Open Access. Powered by Scholars. Published by Universities.®
Biological and Chemical Physics Commons™
Open Access. Powered by Scholars. Published by Universities.®
- Institution
- Publication
- Publication Type
Articles 1 - 5 of 5
Full-Text Articles in Biological and Chemical Physics
Toward Improving Understanding Of The Structure And Biophysics Of Glycosaminoglycans, Elizabeth K. Whitmore
Toward Improving Understanding Of The Structure And Biophysics Of Glycosaminoglycans, Elizabeth K. Whitmore
Electronic Theses and Dissertations
Glycosaminoglycans (GAGs) are the linear carbohydrate components of proteoglycans (PGs) that mediate PG bioactivities, including signal transduction, tissue morphogenesis, and matrix assembly. To understand GAG function, it is important to understand GAG structure and biophysics at atomic resolution. This is a challenge for existing experimental and computational methods because GAGs are heterogeneous, conformationally complex, and polydisperse, containing up to 200 monosaccharides. Molecular dynamics (MD) simulations come close to overcoming this challenge but are only feasible for short GAG polymers. To address this problem, we developed an algorithm that applies conformations from unbiased all-atom explicit-solvent MD simulations of short GAG polymers …
Transport Of Water And Ions Through Single-Walled Armchair Carbon Nanotubes: A Molecular Dynamics Study, Michelle Patricia Aranha
Transport Of Water And Ions Through Single-Walled Armchair Carbon Nanotubes: A Molecular Dynamics Study, Michelle Patricia Aranha
Doctoral Dissertations
The narrow hydrophobic interior of a carbon nanotube (CNT) poses a barrier to the transport of water and ions, and yet, unexpectedly, numerous experimental and simulation studies have confirmed fast water transport rates comparable to those seen in biological aquaporin channels. These outstanding features of high water permeability and high solute rejection of even dissolved ions that would typically require a lot of energy for separation in commercial processes makes carbon nanotubes an exciting candidate for desalination membranes. Extending ion exclusion beyond simple mechanical sieving by the inclusion of electrostatics via added functionality to the nanotube bears promise to not …
Experimental And Theoretical Investigation Of Molecular Field Effects By Polarization-Resolved Resonant Inelastic X-Ray Scattering, Stephane Carniato, Renaud Guillemin, Wayne C. Stolte, Loic Journel, Richard Taieb, Dennis W. Lindle, Marc Simon
Experimental And Theoretical Investigation Of Molecular Field Effects By Polarization-Resolved Resonant Inelastic X-Ray Scattering, Stephane Carniato, Renaud Guillemin, Wayne C. Stolte, Loic Journel, Richard Taieb, Dennis W. Lindle, Marc Simon
Chemistry and Biochemistry Faculty Research
We present a combined theoretical and experimental study of molecular field effects on molecular core levels. Polarization-dependent resonant inelastic x-ray scattering is observed experimentally after resonant K-shell excitation of CF3Cl and HCl. We explain the linear dichroism observed in spin-orbit level intensities as due to molecular field effects, including singlet-triplet exchange, and interpret this behavior in terms of population differences in the 2px,y,z inner-shell orbitals. We investigate theoretically the different factors that can affect the electronic populations and the dynamical R dependence of the spin-orbit ratio. Finally, the results obtained are used to interpret the L-shell …
The Spectroscopy And Molecular Dynamics Of The High Frequency Ν1 6 Intermolecular Vibrations In Hcn‐‐‐Hf And Dcn‐‐‐Df, B. A. Wofford, M. W. Jackson, Shannon Lieb, J. W. Bevan
The Spectroscopy And Molecular Dynamics Of The High Frequency Ν1 6 Intermolecular Vibrations In Hcn‐‐‐Hf And Dcn‐‐‐Df, B. A. Wofford, M. W. Jackson, Shannon Lieb, J. W. Bevan
Scholarship and Professional Work - LAS
Gas phase rovibrational analysis of the high frequency intermolecular hydrogen bonded bending overtone 2ν0 6 [ν0=1132.4783(2) cm− 1] in HCN‐‐‐HF and its corresponding perdeuterated fundamental ν1 6 [ν0=409.1660(2) cm− 1] are reported. Evaluated rovibrational parameters provide the basis for quantitative modeling of the molecular dynamics associated with this vibration. A quantum mechanical calculation permits determination of the quadratic and quartic force constants K 6 6=537(17) and K 6 6 6 6=4.98(12) cm− 1 which in turn are used to estimate the pertinent cubic band stretching interaction constants …
Molecular Dynamics In Hydrogen‐Bonded Interactions: A Preliminary Experimentally Determined Harmonic Stretching Force Field For Hcn‐‐‐Hf, B. A. Wofford, Shannon Lieb, J. W. Bevan
Molecular Dynamics In Hydrogen‐Bonded Interactions: A Preliminary Experimentally Determined Harmonic Stretching Force Field For Hcn‐‐‐Hf, B. A. Wofford, Shannon Lieb, J. W. Bevan
Scholarship and Professional Work - LAS
Observation of the 2ν1 overtone band in the hydrogen‐bonded complex HCN‐‐‐HF permits evaluation of the anharmonicity constant X 1 1=−116.9(1) cm− 1 and determination of the anharmonicity corrected fundamental frequency ω1. This information, and available data from previous rovibrational analyses in the common and perdeuterated isotopic species of HCN‐‐‐HF, offer an opportunity for calculation of an approximate stretching harmonic force field. With the assumptions f 1 2=f 2 4=0.0, the remaining force constants (in mdyn/Å) are evaluated as: f 1 1=8.600(20), f 2 2=6.228(9), f 3 3=19.115(40), f 4 …