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2007

Biological and Chemical Physics

Articles 1 - 16 of 16

Full-Text Articles in Physics

Optimization Of Electrostatic Interactions In Protein-Protein Complexes, Kelly Brock, Kemper Talley, Kacey Coley, Petras Kundrotas, Emil Alexov Nov 2007

Optimization Of Electrostatic Interactions In Protein-Protein Complexes, Kelly Brock, Kemper Talley, Kacey Coley, Petras Kundrotas, Emil Alexov

Publications

In this article, we present a statistical analysis of the electrostatic properties of 298 protein-protein complexes and 356 domain-domain structures extracted from the previously developed database of protein complexes (ProtCom, http://www.ces.clemson.edu/compbio/protcom). For each structure in the dataset we calculated the total electrostatic energy of the binding and its two components, Coulombic and reaction field energy. It was found that in a vast majority of the cases (>90%), the total electrostatic component of the binding energy was unfavorable. At the same time, the Coulombic component of the binding energy was found to favor the complex ...


Btec Thermal Model, Lance J. Irving, Jack Maseberg, Gavin D. Buffington, Clifton D. Clark, Robert J. Thomas, Michael L. Edwards, Jacob Stolarski Oct 2007

Btec Thermal Model, Lance J. Irving, Jack Maseberg, Gavin D. Buffington, Clifton D. Clark, Robert J. Thomas, Michael L. Edwards, Jacob Stolarski

Physics Faculty Publications

AFRL/RHDO has developed a configurable, laser-tissue interaction model that includes components from various areas of Biophysics. The model predicts heat transfer in biological tissue, in either one-dimension or two-dimensional cylindrical coordinates, and is coupled to an Arrhenius damage model. A simulation can be configured as a single run, or a damage-threshold search. Multiple models for describing the laser-tissue interaction are available, including linear absorption (1D, 2D), Monte Carlo scattering (2D) and Beam Propagation Methods using Finite Difference approximations or Hankel Transform methods (2D).


A Novel Empirical Free Energy Function That Explains And Predicts Protein–Protein Binding Affinities, Joseph Audie, Suzanne Scarlata Sep 2007

A Novel Empirical Free Energy Function That Explains And Predicts Protein–Protein Binding Affinities, Joseph Audie, Suzanne Scarlata

Chemistry & Physics Faculty Publications

A free energy function can be defined as a mathematical expression that relates macroscopic free energy changes to microscopic or molecular properties. Free energy functions can be used to explain and predict the affinity of a ligand for a protein and to score and discriminate between native and non-native binding modes. However, there is a natural tension between developing a function fast enough to solve the scoring problem but rigorous enough to explain and predict binding affinities. Here, we present a novel, physics-based free energy function that is computationally inexpensive, yet explanatory and predictive. The function results from a derivation ...


Carbon Nanomaterials In Biological Systems, Sijie Lin Aug 2007

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 ...


Kinetic Monte Carlo Simulation Of Epitaxial Thin Film Growth: Formation Of Submonolayer Islands And Multilayer Mounds, James W. Evans, Patricia A. Thiel, Maozhi Li Aug 2007

Kinetic Monte Carlo Simulation Of Epitaxial Thin Film Growth: Formation Of Submonolayer Islands And Multilayer Mounds, James W. Evans, Patricia A. Thiel, Maozhi Li

Chemistry Conference Papers, Posters and Presentations

No abstract provided.


Inter-Dna Attraction Mediated By Divalent Counterions, Xiangyun Qiu, Kurt Andresen, Lisa W. Kwok, Jessica S. Lamb, Hye Yoon Park, Lois Pollack Jul 2007

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.


Generic Two-Phase Coexistence, Relaxation Kinetics, And Interface Propagation In The Quadratic Contact Process: Simulation Studies, Xiaofang Guo, Da-Jiang Liu, James W. Evans Jun 2007

Generic Two-Phase Coexistence, Relaxation Kinetics, And Interface Propagation In The Quadratic Contact Process: Simulation Studies, Xiaofang Guo, Da-Jiang Liu, James W. Evans

Physics and Astronomy Publications

The quadratic contact process is formulated as an adsorption-desorption model on a two-dimensional square lattice. It involves random adsorption at empty sites and correlated desorption requiring diagonally adjacent pairs of empty neighbors. We assess the model behavior utilizing kinetic Monte Carlo simulations. One finds generic two-phase coexistence between a low-coverage active steady state and a completely covered or "poisoned" absorbing steady state; i.e., both states are stable over a finite range of adsorption rates or "pressures." This behavior is in marked contrast to that for equilibrium phase separation. For spatially homogeneous systems, we provide a comprehensive characterization of the ...


Poisson-Boltzmann Calculations Of Nonspecific Salt Effects On Protein-Protein Binding Free Energies, Claudia Bertonati, Barry Honig, Emil Alexov Mar 2007

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 ...


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 Feb 2007

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.


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 Feb 2007

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.


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 Jan 2007

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 ...


Self-Assembling Dna Dendrimers: A Numerical Study, L. Largo, Francis Starr, F. Sciortino Jan 2007

Self-Assembling Dna Dendrimers: A Numerical Study, L. Largo, Francis Starr, F. Sciortino

Francis Starr

No abstract provided.


Preliminary Structural Studies Of The Transcriptional Regulator Cmer From Campylobacter Jejuni, Chih-Chia Su, Feng Shi, Ruoyu Gu, Ming Li, Gerry Mcdermott, Edward Yu, Qijing Zhang Jan 2007

Preliminary Structural Studies Of The Transcriptional Regulator Cmer From Campylobacter Jejuni, Chih-Chia Su, Feng Shi, Ruoyu Gu, Ming Li, Gerry Mcdermott, Edward Yu, Qijing Zhang

Physics and Astronomy Publications

In Campylobacter jejuni, a Gram-negative bacterial pathogen causing gastroenteritis in humans, the CmeR regulatory protein controls transcription of the multidrug transporter gene operon cmeABC. CmeR belongs to the TetR family of transcriptional regulators. The 210-residue CmeR consists of two functional motifs: an N-terminal DNA-binding domain and a C-terminal ligand-binding domain. It is predicted that the DNA-binding domain interacts directly with target promoters, while the C-terminal motif interacts with inducing ligands (such as bile salts). As an initial step towards confirming this structural model, recombinant CmeR protein containing a 6×His tag at the N-terminus was crystallized. Crystals of ligand-free CmeR ...


Development Of A Novel Modular Mid-Infrared Sensor For The In-Situ Detection Of The Btex Compounds In Water, Raymond Mccue Jan 2007

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 ...


Design And Performance Of A Curved-Crystal X-Ray Emission Spectrometer, A. C. Hudson, Wayne C. Stolte, Dennis W. Lindle, Renaud Guillemin Jan 2007

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 Publications

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.


Colour Doppler Spatial Resolution Performance Testing, Jacinta Browne, Ian Brown, Peter Hoskins, Amanda Watson, Alex Elliott Jan 2007

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

Articles

No abstract available