Bulletin of the American Physical Society
2009 APS March Meeting
Volume 54, Number 1
Monday–Friday, March 16–20, 2009; Pittsburgh, Pennsylvania
Session H40: Biological Physics I |
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Sponsoring Units: DBP Chair: David Weitz, Harvard University Room: 412 |
Tuesday, March 17, 2009 8:00AM - 8:12AM |
H40.00001: Application of EPR studies on Biologically Important Copper Acetyl Acetonate and Copper Tetraphenyl Porphyrin via Bayesian Inference and Density Functional Theory Laxman Mainali, Indra Sahu, Keith Earle Quantitative lineshape analysis can allow one to infer information about spin probe structure and dynamics. Experiments were performed at different frequencies (S, X, K, Q, and W Band) for Copper acetyl acetonate (Cu(acac)$_{2})$ and 5,10,15,20 - Tetraphenyl - 21H,23H -porphine copper(II) (CuTPP) in toluene at different temperatures. In order to obtain unbiased estimates of model parameters within the context of a given model, EPR spectra were analyzed via methods of Bayesian Inference. Four different sets of model parameters used to describe cw EPR spectra for two different probe symmetries (axial and rhombic) were explored using a model for rotational diffusion that was analyzed via Stochastic Liouville Equation. The optimized magnetic and dynamic tensor parameters were inferred from individual and simultaneous multifrequency fits and were compared with the values obtained from density functional theory (DFT). The isotropic g values estimated with PW1PW for Cu(acac)$_{2}$ and CuTPP with the respective basis sets 6-31G and 6-31G(d) agree well with the experimental values, whereas the isotropic A values for Cu(acac)$_{2}$ and CuTPP estimated with Local and gradient corrected functionals PWP and Ahlrichs basis set DZ agree well with the experimental values. [Preview Abstract] |
Tuesday, March 17, 2009 8:12AM - 8:24AM |
H40.00002: Application of Bayesian Inference and Relativistic Density Functional Theory on EPR Study of Biologically important Transition Metal (Vanadium) Compounds Indra Sahu, Laxman Mainali, Keith Earle Quantitative lineshape analysis based on the stochastic Liouville equation allows one to infer information about spin probe structure and dynamics. The EPR parameters extracted from Experimental spectra can be used to check theoretical calculation based on Relativistic Density Functional Theory. Experiments on Vanadyl acetylacetonate [VO(acac)$_{2}$] and Vanadyl mesotetraphenyl porphine [VO(TPP)] in toluene at different temperatures were performed at five different frequencies(S,X,K,Q {\&} W-band). Spectral Analysis was performed using methods of Bayesian Inference at the various frequencies, both independently and in a simultaneous multifrequency fit. Rotational diffusion parameters were inferred for two symmetries (Axial and Rhombic). The isotropic A value (A$_{iso})$ calculated for VO(acac)$_{2 }$ with unrestricted and hybrid-functional PW1PW and for VO (TPP) with unrestricted and hybrid functional BHLYP and Pople style basis set with polarization function 6-311G(3df,3pd), deviated by 0.95{\%} and 0.23{\%} respectively compared to experimental Aiso values. The isotropic g values (g$_{iso})$ calculated for VO (acac)$_{2}$ and VO(TPP) with unrestricted and hybrid-functional PW1PW and Ahlrichs basis set TZV, deviated by 0.18{\%} and 0.05{\%} respectively compared to experimental g$_{iso}$ values. [Preview Abstract] |
Tuesday, March 17, 2009 8:24AM - 8:36AM |
H40.00003: Electrically stimulated contractions of Vorticella convallaria Deependra Kantha, David Van Winkle The contraction of \textit{Vorticella convallaria }was triggered by applying a voltage pulse in its host culturing medium. The 50V, 1ms wide pulse was applied across platinum wires separated by 0.7 cm on a microscope slide. The contractions were recorded as cines (image sequences) by a Phantom V5 camera (Vision Research) on a bright field microscope with 20X objective, with the image size of 256 pixels $\times $ 128 pixels at 7352 pictures per second. The starting time of the cines was synchronized with the starting of the electrical pulse. We recorded five contractions of each of 12 organisms. The cines were analyzed to obtain the initiation time, defined as the difference in time between the leading edge of the electrical pulse and the first frame showing zooid movement. From multiple contractions of same organism, we found the initiation time is reproducible. In comparing different organisms, we found the average initiation time of 1.73 ms with a standard deviation of 0.63 ms. This research is supported by the state of Florida (MARTECH) and Research Corporation. [Preview Abstract] |
Tuesday, March 17, 2009 8:36AM - 8:48AM |
H40.00004: Pressure Effects on the Morphology of Mammalian Cells John Schroeder, Charles R. Keese, Ivar Giaever Living mammalian cells can be perturbed by high pressure in a continuous and controlled manner. The effects can be easily measured and quantified using the well-established method of Electric Cell-substrate Impedance Sensing (ECIS). ECIS is an electrical biosensor that quantitatively monitors behaviours of living cells including spreading and adhesion, micromotion and migration. Here we describe the experimental set-up of the pressure equipment and how ECIS is adapted to data collection under these conditions. Preliminary results suggest that high pressure affects the cell attachment and spreading and causes well-attached cells to round up. Results will be presented on the behavior of monolayers of BSC-1 cells upon application of pressures up to 2 kbars of nitrogen gas.. [Preview Abstract] |
Tuesday, March 17, 2009 8:48AM - 9:00AM |
H40.00005: The electronic properties of microbial nanowires: An STM investigation Josh Veazey, Becky Steidl, Gemma Reguera, Stuart Tessmer \textit{Geobacter} species of bacteria present the prospect of an interesting physical system through the expression of pili that act as electrically conductive nanowires. These nanowires serve the biological role of transporting metabolically generated electrons outside the cell body to electron acceptors in the organism's native environment. We have performed scanning tunneling microscopy and spectroscopy on \textit{Geobacter sulferreducens} in an effort to elucidate the mechanism of conductivity. Understanding this system may lead to the enhancement in the effectiveness of \textit{Geobacter} species' roles in microbial fuel cells and the bioremediation of hazardous waste, such as uranium and petroleum. [Preview Abstract] |
Tuesday, March 17, 2009 9:00AM - 9:12AM |
H40.00006: Probing Ion Channel Insertion into a Bilipid Membranes with a Radio Frequency Tank Circuit Hyun Cheol Shin, Eric Stava, Minrui Yu, Hua Qin, Hyun-Seok Kim, Robert Blick We fabricated a radio frequency resonant circuit which can be applied for probing ion channels formed in bilipid membranes. The insertion of ion channels can be probed by monitoring the resonant response of the tank circuit. The circuit itself is realized on a glass chip, which simultaneously uses DC channel recordings (i.e. conventional on-chip patch clamping) and RF detection. The direct current recordings of the ion channels responses allows for the calibration of the radio frequency signal. Such radio frequency recordings of ion channel activity have great potential for high-throughput drug screening. [Preview Abstract] |
Tuesday, March 17, 2009 9:12AM - 9:24AM |
H40.00007: Highly oil-producing microalgae selected through directed-evolution on a microfludic chip Troy Mestler, Andre Estevez-Torres, Guillaume Lambert, Robert H. Austin Some species of photosynthetic microalgae produce signi?cant amounts of oil which can be easily converted to diesel fuel. However, as it stands today, biodiesel is signi?cantly more expensive than fossil fuels. We wish to improve the oil yield and production rate of a single species of microalgae through directed evolution. We propose to utilize our microfabication technology to create microhabitats to control the nutrient environment of the species, monitor oil production through Raman Spectroscopy, and punish colonies of algae which have low oil yield. We believe this process will produce a mutant species with a high oil yield. [Preview Abstract] |
Tuesday, March 17, 2009 9:24AM - 9:36AM |
H40.00008: Structural Color of Biological and Biomimetic Amorphous Nanostructures Jason Forster, Heeso Noh, Vinodkumar Saranathan, Hui Cao, Simon Mochrie, Chinedum Osuji, Richard Prum, Eric Dufresne The feathers of many bird species have amorphous nanostructures of beta-keratin and air that produce non-iridescent color. These structural colors are the result of wavelength-selective scattering from nanostructures which have well-defined length scales but no long-range translational order. We quantify the optical properties of feathers with angle-resolved reflectance spectra and compare them to the nanoscale structures observed with X-ray scattering. We are exploiting self-assembly of polymeric and colloidal systems to create biomimetic nanostructures that capture the essential optical properties of bird feathers. By varying the characteristic length scale and index of refraction contrast of these structures we aim to enhance and tune wavelength selectivity. [Preview Abstract] |
Tuesday, March 17, 2009 9:36AM - 9:48AM |
H40.00009: Directed Fluid Transport and Mixing with Biomimetic Cilia Arrays A.R. Shields, B.A. Evans, B.L. Carstens, M.R. Falvo, S. Washburn, R. Superfine We present results on the long-range, directed fluid transport and fluidic mixing produced by the collective beating of arrays of biomimetic cilia. These artificial cilia are arrays of free-standing nanorods roughly the size of biological cilia, which we fabricate from a polymer-magnetic nanoparticle composite material and actuate with permanent magnets to mimic biological cilia. Biological cilia have evolved to produce microscale fluid transport and are increasingly being recognized as critical components in a wide range of biological systems. However, despite much effort cilia generated fluid flows remain an area of active study. In the last decade, cilia-driven fluid flow in the embryonic node of vertebrates has been implicated as the initial left-right symmetry breaking event in these embryos. With silia we generate directional fluid transport by mimicking the tilted conical beating of these nodal cilia. By seeding fluorescent microparticles into the fluid we have noted the existence of two distinct flow regimes. The fluid flow is directional and coherent above the cilia tips, while between the cilia tips and the floor particle motion is complicated and suggestive of chaotic advection. [Preview Abstract] |
Tuesday, March 17, 2009 9:48AM - 10:00AM |
H40.00010: Physics of phagocytosis of foreign versus self-tolerance Richard Tsai, Pia Rodriguez, Dennis Discher The first cells to `attack' an implanted or injected foreign material or microbe are phagocytic cells of the innate immune system. These cells actively and rapidly phagocytose foreign cells, surfaces, or particles, but the process that is inefficient when faced with ``self'' cells. We have examined the biochemistry and some of the physics of this decision to eat or not eat. One particular protein on all animal cell membranes, called CD47, seems to engage phagocytic cell couter-receptors, and deactivate the force-generating myosin machinery that otherwise makes phagocytosis efficient. We will map the phagocytic synapse between phagocytes and particles or cells and describe the physicochemical dynamics that mediate this key decision in compatability. [Preview Abstract] |
Tuesday, March 17, 2009 10:00AM - 10:12AM |
H40.00011: The Dynamics of Foraging Ants G. William Baxter We experimentally study the foraging of small black ants, Formicinae lasius flavus, in order to describe their foraging behavior mathematically. Individual ants are allowed to forage on a two-dimensional surface in the {\it absence} of any food sources. The position of the ant as a function of time is determined using a high-resolution digital camera. Analysis of the average square displacements of many ants suggests that the foraging strategy is a non-reversing random walk. Moreover, the ants do not retrace their steps to return home but instead continue the random walk until it brings them back near their starting point. [Preview Abstract] |
Tuesday, March 17, 2009 10:12AM - 10:24AM |
H40.00012: Elasticity in Ionically Cross-Linked Neurofilament Networks Norman Yao, Yi-Chia Lin, Chase Broedersz, Karen Kasza, Frederick MacKintosh, David Weitz Neurofilaments are found in abundance in the cytoskeleton of neurons, where they act as an intracellular framework protecting the neuron from external stresses. To elucidate the nature of the mechanical properties that provide this protection, we measure the linear and nonlinear viscoelastic properties of networks of neurofilaments. These networks are soft solids that exhibit dramatic strain stiffening above critical strains of 30-70{\%}. Surprisingly, divalent ions, such as Mg$^{2+}$, Ca$^{2+}$, and Zn$^{2+}$, act as effective cross-linkers for neurofilament networks, controlling their solid-like elastic response. This behavior is comparable to that of actin-binding proteins in reconstituted filamentous actin. We show that the elasticity of neurofilament networks is entropic in origin and is consistent with a model for cross-linked semiflexible networks, which we use to quantify the cross-linking by divalent ions. Ultimately, we are able to extract microstructural network parameters such as the persistence length and the average distance between cross-links directly from bulk rheology. [Preview Abstract] |
Tuesday, March 17, 2009 10:24AM - 10:36AM |
H40.00013: Exploring Cell-Assisted Cell Growth Elijah Bogart, Sharon Lau, Amrish Deshmukh, Carl Franck The population dynamics of microbial life in sheared liquid suspension affords opportunities to explore the ways in which cells encourage each other to proliferate. Such elegant systems continue to inspire us to develop and test simple theories for cooperative behavior (e.g. Phys. Rev. E v. 77, p. 041905 (2008)) in living matter. We report on new insight afforded by the observation of the amoebae Dictyostelium discoideum of the effect on population growth of the introduction of adhesive contacts of cells with each other as well as solid substrates. Through a hydrodynamic scaling argument we find that that mechanical triggers provided by intercellular collisions are more important than collisions with container walls in encouraging growth. Finally, we confirm the discovery of a strain that lacks growth regulation due to density sensing. This work was supported by the NIH (P01 GM078586). [Preview Abstract] |
Tuesday, March 17, 2009 10:36AM - 10:48AM |
H40.00014: Small Molecules Target Carcinogenic Proteins Claudiu Gradinaru An ingenious cellular mechanism of effecting protein localization is prenylation: the covalent attachment of a hydrophobic prenyl group to a protein that facilitates protein association with cell membranes. Fluorescence microscopy was used to investigate whether the oncogenic Stat3 protein can undergo artificial prenylation via high-affinity prenylated small-molecule binding agents and thus be rendered inactive by localization at the plasma membrane instead of nucleus. The measurements were performed on a home-built instrument capable of recording simultaneously several optical parameters (lifetime, polarization, color, etc) and with single-molecule sensitivity. A pH-invariant fluorescein derivative with double moiety was designed to bridge a prenyl group and a small peptide that binds Stat3 with high affinity. Confocal fluorescence images show effective localization of the ligand to the membrane of liposomes. Stat3 predominantly localizes at the membrane only in the presence of the prenylated ligand. Single-molecule FRET (fluorescence resonance energy transfer) between donor-labeled prenylated agents and acceptor-labeled, surface tethered Stat3 protein is used to determine the dynamic heterogeneity of the protein-ligand interaction and follow individual binding-unbinding events in real time. The data indicates that molecules can effect protein localization, validating a therapeutic design that influences protein activity via induced localization. [Preview Abstract] |
Tuesday, March 17, 2009 10:48AM - 11:00AM |
H40.00015: Direct observation of DNA dynamics toward solid state nanopore studied by fluorescence microscopy Tomoharu Takita, Noriyuki Toyama, Kaya Kobayashi, Toshiyuki Mitsui Translocation of single DNA through a solid state nanopore provides information of the length and the folding configuration of the DNA by sensing the ionic current profile. This sensing method opens the possibility to characterize individual polynucleotide molecule such as DNA and RNA and their interaction with various proteins. The interesting phenomena related to the nanopore based DNA sensing with the translocating ionic current have been reported recently and we also have found unexpected clogging probability of DNA into pore as a function of the biased voltage across the pore membrane. To visualize these phenomena as the dynamics of individual DNA molecule near nanopore, we have used fluorescence microscopy. The acceleration of DNA caused by an attractive force toward nanopore was observed in sequential sets of the microscope images. By applying the langevin equations to follow the dynamical motion of DNA, the electric fields near the nanopore under the various biased voltages and ionic concentrations were estimated in DNA solution. In this presentation, we will report the results of the estimated electric fields near nanopore and discuss the shape of the potential. [Preview Abstract] |
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