Bulletin of the American Physical Society
12th Annual Meeting of the Northwest Section of the APS
Volume 55, Number 6
Friday–Saturday, October 1–2, 2010; Walla Walla, Washington
Session C2: Biophysics, Fluids, and Fields |
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Chair: Bethe Scaletter, Lewis and Clark College Room: Science 376 (before break) and Science 151 (after break) |
Friday, October 1, 2010 1:30PM - 2:06PM |
C2.00001: Using optical forces to probe mechanical response from single molecules to biomaterials Invited Speaker: In the past decade, the ability to manipulate and measure forces exerted by single biological molecules has transformed our understanding of their mechanical response, stability, and the mechanisms by which they operate. One of the essential tools in this revolution has been optical tweezers, which use a focused laser beam to ``trap'' (hold stably in three dimensions) micrometer-sized refractive particles. In this talk, I will briefly describe how optical tweezers work and how they can be used to manipulate and probe the mechanical response of single DNA and protein molecules. I will then describe the technique of holographic optical tweezers, which modify the phase of a laser beam in order to generate multiple optical traps at specified locations in three dimensions within a sample. I will discuss our work towards applying this technique to mechanical studies of protein-based biomaterials on the microscale. [Preview Abstract] |
Friday, October 1, 2010 2:06PM - 2:42PM |
C2.00002: Dynamics of protein conformations Invited Speaker: A novel theoretical methodology is introduced to identify dynamic structural domains and analyze local flexibility in proteins. The methodology employs a multiscale approach combining identification of essential collective coordinates based on the covariance analysis of molecular dynamics trajectories, construction of the Mori projection operator with these essential coordinates, and analysis of the corresponding generalized Langevin equations [M.Stepanova, Phys.Rev.E 76(2007)051918]. Because the approach employs a rigorous theory, the outcomes are physically transparent: the dynamic domains are associated with regions of relative rigidity in the protein, whereas off-domain regions are relatively soft. This also allows scoring the flexibility in the macromolecule with atomic-level resolution [N.Blinov, M.Berjanskii, D.S.Wishart, and M.Stepanova, Biochemistry, 48(2009)1488]. The applications include the domain coarse-graining and characterization of conformational stability in protein G and prion proteins. The results are compared with published NMR experiments. Potential applications for structural biology, bioinformatics, and drug design are discussed. [Preview Abstract] |
Friday, October 1, 2010 2:42PM - 3:10PM |
C2.00003: BREAK
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Friday, October 1, 2010 3:10PM - 3:22PM |
C2.00004: On the magnetic field near the center of Helmholtz coils Michael Crosser, Steven Scott, Adam Clark, Marshall Wilt We develop a series expansion for the calculation of the magnetic field near the center of Helmholtz coils and apply the result to a magnet of our design. Our analysis considers geometric details of the coils, the magnetic properties of the form and windings, conductor insulation effects, and several winding imperfections. We also consider the relaxation of coil symmetry which happens when the mean radius of each coil and the coil midplane separation distance are unequal. We compute the field uniformity near the coil's center for three cases, including one where axial symmetry remains but geometric imperfections of the order of 10$^{-3}$ of the coil ``radius'' exist. [Preview Abstract] |
Friday, October 1, 2010 3:22PM - 3:34PM |
C2.00005: Acoustic Target Location and Scattering Feature identification for a solid cylinder utilizing reversible Synthetic Aperture Sonar filtering Grant Eastland, Timothy Marston, Philip Marston Understanding the scattering features of proud and partially exposed cylinders is relevant to understanding the high frequency scattering by a variety of simple targets. We performed various experiments where partial exposure was studied by lowering a solid aluminum cylinder through a flat free surface into a tank of water insonified at grazing incidence with short pulses to identify different features while monitoring evolution of the scattering as a function of the amount of exposure. The present investigation also allows for the recording of bistatic scattering and reversible filtering based on a form of synthetic aperture sonar (SAS). The slope of the feature timing, derived using ray theory, expressed by the derivative dt/dh where t is the measured time of the feature, depends on the feature type as well as the source and receiver grazing angles. Free surface interactions for features revealed by the slopes are accurately identified using reversible SAS filtering. [Preview Abstract] |
Friday, October 1, 2010 3:34PM - 3:46PM |
C2.00006: Are random wave fields filamentary? Alexander Davis, Steven Tomsovic O'Connor, Gehlen, and Heller [1] studied random superpositions of plane waves, mostly numerically, to understand the eigenstates of quantum chaotic systems better. They argued that the random states have ridges, which exhibit a filamentary-like structure. This begs the question as to how to detect whether data exhibits a filamentary nature. A number of algorithms to construct filaments from data have been introduced, but apparently little work has concentrated on the simpler question, ``how filamentary is some data set?'' We introduce a particularly simple use of the dot product formed from two vectors defined by any three local intensity maxima. Excess alignment relative to random data would generate higher probabilities of finding angles near 0 and 180 degrees. We show results for random superpositions of plane waves using the locations of local intensity maxima and also consider correlations between positions of local intensity maxima and their intensities. \\[4pt] [1] P. W. O'Connor, J. Gehlen, and E. J. Heller, Phys. Rev. Lett. 58,1296 (1987). [Preview Abstract] |
Friday, October 1, 2010 3:46PM - 3:58PM |
C2.00007: Capillary wave scattering by an infinitesimal barrier: effect of contact line dynamics Likun Zhang, David Thiessen In microgravity, capillary instabilities could be countered by minimal solid support structures such that novel fluid configurations are possible. A capillary channel that could be easily realized consists of an array of solid rings or a helix to stabilize large aspect ratio liquid cylinders. The propagation of capillary waves on such channels is of importance for some envisioned applications. In this work, the scattering of capillary waves on liquid cylinder by an infinitesimal transverse barrier is considered theoretically by the method of matched evanescent wave expansion. To account for contact line dynamics on the barrier, an effective-slip boundary condition is applied which assumes that the contact-line velocity is proportional to the deviation of the contact angle from its equilibrium value. We find that energy dissipation at the barrier is most effective for incident waves whose phase velocity is close to the phenomenological slip coefficient. The scattering agrees in the short-wave limit with the theory of gravity-capillary wave scattering by a transverse surface-piercing vertical barrier in the limit of zero barrier depth and zero gravity. [Preview Abstract] |
Friday, October 1, 2010 3:58PM - 4:10PM |
C2.00008: Capillary wave measurements on helically-supported capillary channels Fahim Chandurwala, David Thiessen NASA is considering power generation by the Rankine cycle to save weight on long-duration manned missions to the moon or Mars. Phase separation technology is critical to this process in microgravity. Arrays of capillary channels might be useful for filtering liquid drops from a flowing vapor. The efficiency of droplet capture by a helically-supported capillary channel is being studied. A droplet impinging on the channel launches capillary waves that propagate down the channel helping to dissipate some of the drop's kinetic energy. High-speed video of the channel combined with image processing allows for measurement of the amplitude and speed of the wave packets. Increasing the pitch of the support structure decreases the wave speed. An understanding of the dynamic response of the channel to drop impact is a first step in predicting drop-capture efficiency. [Preview Abstract] |
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