Biological and Chemical Physics Commons^™

Carbon Nanomaterials In Biological Systems, Sijie Lin

All Theses

ABSTRACT


This thesis intends to present, from the biophysical viewpoint, my study on understanding carbon nanomaterials in biological and environmental systems. Carbon nanotubes and fullerenes represent a major family of carbon nanoparticles which possess distinct electrical, optical and mechanical properties. However, the major hurdle for making carbon nanomaterials bioavailable lies in their tendency toward bundling, driven by hydrophobic interaction, van der Waals force, and pi-stacking. To overcome this problem, we used non-covalent binding of zwitterionic lysophopholipids (LPL) onto the external surfaces of single-walled carbon nanotubes (SWNTs). This method affords superior SWNT solubility in aqueous solution. The stability of SWNT-LPL complex …

Inter-Dna Attraction Mediated By Divalent Counterions, Xiangyun Qiu, Kurt Andresen, Lisa W. Kwok, Jessica S. Lamb, Hye Yoon Park, Lois Pollack

Physics and Astronomy Faculty Publications

Can nonspecifically bound divalent counterions induce attraction between DNA strands? Here, we present experimental evidence demonstrating attraction between short DNA strands mediated by Mg2 ions. Solution small angle x-ray scattering data collected as a function of DNA concentration enable model independent extraction of the second virial coefficient. As the [Mg2] increases, this coefficient turns from positive to negative reflecting the transition from repulsive to attractive inter-DNA interaction. This surprising observation is corroborated by independent light scattering experiments. The dependence of the observed attraction on experimental parameters including DNA length provides valuable clues to its origin.

Poisson-Boltzmann Calculations Of Nonspecific Salt Effects On Protein-Protein Binding Free Energies, Claudia Bertonati, Barry Honig, Emil Alexov

Publications

The salt dependence of the binding free energy of five protein-protein hetero-dimers and two homo-dimers/tetramers was calculated from numerical solutions to the Poisson-Boltzmann equation. Overall, the agreement with experimental values is very good. In all cases except one involving the highly charged lactoglobulin homo-dimer, increasing the salt concentration is found both experimentally and theoretically to decrease the binding affinity. To clarify the source of salt effects, the salt-dependent free energy of binding is partitioned into screening terms and to self-energy terms that involve the interaction of the charge distribution of a monomer with its own ion atmosphere. In six of …

Focusing Capillary Optics For Use In Solution Small-Angle X-Ray Scattering, Jessica S. Lamb, Sterling Cornaby, Kurt Andresen, Lisa W. Kwok, Hye Yoon Park, Xiangyun Qiu, Detlef-M. Smilgies, Donald H. Bilderback, Lois Pollack

Physics and Astronomy Faculty Publications

Measurements of the global conformation of macromolecules can be carried out using small-angle X-ray scattering (SAXS). Glass focusing capillaries, manufactured at the Cornell High Energy Synchrotron Source (CHESS), have been successfully employed for SAXS measurements on the heme protein cytochrome c. These capillaries provide high X-ray flux into a spot size of tens of micrometres, permitting short exposures of small-volume samples. Such a capability is ideal for use in conjunction with microfluidic mixers, where time resolution may be determined by beam size and sample volumes are kept small to facilitate mixing and conserve material.

Fragmentation Of Methyl Chloride Studied By Partial Positive And Negative Ion Yield Spectroscopy, D. Ceolin, Maria Novella Piancastelli, Renaud Guillemin, Wayne C. Stolte, S-W Yu, Oliver Hemmers, Dennis W. Lindle

Environmental Studies Faculty Publications

The authors present partial-ion-yield experiments on the methyl chloride molecule excited in the vicinity of the Cl2p and C1s inner shells. A large number of fragments, cations produced by dissociation or recombination processes, as well as anionic species, have been detected. Although the spectra exhibit different intensity distributions depending on the core-excited atom, general observations include strong site-selective fragmentation along the C–Cl bond axis and a strong intensity dependence of transitions involving Rydberg series on fragment size.

Exploring Renner-Teller Induced Quenching In The Reaction H(2S)+Nh(A1Δ): A Combined Experimental And Theoretical Study, L. Adam, W. Hack, George C. Mcbane, H. Zhu, Z.-W. Qu, Reinhard Schinke

Peer Reviewed Articles

Experimental rate coefficients for the removal of NH(a¹Δ) and ND(a¹Δ) in collisions with H and D atoms are presented; all four isotope combinations are considered: NH+H, NH+D, ND+H, and ND+D. The experiments were performed in a quasistatic laser-flash photolysis/laser-induced fluorescence system at low pressures. NH(a¹Δ) and ND(a¹Δ) were generated by photolysis of HN₃ and DN₃, respectively. The total removal rate coefficients at room temperature are in the range of (3-5) x 10¹³ cm³ mol^-1 s^-1. For two isotope combinations, NH+H …

Design And Performance Of A Curved-Crystal X-Ray Emission Spectrometer, A. C. Hudson, Wayne C. Stolte, Dennis W. Lindle, Renaud Guillemin

Chemistry and Biochemistry Faculty Research

A curved-crystal x-ray emission spectrometer has been designed and built to measure 2–5 keV x-ray fluorescence resulting from a core-level excitation of gas phase species. The spectrometer can rotate 180°, allowing detection of emitted x rays with variable polarization angles, and is capable of collecting spectra over a wide energy range (20 eV wide with 0.5 eV resolution at the Cl K edge) simultaneously. In addition, the entire experimental chamber can be rotated about the incident-radiation axis by nearly 360° while maintaining vacuum, permitting measurements of angular distributions of emitted x rays.

Development Of A Novel Modular Mid-Infrared Sensor For The In-Situ Detection Of The Btex Compounds In Water, Raymond Mccue

Doctoral

This research thesis describes the design, construction and testing of a novel modular mid-infrared fibre optic sensing system for the detection of hydrocarbons in water. It is the adverse effects to these hydrocarbon pollutants on flora and fauna that has led to the development of sensing systems for their detection and quantification. The key sensor design feature, its modularity, utilises simple low cost commercially available optical components, which are inherently suited to construct compact rugged sensing systems to perform in-situ measurements which are ideally preferred for environmental sensing. The various laboratory-based prototypes constructed weee calibrated for two target analytes over …

Colour Doppler Spatial Resolution Performance Testing, Jacinta Browne, Ian Brown, Peter Hoskins, Amanda Watson, Alex Elliott

Articles

No abstract available

Structure Inhomogeneities, Shallow Defects, And Charge Transport In The Series Of Thermoelectric Materials K2bi8−Xsbxse13, Jeffrey S. Dyck, T. Kyratski, E. Hatzikraniotis, K. M. Paraskevopoulos, C. D. Malliakas, C. Uher, M. G. Kanatzidis

Physics

The charge transport properties of the low-dimensional thermoelectric materials K₂Bi_8-xSb_xSe₁₃ (02Bi_8-xSb_xSe₁₃ was analyzed on the basis of the classical semiconductor theory and discussed in the context of recent band calculations. The results suggest that the K₂Bi_8-xSb_xSe₁₃ materials possess coexisting domains with semimetallic and semiconducting characters whose ratio is influenced by the value of x and by local defects. The extent and relative distribution of these domains control the charge transport properties. Electron diffraction experiments performed on samples of K_{2 …}

Predicting Residue Contacts Using Pragmatic Correlated Mutations Method: Reducing The False Positives, Petras J. Kundrotas, Emil Alexov

Publications

Background

Predicting residues' contacts using primary amino acid sequence alone is an important task that can guide 3D structure modeling and can verify the quality of the predicted 3D structures. The correlated mutations (CM) method serves as the most promising approach and it has been used to predict amino acids pairs that are distant in the primary sequence but form contacts in the native 3D structure of homologous proteins.

Results

Here we report a new implementation of the CM method with an added set of selection rules (filters). The parameters of the algorithm were optimized against fifteen high resolution crystal …

Protcom: Searchable Database Of Protein Complexes Enhanced With Domain-Domain Structures, Petras Kundrotas, Emil Alexov

Publications

The database of protein complexes (PROTCOM) is a compilation of known 3D structures of protein–protein complexes enriched with artificially created domain–domain structures using the available entries in the Protein Data Bank. The domain–domain structures are generated by parsing single chain structures into loosely connected domains and are important features of the database. The database (http://www.ces.clemson.edu/compbio/protcom) could be used for benchmarking purposes of the docking and other algorithms for predicting 3D structures of protein–protein complexes. The database can be utilized as a template database in the homology or threading methods for modeling the 3D structures of unknown protein–protein complexes. …

Electrostatic Properties Of Protein-Protein Complexes, Petras J. Kundrotas, Emil Alexov

Publications

Statistical electrostatic analysis of 37 protein-protein complexes extracted from the previously developed database of protein complexes (ProtCom, http://www.ces.clemson.edu/compbio/protcom) is presented. It is shown that small interfaces have a higher content of charged and polar groups compared to large interfaces. In a vast majority of the cases the average pK_a shifts for acidic residues induced by the complex formation are negative, indicating that complex formation stabilizes their ionizable states, whereas the histidines are predicted to destabilize the complex. The individual pK_a shifts show the same tendency since 80% of the interfacial acidic groups were found to lower their …

Measuring Inter-Dna Potentials In Solution, Xiangyun Qiu, Lisa W. Kwok, Hye Yoon Park, Jessica S. Lamb, Kurt Andresen, Lois Pollack

Physics and Astronomy Faculty Publications

Interactions between short strands of DNA can be tuned from repulsive to attractive by varying solution conditions and have been quantified using small angle x-ray scattering techniques. The effective DNA interaction charge was extracted by fitting the scattering profiles with the generalized one-component method and inter-DNA Yukawa pair potentials. A significant charge is measured at low to moderate monovalent counterion concentrations, resulting in strong inter-DNA repulsion. The charge and repulsion diminish rapidly upon the addition of divalent counterions. An intriguing short range attraction is observed at surprisingly low divalent cation concentrations, ~16 mM Mg2+. Quantitative measurements of inter- DNA potentials …

Development Of A High Spatial Selectivity Tri-Polar Concentric Ring Electrode For Laplacian Electroencephalography (Leeg) System, Kanthaiah Koka

Doctoral Dissertations

Brain activity generates electrical potentials that are spatio-temporal in nature. Electroencephalography (EEG) is the least costly and most widely used non-invasive technique for diagnosing many brain problems. It has high temporal resolution but lacks high spatial resolution.

The surface Laplacian will enhance the spatial resolution of EEG as it performs the second spatial derivative of the surface potentials. In an attempt to increase the spatial selectivity, researchers introduced a bipolar electrode configuration using a five point finite difference method (FPM) and others applied a quasi-bipolar (tri-polar with two elements shorted) concentric electrode configuration. To further increase the spatial resolution, the …

Erratum: The Structure Of Alkali Halide Dimers: A Critical Test Of Ionic Models And New Ab Initio Results, T. Törring, S. Biermann, J. Hoeft, Richard J. Mawhorter, Robert J. Cave, C. Szemenyei

All HMC Faculty Publications and Research

It has come to our attention that some of the ab initio results presented are incorrect due to errors in the Cs and C1 basis sets, and a small error in the binding energy of Rb2F2. The corrected results are presented below for the species that were affected, modifying the results in Table III of the original paper. Only those values which are different from the results of the original Table III are included. Note that some of these results are used for comparison with the ionic models in later tables. In addition, some HF data quoted in Tables V …

Femtosecond Nuclear Motion Of Hcl Probed By Resonant X-Ray Raman Scattering In The Cl 1s Region, Marc Simon, Loic Journel, Stephane Carniato, Richard Taieb, I. Minkov, Faris Gel'mukhanov, P. Salek, H. Agren, Renaud Guillemin, Wayne C. Stolte, A. C. Hudson, Dennis W. Lindle

Chemistry and Biochemistry Faculty Research

Femtosecond dynamics are observed by resonant x-ray Raman scattering (RXS) after excitation along the dissociative Cl 1s→6ơ* resonance of gas-phase HCl. The short core-hole lifetime results in a complete breakdown of the common nondispersive behavior of soft-x-ray transitions between parallel potentials. We evidence a general phenomenon of RXS in the hard-x-ray region: a complete quenching of vibrational broadening. This opens up a unique opportunity for superhigh resolution x-ray spectroscopy beyond vibrational and lifetime limitations.

A Hierarchical Family Of Three-Dimensional Potential Energy Surfaces For He-Co, Kirk A. Peterson, George C. Mcbane

Peer Reviewed Articles

A hierarchical family of five three-dimensional potential energy surfaces has been developed for the benchmark He-CO system. Four surfaces were obtained at the coupled cluster singles and doubles level of theory with a perturbational estimate of triple excitations, CCSD(T), and range in quality from the doubly augmented double-zeta basis set to the complete basis set (CBS) limit. The fifth corresponds to an approximate CCSDT/CBS surface (CCSD with iterative triples/CBS, denoted CBS+corr). The CBS limit results were obtained by pointwise basis set extrapolations of the individual counterpoise-corrected interaction energies. For each surface, over 1000 interaction energies were accurately interpolated using a …

Radiative Neutron Β-Decay In Effective Field Theory, Susan Gardner, Véronique Bernard, Ulf-G. Meißner, Chi Zhang

Center for Plant Science Innovation: Faculty Publications

In summary, we have computed the photon energy spectrum and photon polarization in neutron radiative β-decay in an effective field theory approach, utilizing HBCHPT and the SSE, including all terms in O(1/M). The leading contribution to the photon energy spectrum has been calculated previously [4]; we agree with the expression in Ref. [4] for Σ_spins |M|², though we disagree with their numerical results for the photon energy spectrum. Moreover, we find that the O(1/M) terms are numerically quite small, generating contributions no larger than O(0.5 %), so that radiative neutron β-decay is quite insensitive to nucleon structure …

Photo-Induced Current Measurements In Chlamydomonas Cell Suspensions, Collin D. Capano

Renée Crown University Honors Thesis Projects - All

In order to fully understand the principles behind phototaxis in flagellate algae, it is necessary to measure the electric currents these cells create when processing light stimuli. Many different techniques have been developed to do this. One of these techniques, measuring from cell suspensions, has a number of advantages over the others that makes it highly desirable. However, the lab that first developed this method of recording did not describe the setup very well. The result is that in the thirteen years since it was first reported, only one other independent lab has been able to reproduce the results despite …

Detection Of Bacillus Spores By Aptamer Selectivity Using Atomic Force Microscopy, Nina M. Houtkooper

Theses and Dissertations

The anthrax attack of Oct 2001 demonstrates the need for a rapid detector for spores of Bacillus anthracis (BA). Current technology requires cultures of BA to be grown for 24 hours. Using aptamers, a type of nucleic acid ligand selective for a target molecule, to select BA spores for measurement without culturing is a possible solution for quicker detection. An aptamer having a specially selected structure is expected to selectively bind to the surface of its target spore, separating it from other material. An atomic force microscopy (AFM) method was developed to test this selectivity. Aptamers having structure selected to …

Lethality Of Bacillus Anthracis Spores Due To Short Duration Heating Measured Using Infrared Spectroscopy, Kristina M. Goetz

Theses and Dissertations

There are a number of analytical and semi-empirical models that describe the behavior of particulate matter in the atmosphere. Many of these require modification for all types of weather, dry versus wet deposition, and overall effects can be quite non-linear. Rainfall (rate, drop size, etc.), snowfall (rate, flake size, etc.), humidity, pressure, temperature, and combination of these greatly affect particle settling and washout rates. To that end, a method for tracking released constituents using the Regional Atmospheric Modeling System (RAMS) microphysics package is developed by modifying one of the hydrometeor categories (hail) in the microphysics package. The RAMS microphysics package …

Molecular Dynamics Simulations Of Amphiphilic Molecules, Roger L. Mcmullen Jr.

Seton Hall University Dissertations and Theses (ETDs)

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Near-Edge X-Ray Absorption Fine Structure Study Of Ion-Beam-Induced Phase Transformation In Gd2(Ti1-Yzry)2o7, Ponnusamy Nachimuthu, S. Thevuthasan, V. Shutthanandan, E. M. Adams, W. J. Weber, B. D. Begg, D. K. Shuh, Dennis W. Lindle, Eric M. Gullikson, Rupert C. Perera

Chemistry and Biochemistry Faculty Research

The structural and electronic properties of Gd₂(Ti_1−yZr_y)₂O₇ (y=0–1) pyrochlores following a 2.0-MeV Au²⁺ ion-beam irradiation (~5.0 X 10¹⁴ Au²⁺/cm²) have been investigated by Ti 2p and O 1s near-edge x-ray absorption fine structure (NEXAFS). The irradiation of Gd₂(Ti_1−yZr_y)₂O₇ leads to the phase transformation from the ordered pyrochlore structure (Fd3m) to the defect fluorite structure (Fm3m) regardless of Zr concentration. Irradiated Gd₂(Ti_{1−y …}

Fragmentation Dynamics Of H2s Following S 2p Photoexcitation, Renaud Guillemin, S-W Yu, Wayne C. Stolte, Dennis W. Lindle

Chemistry and Biochemistry Faculty Research

The fragmentation dynamics of core-excited H₂S has been studied by means of partial anion and cation yield measurements around the S L_2,3-subshell ionization thresholds. All detectable ionic fragments are reported, and significant differences between partial ion yields are observed. Possible dissociation pathways are discussed by comparison to previous studies of electron spectra.

Anion And Cation-Yield Spectroscopy Of Core-Excited Sf6, Maria Novella Piancastelli, Wayne C. Stolte, Renaud Guillemin, A. Wolska, M. M. Sant'anna, Dennis W. Lindle

Chemistry and Biochemistry Faculty Research

We report an extensive study on total and partial-ion-yield spectroscopy around both the S 2p and F 1s thresholds in SF₆. All positive and negative single-ion channels have been measured. Below the F 1s threshold we detect a large variation in relative intensity of the resonant structures according to the specific channel monitored, indicating selective fragmentation. Above threshold, at variance with previous cases described by us, we detect high-intensity structures related to shape resonances not only in the cation channels but also for the anions. We discuss the applicability and limits of a model we …

Spatial Distribution Of Competing Ions Around Dna In Solution, Kurt Andresen, R. Das, Hye Yoon Park, H. Smith, Lisa W. Kwok, Jessica S. Lamb, E. J. Kirkland, D. Herschlag, K. D. Finkelstein, Lois Pollack

Physics and Astronomy Faculty Publications

The competition of monovalent and divalent cations for proximity to negatively charged DNA is of biological importance and can provide strong constraints for theoretical treatments of polyelectrolytes. Resonant x-ray scattering experiments have allowed us to monitor the number and distribution of each cation in a mixed ion cloud around DNA. These measurements provide experimental evidence to support a general theoretical prediction: the normalized distribution of each ion around polyelectrolytes remains constant when ions are mixed at different ratios. In addition, the amplitudes of the scattering signals throughout the competition provide a measurement of the surface concentration parameter that predicts the …

Probing Cation Antisite Disorder In Gd2ti2o7 Pyrochlore By Site-Specific Nexafs And Xps, Ponnusamy Nachimuthu, S. Thevuthasan, Mark H. Engelhard, W. J. Weber, D. K. Shuh, N. M. Hamdan, B. S. Mun, E. M. Adams, D. E. Mccready, V. Shutthanandan, Dennis W. Lindle, G. Balakrishnan, R. C. Ewing

Chemistry and Biochemistry Faculty Research

Disorder in Gd₂Ti₂O₇ is investigated by near-edge x-ray-absorption fine structure (NEXAFS) and x-ray photoelectron spectroscopy (XPS). NEXAFS shows Ti⁴⁺ ions occupy octahedral sites with a tetragonal distortion induced by vacant oxygen sites. O 1s XPS spectra obtained with a charge neutralization system from Gd₂Ti₂O₇(100) and the Gd₂Ti₂O₇ pyrochlore used by Chen et al. [Phys. Rev. Lett. 88, 105901 (2002)], both yielded a single peak, unlike the previous result on the latter that found two peaks. The current results give no evidence for …

Spectroscopic And Microscopic Investigation Of The Corrosion Of 316/316l Stainless Steel By Lead-Bismuth Eutectic (Lbe) At Elevated Temperatures: Importance Of Surface Preparation, Allen L. Johnson, Denise Parsons, Julia Manzerova, Dale L. Perry, Daniel Koury, Brian D. Hosterman, John Farley

Transmutation Sciences Materials (TRP)

The corrosion of steel by lead–bismuth eutectic (LBE) is an important issue in proposed nuclear transmutation schemes. Russian scientists at the IPPE exposed steel samples to oxygen-controlled LBE at temperatures up to 823 K and exposure times up to 3000 h. We have characterized these post-exposure steel samples and unexposed controls, using scanning electron microscopy (SEM), energy-dispersive X-ray analysis (EDAX) and X-ray photoelectron spectroscopy (XPS). Previous researchers have investigated the corrosion by LBE of steel of varying composition. In the present work, we compared two samples having the same composition (standard nuclear grade 316/316L) but different surface preparation: a cold-rolled …

Growth And Transport Properties Of Complementary Germanium Nanowire Field Effect Transistors, Andrew B. Greytak, Lincoln J. Lauhon, Mark S. Gudiksen, Charles M. Lieber

Faculty Publications

n- and p-type Ge nanowires were synthesized by a multistep process in which axial elongation, via vapor–liquid–solid (VLS) growth, and doping were accomplished in separate chemical vapor deposition steps. Intrinsic, single-crystal, Ge nanowires prepared by Au nanocluster-mediated VLS growth were surface-doped in situ using diborane or phosphine, and then radial growth of an epitaxial Ge shell was used to cap the dopant layer. Field-effect transistors prepared from these Ge nanowires exhibited on currents and transconductances up to 850 µA/µm and 4.9 µA/V, respectively, with device yields of >85%.