Bulletin of the American Physical Society
16th Annual Meeting of the Northwest Section of the APS
Volume 60, Number 6
Thursday–Saturday, May 14–16, 2015; Pullman, Washington
Session B5: Biophysics |
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Chair: Douglas Juers, Whitman College Room: Smith Center for Undergraduate Education (CUE) 209 |
Friday, May 15, 2015 1:30PM - 2:00PM |
B5.00001: A Primer on Optical Nanoscopy Invited Speaker: Bethe Scalettar For nearly a century, diffraction has imposed an essentially impenetrable barrier of $\sim$200 nm on the lateral resolution of far-field optical microscopy. However, in the mid 1990's this barrier began to crumble, and $\sim$20 nm lateral resolution now can be achieved with fluorescence microscopy by switching between bright and dark states of fluorescent markers. The significance of this achievement is immense, as exemplified by the fact that pioneers in ``optical nanoscopy'' were awarded the 2014 Nobel Prize in Chemistry. In this talk, I will present a primer on optical nanoscopy and show how we have used this technique to elucidate attributes of proteins involved in learning and memory formation. [Preview Abstract] |
Friday, May 15, 2015 2:00PM - 2:12PM |
B5.00002: Vegetative Rhombic Pattern Formation Driven by Root Suction for an Interaction-Diffusion Plant-Ground Water Model System in an Arid Flat Environment David Wollkind, Inthira Chaiya, Richard Cangelosi, Bonni Dichone, Chontita Rattanakul A rhombic planform nonlinear cross-diffusive instability analysis is applied to an interaction-diffusion plant-ground water model system in an arid flat environment containing a root suction effect. A threshold-dependent paradigm is introduced to interpret stable rhombic patterns driven by this plant root suction effect in the ground water equation. The results of that analysis are represented by plots in a root suction coefficient versus rainfall rate dimensionless parameter space. From those plots regions corresponding to bare ground and vegetative patterns consisting of isolated patches, rhombic arrays of pseudo spots or gaps separated by an intermediate rectangular state, and homogeneous distributions from low to high density are identified in this parameter space. Then that morphological sequence, produced upon traversing an experimentally determined root suction characteristic curve, is compared with observational evidence relevant to the occurrence of leopard, pearled, or labyrinthine-type tiger bush and used to motivate an aridity classification scheme. [Preview Abstract] |
Friday, May 15, 2015 2:12PM - 2:24PM |
B5.00003: Coarse-Grained Molecular Simulations of Allosteric Cooperativity Prithviraj Nandigrami, John Portman We develop a mixed Monte Carlo-Molecular Dynamics scheme to simulate the classic Monod-Wyman-Changeux (MWC) model of allostery at the molecular level. Ligand binding in this model is cooperative due to the coupling between the binding sites provided by the conformational transition of the protein. We present results for calcium binding to the two binding loops within each domain of Calmodulin (CaM). We find that relative binding free energies of an individual loop is determined by the conformational compatibility of the binding site in the bound conformation, as well as the conformational flexibility of the binding site in the unbound conformation. This simple coarse-grained model captures the qualitative differences for calcium binding to the isolated domains of CaM such as overall affinity and the relative binding cooperativity. A simple two state MWC model provides an accurate description of the simulated population for the ligation states of each domain as a function of concentration. [Preview Abstract] |
Friday, May 15, 2015 2:24PM - 2:36PM |
B5.00004: 3D Contraction Force in Different Morphology of Cancer Cell Jihan Kim, Nicholas Groves, Bo Sun Cell migration is an integrated process that is important in life. Migration is essential for embryonic development as well as homeostatic processes such as wound healing and immune responses. Unlike normal migration process, we have seen that aberrant behavior in cancer cell. In this experiment we focused on its behavior through connective extracellular matrix (ECM). When cell migrates through 3D ECM, it deforms the matrix by applying forces around its environment. To obtain traction forces, we computed deformation field of the matrix around a cell. The existing experiment had been done with analysis on elongated-shape of MDA-MB-231 breast cancer cell. And highly dense fluorescent particles embedded in 3D collagen were used to capture a deformation field of matrix. In this experiment we developed a technique to capture the deformation field without introducing particles inside of collagen gel. This method can eliminate any interactions between particles and collagen fibers. In addition, we obtained deformation field of different morphology of breast cancer cells. Finally we were able to determine the topology of traction forces in cancer cell based on its shapes. [Preview Abstract] |
Friday, May 15, 2015 2:36PM - 3:06PM |
B5.00005: Using computational biophysics to study protein structure, function and evolution Invited Speaker: F. Marty Ytreberg Understanding how proteins evolve and function is vital for developing better drugs and for predicting and controlling the outbreak of disease. Yet, the biophysical implications of protein evolution are often not well understood. Computational biophysics has emerged as a useful tool in this area due to its unique ability to obtain an atomically detailed view of proteins and how they interact with other biomolecules. I will give examples from our studies where computational biophysics has provided valuable insight into protein evolution, and has been used to determine and analyze structural ensembles for intrinsically disordered proteins. [Preview Abstract] |
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