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Articles 1 - 11 of 11
Full-Text Articles in Physics
Optimization Of Electrostatic Interactions In Protein-Protein Complexes, Kelly Brock, Kemper Talley, Kacey Coley, Petras Kundrotas, Emil Alexov
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 formation while …
Btec Thermal Model, Lance J. Irving, Jack Maseberg, Gavin D. Buffington, Clifton D. Clark, Robert J. Thomas, Michael L. Edwards, Jacob Stolarski
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
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 …
Inter-Dna Attraction Mediated By Divalent Counterions, Xiangyun Qiu, Kurt Andresen, Lisa W. Kwok, Jessica S. Lamb, Hye Yoon Park, Lois Pollack
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
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 …
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
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
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
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 …
Development Of A Novel Modular Mid-Infrared Sensor For The In-Situ Detection Of The Btex Compounds In Water, Raymond Mccue
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
Colour Doppler Spatial Resolution Performance Testing, Jacinta Browne, Ian Brown, Peter Hoskins, Amanda Watson, Alex Elliott
Articles
No abstract available
Design And Performance Of A Curved-Crystal X-Ray Emission Spectrometer, A. C. Hudson, Wayne C. Stolte, Dennis W. Lindle, Renaud Guillemin
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.