands exhibit zigzag edges, which exhibits unique electronic structures compared with the center areas of the islands.

This thesis studies electronic properties of molecular devices in the limiting cases of strong and weak electrode-molecule coupling. In these two limits, we use the complementary techniques of X-Ray spectroscopy and Scanning Tunneling Microscopy (STM) to understand the mechanisms for electrode-molecule bond formation, the energy level realignment due to metal-molecule bonds, the effect of coupling strength on single-molecule conductance in low-bias measurements, and the effect of coupling on transport under high-bias. We also introduce molecular designs with inherent asymmetries, and develop an analytical method to determine the effect of these features on high-bias conductance. This understanding of the role of electrode-molecule coupling in high-bias regimes enables us to develop a series of functional electronic devices whose properties can be predictably tuned through chemical design. First, we explore the weak electrode-molecule coupling regime by studing the interaction of two types of paracyclophane derivates that are coupled `through-space' to underlying gold substrates. The two paracyclophane derivatives differ in the strength of their intramolecular through-space coupling. X-Ray photoemission spectroscopy (XPS) and Near-Edge X-ray Absorbance Fine Structure (NEXAFS) spectroscopy allows us to determine the orientation of both molecules; Resonant Photoemission Spectroscopy (RPES) then allows us to measure charge transfer time from molecule to metal for both molecules. This study provides a quantititative measure of charge transfer time as a function of through-space coupling strength. Next we use this understanding in STM based single-molecule current-voltage measurements of a series of molecules that couple through-space to one electrode, and through-bond to the other. We find that in the high-bias regime, these molecules respond differently depending on the direction of the applied field. This asymmetric response to electric field direction results in diode-like behavior. We vary the length of these asymmetrically coupled molecules, and find that we can increase the rectifying characteristics of these molecules by increasing length. Next, we explore the strong-coupling regime with an X-Ray spectroscopy study of the formation of covalent gold-carbon bonds using benzyltrimethyltin molecules on gold surfaces in ultra high vacuum conditions. Through X-ray Photoemission Spectroscopy (XPS) and X-ray absorption measurements, we find that the molecule fragments at the Sn-Benzyl bond when exposed to gold and the resulting benzyl species only forms covalent Au-C bonds on less coordinated Au surfaces like Au(110). We also find spectroscopic evidence for a gap state localized on the Au-C bond that results from the covalent nature of the bond. Finally, we use Density Functional Theory based Nudged Elastic Band methods to find reaction pathways and energy barriers for this reaction. We use our knowledge of the electronic structure of these bonds to create single-molecule junctions containing Au-C bonds in STM-based break junction experiments. In analogy with our approach for the weakly coupled `through-space' systems, we study the high-bias current-voltage characteristics of molecules with one strong Au-C bond, and one weaker donor-acceptor bond. These experiments reveal that the `gap state' created due to the covalent nature of the Au-C bond remains essentially pinned to the Fermi level of its corresponding electrode, and that most of the electric potential drop in the junction occurs on the donor-acceptor bond; as a result, these molecules behave like rectifiers. We use this principle to create a series of three molecular rectifiers, and show that the unique properties of the Au-C bond allow us to easily tune the rectification ratio by modifying a single electronic parameter. We then explore the process of molecular self-assembly to create organic electronic structures on metal surfaces. Specifically, we study the formation of graphene nanoribbons using a brominated precursor deposited on Au(111) surface in ultra high vacuum. We find that the halogen atoms cleave from the precursors at surprisingly low temperatures of <100C, and find that the resulting radicals bind to Au, forming Au-C and Au-Br bonds. We show that the Br desorbs at relatively low temperatures of <250C, and that polymerization of the precursor molecules to form nanoribbons proceeds only after the debrominization of the surface. Finally, with Angle-Resolved Photoemission and Density Functional Theory calculations, we quantify the interaction strength of the resulting nanoribbons with the underlying gold substrate. Taken together, the results presented in this thesis offer a mechanistic understanding of the formation of electrode-molecule bonds, and also an insight into the high-bias behavior of molecular junctions as a function of electrode-molecule coupling. In addition, our work in developing tunable, functional electronic devices serves as a framework for future technological advances towards molecule-based computation.

Molecular modeling of proteins and DNA is an attractive goal because it allows to gain insight into dynamic behavior of molecules on atomistic level. Such studies have a great potential to complement existing experimental techniques in investigating mechanisms of biomolecular phenomena. However, due to large size and ruggedness of free energy landscapes of biopolymers, simulations of long-time scale events often suffer from the pseudoergodicity problem, which manifests as inability to explore configurational space of interest within available computation time. The studies presented here reflect efforts to resolve this problem both by exploring advantages and limitations of the existing simulation techniques in studying behavior of specific biomolecular systems, and by testing new simulation methodologies. Part I is concerned with the mechanism of 8-oxoguanine DNA lesion recognition by the bacterial DNA repair enzyme MutM. Two qualitative studies using the Targeted Molecular Dynamics technique explore possible molecular interactions in the MutM/DNA complex associated with the enzyme's sliding along the ds-DNA and the extrusion of the interrogated base into the MutM's catalytic pocket. The findings suggest that MutM may require rocking motion of the bases encountered in its sliding along the DNA. The rocking motion of the oxoguanine is likely to be restricted due to repulsive electrostatic interactions of its O8 atom with the DNA phosphate backbone and may result in braking of the sliding motion of the MutM. This led to the proposal of the braking recognition mechanism in which recognition occurs due to arrest of the sliding process at the lesion site, which makes possible the otherwise slower process of extruding the base into the catalytic pocket of the MutM for excision. The second study suggests that binding between the conserved Arg 112 residue of MutM and the cytosine estranged during the oxoguanine extrusion may be important to prevent partial oxoguanine extrusion from becoming an alternative sliding pathway. Chapter 1.4 describes an attempt to investigate a possibility of long-range lesion recognition by MutM by computing free energy of MutM/DNA complexes. The Orthogonal Space Random Walk technique used for the free energy calculations in this experiment represents one of recent advancements in the generalized ensemble simulation methodology. Failure to obtain converged free energy estimates for the MutM/DNA complexes led to the discussion of possible limitations of this technique and to the proposal that MutM binding to the DNA in the vicinity of a lesion may require a global conformational reorganization of the DNA in comparison to lesion-free MutM/DNA complexes. Part II presents three small model systems studies of the efficiency of generalized ensemble simulation techniques and reflects a part of the recent methodological development in this field. The generalized ensemble techniques utilize sampling of the configrational space with modified probabilities in order to overcome the barrier crossing problem. Chapters 2.2 and 2.4 are concerned with history-dependant methods of formulating a priory unknown efficient probability modifications. In these studies the use of the Wang-Landau recursion approach in the metadynamics technique and the hybrid Wang-Landau recursion / adaptive reweighing approach for the Simulated Scaling technique are tested. The chapter 2.3 is concerned with an attempt of resolving the diffusion sampling problem associated with the generalized ensemble methods by implementing the Self-Guided Langevin dynamics approach for the Essential Energy Space modality of the metadynamics technique. All three studies demonstrated superior sampling efficiency of the proposed method enhancements for the selected model systems. / A Dissertation submitted to the Institute of Molecular Biophysics in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester, 2009. / June 22, 2009. / DNA Glycosylases, Orthogonal Space Random Walk, Simulated Scaling Metadynamics, Enhanced Sampling, MutM, Generalized Ensemble, Fpg / Includes bibliographical references. / Wei Yang, Professor Directing Dissertation; Ming Ye, Outside Committee Member; Rafael Bruschweiler, Committee Member; Hong Li, Committee Member; Marcia Fenley, Committee Member.

Anthracis Repressor (AntR) is a Mn(II) activated DNA binding protein that is involved in the regulation of Mn(II) homeostasis in Bacillus anthracis. AntR is a member of the Diphtheria Toxin Repressor (DtxR) family of proteins. These proteins function as sensors of intracellular Fe(II) or Mn(II) levels and effect the metal regulated expression of many genes, frequently including virulence related genes. Our studies on AntR focus on metal regulated activation of the protein. We have determined the Mn(II) binding stoichiometry, equilibrium binding constants, and associated kinetic rate constants in AntR using a variety of electron paramagnetic resonance methods. Two divalent manganese ions were observed to bind AntR with positive cooperativity and apparent dissociation constants of 210 ± 18 μM and 16.6 ± 1.0 μM. Binding rates were in the sub-millisecond range, and dissociation rates were characterized by rate constants 35.7 ± 12.1 s-1 and 0.115 ± 0.009 s-1. We probed the nature of the metal binding site with EPR for comparison with the crystal structures of homologous manganese transport regulator (MntR) from Bacillus subtilis. The spectra were not consistent with a binuclear Mn(II) cluster as seen in MntR structures. Gel filtration, continuous wave EPR, and Pulsed EPR methods were used to investigate possible structural changes in response to metal binding. We found that AntR is exclusively dimeric in absence of Mn(II). Double electron-electron resonance (DEER) was employed to measure spin-spin distance of strategically placed nitroxide spin labels in dimeric AntR. To realize the full potential of DEER, an analysis software with graphical user interface was developed. The data indicated the presence of multiple conformations for each spin label pair in apo-AntR. Metal binding had little effect on these conformations, except near the putative DNA-binding helixes, where metal binding sharpened the distribution of conformers, and decreased the distance between DNA binding regions of AntR dimer. We also showed that the AntR backbone dynamics change considerably upon metal binding. A structure model for AntR was built from homology to MntR, and the experimentally measured distances were simulated. This model only partially agreed with the DEER results, suggesting structural differences between AntR and MntR. These results allow us to develop a model for the Mn(II) induced activation of the repressor. / A Dissertation Submitted to the Institute of Molecular Biophysics in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy. / Spring Semester, 2007. / January 12, 2007. / Manganese, MntR / Includes bibliographical references. / Piotr G. Fajer, Professor Co-Directing Dissertation; Timothy M. Logan, Professor Co-Directing Dissertation; Michael Blaber, Outside Committee Member; Richard Bertram, Committee Member; Hugh Nymeyer, Committee Member.

The Iron-dependent Regulator (IdeR) is a 230-amino acid transcriptional repressor that regulates iron homeostasis, oxidative stress response and virulence in Mycobacterium tuberculosis. The importance of IdeR for mycobacterial metabolism, virulence, and survival in the host cell suggests that the protein may have a potential as a therapeutic target. The natural ligand for IdeR is Fe(II), but Ni(II), Co(II), Cd(II), Mn(II), and Zn(II) also bind to and activate the protein in vitro. Protein activation by metal is complex process involving metal-induced folding of the N-terminal domain, changes in the interaction between the N- and C-terminal domains, and formation of homodimers. The objective of this work was to characterize the molecular details of IdeR activation in vitro. The dimerization energetics were determined as a function of metal binding using equilibrium analytical ultracentrifugation. The dissociation constant was strongly dependent on the metal ligation state of the protein. Addition of Ni(II) induced changes in fluorescence intensity and emission maximum of the tryptophan residues that strongly depended on protein concentration. Mutational analysis suggested that both tryptophan residues in IdeR are sensitive to folding, dimerization and metal binding. Metal binding affinity was measured quantitatively using equilibrium dialysis. The results showed strongly positive cooperative binding of three equivalents of metal per monomer. Metal binding was not cooperative in an IdeR variant that showed reduced affinity for dimer formation. The results of this study establish the positive cooperative nature of metal binding by IdeR and suggest that dimerization contributes significantly to the cooperative binding. Equilibrium binding studies together with fluorescence titration and isothermal titration calorimetry experiments performed in metal binding mutants revealed equal importance of the primary and ancillary metal binding sites for cooperativity of metal binding, in contrast to the differential role of each site in repressor activity in vitro. The strong coupling between metal binding and dimerization establishes "all or nothing" mechanism for regulation of repressor activity under the conditions of constantly changing free metal concentration, providing greater control over the metal-dependent DNA binding activity of IdeR. Our findings place specific constraints on the activation mechanism, simplifying the existing model. / A Dissertation Submitted to the Institute of Molecular Biophysics in Partial Fulfillment of the Degree of Doctor of Philosophy. / Fall Semester, 2006. / July 13, 2006. / Dimerization, Ligand Binding, Cooperativity, Repressor / Includes bibliographical references. / Timothy M. Logan, Professor Directing Dissertation; Albert E. Stiegman, 1953-, Outside Committee Member; Michael Blaber, Committee Member; Piotr G. Fajer, Committee Member; Hong Li, Committee Member.

Molecules containing the phosphate (O—PO32-) moiety are ubiquitous in biochemistry. Phosphoryl transfer reactions that break and form the O—P phosphoryl bond are central to biological processes as diverse as energy metabolism and signal transduction. As described by Westheimer, the utility of phosphates stem from their ability to be kinetically stable while thermodynamically unstable. This dissertation uses electronic structure theory to investigate, at an elementary chemical level, the thermodynamic and kinetic properties of phosphate esters in an attempt to answer the question, "Why nature chose phosphates?". Chapter 1 formulates the question to be answered. Chapter 2 provides the underlying theoretical background to the computational methods employed. In Chapter 3, the anomeric effect, a stereoelectronic effect is first identified as a contributor to the high-energy status of N-phosphoryl-guanidines using electronic structure methods. In Chapter 4 it is further found that the anomeric effect can contribute to the thermodynamic poise of a range of phosphates. Chapter 5 investigates the connection between phosphoryl transfer mechanisms and the anomeric effect. It is found that the anomeric effect promotes O—P bond cleavage and plays a dominant role in the dissociative mechanism of phosphoryl transfer. The impact of other stereoelectronic effects such as hyperconjugation upon the hydrogen bonding properties of phosphates is also examined in Chapter 6. Compelling evidence is obtained suggesting the role of the O—P bond weakening anomeric effect in discriminating phosphoryl transfer potentials and controlling reaction rates in a range of biologically important phosphoryl compounds. Strong correlations between phosphoryl transfer potentials, rates of reaction in solution, O—P bond weakening, and the magnitude of the n(O)→σ*(O—P) anomeric effect is shown. This dissertation articulates a fundamental property of phosphates that may provide an answer to the age old question of "Why nature chose phosphates". / A Dissertation Submitted to the Program in Molecular Biophysics in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy. / Summer Semester, 2007. / June 11, 2007. / Phosphates, Anomeric Effect / Includes bibliographical references. / Michael S. Chapman, Professor Co-Directing Dissertation; W. Ross Ellington, Professor Co-Directing Dissertation; Robert L. Fulton, Outside Committee Member; Timothy A. Cross, Committee Member; Huan-Xiang Zhou, Committee Member.