Bulletin of the American Physical Society
2009 Joint Spring Meeting of the Ohio Sections of the APS and AAPT
Volume 54, Number 3
Friday–Saturday, April 24–25, 2009; Ada, Ohio
Session C5: Applied Physics and Biophysics |
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Chair: David Weeks, Air Force Institute of Technology Room: McIntosh Center Activities Room |
Saturday, April 25, 2009 8:16AM - 8:28AM |
C5.00001: A Wigner Distribution Analysis of Scattering Dynamics David Weeks, Brent Lacy Using the time dependent Channel Packet Method (CPM),\footnote{D.E.Weeks, T.A.Niday, S.H.Yang, J Chem Phys. \textbf{125}, 164301 (2006).} a Fourier transformation of the correlation function between evolving wave packets is used to compute scattering matrix elements. The correlation function can also be used to compute a Wigner distribution as a function of time and energy. This scattering Wigner distribution is then used to investigate times at which various energetic contributions to the scattering matrix are made during a molecular collision. We compute scattering Wigner distributions for a variety of molecular systems and use them to characterize the associated molecular dynamics. In particular, the square well provides a simple and easily modified potential to study the relationship between the scattering Wigner distribution and wave packet dynamics. Additional systems that are being studied include the collinear H + H$_{2}$ molecular reaction, and the non-adiabatic B + H$_{2}$ molecular collision. [Preview Abstract] |
Saturday, April 25, 2009 8:28AM - 8:40AM |
C5.00002: A Heat Conduction Problem in Laser Ablation William Fuller, Maria Raiti, Ronald Bush Laser ablation of the saphenous vein involves using laser-tipped probes to produce photothermal effects in the vein. We consider the effects of laser-induced thermal heating and conduction on the vein wall. We formulate and solve the relevant two-dimensional heat conduction problem. The solution resolves an aspect of a controversy involving the mechanism of the medical procedure. [Preview Abstract] |
Saturday, April 25, 2009 8:40AM - 8:52AM |
C5.00003: Modeling the output of a TEA CO$_{2}$ laser Daniel Crowder, Thomas Wilson We compare the results of numerical solutions to a set of coupled rate (first-order linear differential) equations in a simplified theoretical model$^{1}$, to experimental measurements of the output of a transversely-excited atmospheric-pressure (TEA) carbon dioxide laser. The model is used to study the influence of the molecular gas ratio (partial pressures of CO$_{2}$, H$_{2}$, and N$_{2})$ and mirror reflectivities on the peak power and energy of the gain-switched pulse. The laser is a vintage \textit{Gentec DD-250}$^{2}$ TEA CO$_{2}$ laser. We use a fast (0.2-ps risetime) room-temperature photoelectromagnetic mode (PEM) HgCdTe detector and a 1-GHz bandwidth digital oscilloscope to sample the gain-switched pulse. We review the model's assumptions of a four-level laser and the various processes involved in the production of the laser output. Good qualitative agreement is observed between theory and experiment, considering the simple assumptions of the model. In both cases, the gain-switched spike, containing several megawatts in $\sim $200-ns duration, is followed by a slower relaxation tail. The length of the lower-power tail scales with increasing N$_{2}$ partial pressure. The model takes no account of the competition between the various longitudinal and transverse modes of the cavity. $^{1}$K.J. Andrews, P.E. Dyer and D.J. James, J. Phys. E: Scientific Instruments \textbf{8}, 493-497 (1975). $^{2}$Gentec Electro-Optics Inc., 445 St. Jean-Baptiste, Suite 160, Quebec, QC, Canada G2E 5N7 [Preview Abstract] |
Saturday, April 25, 2009 8:52AM - 9:04AM |
C5.00004: The Derivation of the Equation of the Damped Harmonic Oscillator from Lagrangian Methods with a Kaluza-Klein-like Hidden Dimension John Brandenburg Lagrangian methods cannot include non-conservative forces and therefore cannot produce a simple derivation of the ubiquitous and very useful damped harmonic oscillator equation. Recently, it has been found that the damping term can be included in a Lagrangian approach by employing a Kaluza-Klein hidden dimension (Klein 1926). In this application of the method, the hidden variable occurs as a ``subscale model'' where the normal Lagrangian for a harmonic oscillator is written .5(mq'$^{2}$ -kq$^{2}$ + 2sq'q* +m*q$_{o}$'$^{2}$ ) where q* is an integral over a short cyclic collision time of subscale molecular model coordinate derivative q$_{o}$' where a molecular coordinate shares velocity with a mass m as it collides and ``sticks'' to it, so that q$_{o}$'=q' during the interval of integration, and finally m* is a very small ``molecular'' mass. This results in the total derivative acquiring the term sq' and the resulting equations mq'' +sq' +kq =0 and m*q$_{o}$'=Constant being recovered. This exercise gives insight to the use of Kaluza-Klein hidden dimension in Gravitational physics and also suggests such hidden dimensions can add a ``thermal bath'' to otherwise conservative problems. Klein O. (1926) ``Quantum Theory and Five-Dimensional Relativity Zeitschrift fur Physik'' \textbf{37}, 895. [Preview Abstract] |
Saturday, April 25, 2009 9:04AM - 9:16AM |
C5.00005: Electron transport through asymmetric DNA molecules Sunhee Lee, Eric Hedin, Yong Joe Stimulated by intriguing experiments of electrical charge transport through single DNA molecules which are trapped between two metal electrodes [1, 2], we investigate quantum mechanical electron transport along the long axis of the DNA molecule with five poly (dG) and poly (dC) base pairs. Using a quasi-one-dimensional tight-binding model, we calculate the electron transmission of one conduction channel of a modified DNA model for the variation of backbone onsite energy, the energy-dependent hopping strength, and the contact coupling between the leads and the DNA molecule. In this symmetry-breaking system, we find that two transmission mini-bands with a gap merge together and eventually disappear, and an extra resonance peak arises in the contour plots of the transmission. Finally, the current-voltage characteristics in a short asymmetric DNA molecule will also be presented. \\[3pt] [1] D. Porath \textit{et al}., Nature \textbf{403}, 635 (2000). \\[0pt] [2] H. Cohen \textit{et al}., Proc. Natl. Acad. Sci. \textbf{102}, 16979 (2005). [Preview Abstract] |
Saturday, April 25, 2009 9:16AM - 9:28AM |
C5.00006: All-or-none protein-like folding of a homopolymer chain Mark Taylor, Wolfgang Paul, Kurt Binder Many small proteins fold via a first-order ``all-or-none'' transition directly from an expanded coil to a compact native state. Here we report an analogous direct freezing transition from an expanded coil to a compact crystallite for a simple flexible homopolymer. Wang-Landau sampling is used to construct the complete density of states for square-well chains up to length 256. Analysis within both the microcanonical and canonical ensembles shows that, for a chain with sufficiently short-range interactions, the usual polymer collapse transition is preempted by a direct freezing transition. Despite the non-unique homopolymer ground state, the thermodynamics of this direct freezing transition are identical to the thermodynamics of two-state protein folding. A free energy barrier separates a high entropy ensemble of unfolded states from a low entropy set of crystallite states and the transition proceeds via the formation of a transition-state folding nucleus. An Arrhenius analysis of the folding/unfolding free energy barrier yields a Chevron plot characteristic of proteins and the model chain satisfies the van't Hoff calorimetric criterion for two-state folding. [Preview Abstract] |
Saturday, April 25, 2009 9:28AM - 9:40AM |
C5.00007: Transitions of a tethered chain under tension Jutta Luettmer-Strathmann, Wolfgang Paul, Kurt Binder An applied tension changes the equilibrium conformations of a tethered polymer chain and thus affects both the adsorption transition and the coil globule transition. Conversely, solvent quality and surface attraction are reflected in equilibrium force-extension curves that can be measured in experiments. In this work, we performed Monte Carlo simulations of the bond-fluctuation model with a Wang-Landau algorithm to determine the density of states in the state space of monomer-monomer contacts, monomer-surface contacts, and chain extension. We study the effect of tension on the collapse and adsorption transitions and calculate force- extension curves that may be compared with experimental data. [Preview Abstract] |
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