Bulletin of the American Physical Society
APS March Meeting 2015
Volume 60, Number 1
Monday–Friday, March 2–6, 2015; San Antonio, Texas
Session F47: Quantum Biology and Sensors |
Hide Abstracts |
Sponsoring Units: DBIO Chair: Steven Schwartz, University of Arizona Room: 217B |
Tuesday, March 3, 2015 8:00AM - 8:12AM |
F47.00001: Docking Prediction of a Water Soluble Porphyrin and Tubulin Assisted with Resonance Raman and Vibrational Mode Analysis Brady McMicken, Lorenzo Brancaleon, Robert Thomas, James Parker The ability to modify protein conformation by controlling its partial unfolding may have practical applications such as diminishing its function or blocking its activity. One method used to induce partial unfolding of a protein involves the use of a photosensitizer non-covalently bound to a protein that triggers photochemical reactions upon irradiation leading to protein conformational changes. We are investigating the photoinduced conformational changes of tubulin mediated by a bound water-soluble porphyrin that acts as a photosensitizer. Analysis of how tubulin conformational changes affect its function including polymeric assembly forming microtubules is of interest to uncover the mechanism responsible for the structural change. Our approach to better understand the conformational change, we first plan to discover the binding location between the porphyrin and protein. Use of vibrational mode analysis using density functional theory and resonance Raman experiments targeting the porphyrin molecule will be used to correlate Raman peaks with vibrational modes. The relative intensities of the porphyrin bound to tubulin can be used to calculate the equilibrium geometry observed from Raman spectra. These data will provide the relative distortion of the porphyrin when bound to tubulin, which will subsequently be used in docking simulations to find the most likely binding configuration. [Preview Abstract] |
Tuesday, March 3, 2015 8:12AM - 8:24AM |
F47.00002: Broad-band opsin for effective stimulation of cells by white light Subrata Batabyal, Gregory Cervenka, Young-tae Kim, Samarendra Mohanty Currently, use of optogenetic sensitization of retinal cells combined with activation/inhibition has potential as alternative to retinal implants that would have required electrodes inside every single neuron for high visual resolution. However, clinical translation of optogenetic activation for restoration of vision suffers from the drawback that narrow spectral sensitivity of opsin requires active stimulation by blue laser or LED having intensity much higher than ambient light. In order to allow ambient-light based stimulation paradigm, here we report development of broad-band opsin that has broad spectral excitability in the entire visible spectrum. The cells sensitized with the broad-band opsin showed order of magnitude higher excitability with white light as compared to that using only the narrow-band light components. The use of broad-band opsin construct will allow higher sensitivity of the opsin-sensitized neurons in degenerated retina to ambient white light, and therefore, significantly lower activation-threshold in contrast to conventional approach of intense, narrow-band light based active-stimulation. [Preview Abstract] |
Tuesday, March 3, 2015 8:24AM - 8:36AM |
F47.00003: Photoconductivity in DNA-Porphyrin Complexes Peco Myint, Emma Oxford, Collence Nyazenga, Walter Smith, Zhengqing Qi, A.T. Johnson We have measured the photoconductivity of $\lambda -$DNA that is modified by intercalating a porphyrin compound, \textit{meso}-tetrakis($N$-methyl-4-pyridiniumyl)porphyrin (TMPyP), into its base stacks. Intercalation was verified by a red shift and hypochromism of the Soret absorption peak. The DNA/porphyrin strands were then deposited onto oxidized silicon substrates which had been patterned with interdigitated electrodes, and blown dry. Electrical measurements were carried out under nitrogen, using illumination from a 445 nm laser; this wavelength falls within the absorption peak of the DNA/porphyrin complexes. When initially measured under dry nitrogen, the complexes show no photoconductivity or dark conductivity. However, at relative humidities of 30{\%} and above, we do observe dark conductivity, and also photoconductivity that grows with time. Photoconductivity gets larger at higher relative humidity. Remarkably, when the humidity is lowered again, some photoconductivity is now observed, indicating a change that persists for more than 24 hours. It may be that the humidity alters the structure of the DNA, perhaps allowing for better alignment of the bases. [Preview Abstract] |
Tuesday, March 3, 2015 8:36AM - 8:48AM |
F47.00004: Optimization of a Quantum Biomimetic Photocell Nathaniel Gabor, Vivek Aji, Yafis Barlas We propose and describe the structure, function, and optimization of a biologically inspired two-channel quantum photocell. The photocell, which operates as a dual quantum heat engine, simultaneously performs the critical tasks of absorption, power conversion, and energy flux regulation. By considering the realistic case of stochastic solar photon irradiance, we determine the spectrum of optimal absorption characteristics and charge transfer probabilities necessary for the input supply to exactly meet the output demand. Strikingly, the regulation optimization spectrum peaks in the red and blue portions of the terrestrial solar irradiance, and exhibits close correspondence to the action spectrum of chlorophyll-based photosynthetic organelle. Moreover, a comparison of structure and function of the proposed two-color photocell to photosynthetic chlorophyll complexes in green plants may answer the question: why on Earth are terrestrial plants green? [Preview Abstract] |
Tuesday, March 3, 2015 8:48AM - 9:00AM |
F47.00005: A Classical Theory of Multichromophoric Resonance Energy Transfer Sebastian Duque, Paul Brumer, Leonardo A. Pachon Based on classical electrodynamics, a classical theory of multichromophoric resonance energy transfer is formulated. In the maximum coupling configuration between $N_{\mathrm{A}}$ acceptors and $N_{\mathrm{D}}$ donors, the present theory predicts a first-order-in-the-interactions enhancement of the energy transfer rate by a factor $N_{\mathrm{A}}$ and additional second-order-in-the-interactions enhancement arising from the interaction between donors. The theory is applied to predict the transfer rate of the LH II and results are found to be in good agreement with experimental results. [Preview Abstract] |
Tuesday, March 3, 2015 9:00AM - 9:12AM |
F47.00006: ABSTRACT WITHDRAWN |
Tuesday, March 3, 2015 9:12AM - 9:24AM |
F47.00007: Coherent dimer dynamics in a dissipative environment maintained by an off-resonant single mode Elliott Levi, Brendon Lovett The role of quantum coherence in efficient energy harvesting has recently been the subject of intense research. In this paper, we explore the extent to which quantum coherence can be induced in a previously incoherent two level system (TLS) by strongly coupling to a single, off-resonant, bosonic mode. The rest of the environment is assumed to comprise a Markovian bath of bosonic modes. The TLS could, for example, represent the position of the exciton in an energy transfer dimer system. The TLS-single mode coupling strength is varied for several different forms of bath spectral density in order to assess whether the coherent dynamics of the TLS are modified. We find a clear renormalisation of the site population oscillation frequency, which also causes an altered interaction with the bath. This new interaction can cause enhanced or reduced coherent behaviour of the TLS depending on the parameters. We will discuss the usefulness and pitfalls of exploiting such a dynamics-altering tool in a quantum device. [Preview Abstract] |
Tuesday, March 3, 2015 9:24AM - 9:36AM |
F47.00008: Identification of nucleobases using variable currents through graphene nanopores: A first principles study J.T. Haraldsen, H. McFarland, T. Ahmed, J.-X. Zhu, A.V. Balatsky Nanopore-based technology has the potential to be an efficient method for DNA/RNA base sequencing, as well as an identifier of other biomolecules. However, the thickness of the nanopore substrate is critical for the identification of individual nucleobases due to resulting noise and resolution problems. Recently, graphene has been suggested as a possible nanopore substrate due to its single atomic thickness and robust strength. In this study, we examine a possible device mechanism for the voltage dependence of nucleobases passing through a graphene nanopore. We utilize density functional theory with a generalized gradient approach on a graphene ribbon with a nucleobase in order to calculate the transmission spectra for each base. Transmission spectra for each base allows for the calculation of the ballistic current and differential current as a function of voltage. We show that applying various bias voltages across a graphene ribbon for the general, energy-minimized position of the translocated nucleobase, it is possible to distinguish individual bases using the resulting current. Overall, our goal is to improve nanopore device design by helping to further DNA/RNA nucleobase identification and sequencing. [Preview Abstract] |
Tuesday, March 3, 2015 9:36AM - 9:48AM |
F47.00009: Physical limits to biomechanical sensing Farzan Beroz, Chase P. Broedersz, Ned S. Wingreen Experiments have shown that eukaryotic cells such as fibroblasts and mesenchymal stem cells are able to accurately probe and respond to the elastic properties of their microenvironment. These cells navigate across gradients in stiffness, a phenomenon that has been called ``durotaxis.'' Spatial heterogeneity in the cell's elastic environment produces sampling noise in local probing of stiffness, which places fundamental limits on the accuracy with which a cell can sense stiffness gradients. To determine the biophysical limits of durotaxis, we develop a quantitative model of a cell as a stiffness-measuring device interacting with a disordered fiber network in two and three dimensions. We find that local stiffness measurements follow a broad distribution spanning several orders of magnitude. [Preview Abstract] |
Tuesday, March 3, 2015 9:48AM - 10:00AM |
F47.00010: Graphene Nanonet for Biological Sensor Narae Shin, Taekyeong Kim, Jaesung Park, Hye Jun Jin, Hyungwoo Lee, Kyung-eun Byun, Chang-seuk Lee, Kwang S. Kim, Byung Hee Hong, Tae Hyun Kim, Seunghun Hong Graphene nanoribbons (GNRs) have been drawing attentions because they exhibited improved transconductances compared with graphene, and their edges could be functionalized with various chemicals or biological molecules. Herein, we developed a facile method to fabricate graphene nanonet (GNN) patterns over a large surface area for biological applications. In this method, the networks of V$_{2}$O$_{5}$ nanowires were adsorbed selectively in the desired regions on a graphene layer, and they were utilized as a shadow mask during the reactive ion etching on the graphene layer. This fabrication process allowed us to prepare large scale patterns of GNN structures which were comprised the continuous networks of GNRs with chemical functional groups on their edges. The chemical functional groups in the GNN could be functionalized with biological molecules such as DNAs for biological applications. Using the GNN-based biochip devices, we have successfully achieved the fluorescence imaging of DNAs on the GNN channels and the electrical detection of the DNAs at 1nM concentrations. Our method could be a powerful strategy to mass-produce GNR-based devices and should enable various practical bio-applications. [Preview Abstract] |
Tuesday, March 3, 2015 10:00AM - 10:12AM |
F47.00011: Optical detection of cellular activation by optical stimulation Sarmishtha Satpathy, Subrata Batbyal, Young-tae Kim, Samarendra Mohanty Despite the many advantages of patch clamp recordings, there have been efforts to find alternative methods for measuring action potentials in neurons as electrode methodologies have limited spatial resolution, rely on mechanical stability, and are hence cumbersome to use. Here, we report use of optical methods that allow detection of cells with increased spatial information. We demonstrate use of calcium dyes or genetic voltage/ion indicators for optical detection of influx of Ca$^{2+}$ions as a measure of optical stimulation. We also show that phase information of light transmitted or reflected from the activated-cell can be used to non-invasively measure changes in optical path length of the cells during optical activation. Further, we report use of polarized light for wide-field detection of optogenetically-stimulated activity in cells, requiring no exogenous labeling, making it possible to detect cellular activity with high spatial and temporal resolution by wide-field polarimetric/phase imaging. With optical detection of neural activities, the whole process of identification, activation and detection can be made non-invasive added with the advantages of high throughput and least requirement of mechanical stability and contamination. [Preview Abstract] |
Tuesday, March 3, 2015 10:12AM - 10:24AM |
F47.00012: Ultra-low field T1 vs. T1rho at 3T and 7T: study of rotationally immobilized protein gels and animal brain tissues Hui Dong, Ben Inglis, Ian Barr, John Clarke Clinical magnetic resonance imaging (MRI) machines operating in static fields of typically 1.5 T or 3 T can capture information on slow molecular dynamics utilizing the so-called T1rho technique. This technique, in which a radiofrequency (RF) spin-lock field is applied with microtesla amplitude, has been used, for example, to determine the onset time of stroke in studies on rats. The long RF pulse, however, may exceed the specific absorption rate (SAR) limit, putting subjects at risk. Ultra-low-field (ULF) MRI, based on Superconducting Quantum Interference Devices (SQUIDs), directly detects proton signals at a static magnetic field of typically 50--250 $\mu $T. Using our ULF MRI system with adjustable static field of typically 55 to 240 $\mu $T, we systematically measured the T1 and T2 dispersion profiles of rotationally immobilized protein gels (bovine serum albumin), ex vivo pig brains, and ex vivo rat brains with induced stroke. Comparing the ULF results with T1rho dispersion obtained at 3 T and 7 T, we find that the degree of protein immobilization determines the frequency-dependence of both T1 and T1rho. Furthermore, T1rho and ULF T1 show similar results for stroke, suggesting that ULF MRI may be used to image traumatic brain injury with negligible SAR. [Preview Abstract] |
Tuesday, March 3, 2015 10:24AM - 10:36AM |
F47.00013: New formulation of Magnetization Equation for Flowing Nuclear Spin under NMR/MRI Excitation(I) Dilip De, Moses Emetere, Victor Omotosho We have obtained for the first time from the Bloch NMR equations the correct dependence of the single component of magnetization, M$_{y}$ and M$_{z}$ at resonance (NMR/MRI) on relaxation times, rf B$_{1}$ field (pulsed or continuous), blood(nuclear spin) flow velocity, etc. in the rotating frame of reference. The equations are applicable for both CW and pulsed NMR experiments with or without flow of spins. Our approaches can be extended easily to include gradient fields and diffusion of spins, if needed in NMR/MRI experiments. We also discuss the application of our equations to a specific case of MR excitation scheme: Free induction decay. The first time new equations of single component of MR magnetization and further equations that can be derived with the methodologies used here, can be applied towards accurate simulation of MR images/signals and extraction of parameters of clinical importance through comparison of the measured and the simulated images/signals. [Preview Abstract] |
(Author Not Attending)
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F47.00014: The reference-probe model in avian magnetoreception Maria Procopio, Thorsten Ritz The sensory mechanism that allows magneto-sensitive organisms to detect the direction of the geomagnetic field for navigation purposes is still largely unclear. One of the two leading hypothesis stipulates that photoindused radical-pair reactions in photoreceptor proteins act as the primary magnetic sensor in migratory birds. In recent years the radical-pair mechanism has been receiving considerable support, qualifying the avian compass for a place in the emerging field of quantum biology. Investigations on such a spin-based sensor have focussed on uncovering the design features for bioinspired technology. The reference-probe model has been suggested as an optimal radical-pair design. Radical-pairs with probe character have been shown to achieve not only optimal but also robust directional sensitivity to weak magnetic fields. However, the relevance of the reference character has not been studied yet. Here we introduce a method to investigate the contribution of the reference character to optimality and robustness. By analytical and computational studies, we find that the probe character is crucial for optimality, while the reference character captures robust features. Our results suggest the reference-probe model to contain both optimal and robust design features. [Preview Abstract] |
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