Publications

2010
Roy S, Prasad M, Topolancik J, Vollmer F. All-optical switching with bacteriorhodopsin protein coated microcavities and its application to low power computing circuits. Journal of Applied Physics 2010;107:053115. 2010_roy_aip.pdf
Gabrielse G, Klothammer WS, McConnell R, Richerme P, Wrubel J, Kalra R, Novitski D, Grzonka D, Oelert W, Sefzick T, Zielinski M, Borbely JS, George MC, Hessels EA, Storry CH, Weel M, Mullers A, Walz J, Speck A. Centrifugal Separation of Antiprotons and Electrons. Phys. Rev. Lett. 2010;105:213002. 2010_gabrielse_prl.pdf
Spicer R, Groover A. Evolution of development of vascular cambia and secondary growth. New Phytol 2010;186(3):577-92.Abstract

Secondary growth from vascular cambia results in radial, woody growth of stems. The innovation of secondary vascular development during plant evolution allowed the production of novel plant forms ranging from massive forest trees to flexible, woody lianas. We present examples of the extensive phylogenetic variation in secondary vascular growth and discuss current knowledge of genes that regulate the development of vascular cambia and woody tissues. From these foundations, we propose strategies for genomics-based research in the evolution of development, which is a next logical step in the study of secondary growth.

2010_spicer_rev._new_phytologist.pdf
Speck A, Mandal P. Half-cycle-pulse-train induced state redistribution of Rydberg atoms. Physical Review A 2010;81:013401. 2010_mandal_pr.pdf
Okada K, Bartolini F, Deaconescu AM, Moseley JB, Dogic Z, Grigorieff N, Gundersen GG, Goode BL. Adenomatous polyposis coli protein nucleates actin assembly and synergizes with the formin mDia1. J Cell Biol 2010;189(7):1087-96.Abstract

The tumor suppressor protein adenomatous polyposis coli (APC) regulates cell protrusion and cell migration, processes that require the coordinated regulation of actin and microtubule dynamics. APC localizes in vivo to microtubule plus ends and actin-rich cortical protrusions, and has well-documented direct effects on microtubule dynamics. However, its potential effects on actin dynamics have remained elusive. Here, we show that the C-terminal "basic" domain of APC (APC-B) potently nucleates the formation of actin filaments in vitro and stimulates actin assembly in cells. Nucleation is achieved by a mechanism involving APC-B dimerization and recruitment of multiple actin monomers. Further, APC-B nucleation activity is synergistic with its in vivo binding partner, the formin mDia1. Together, APC-B and mDia1 overcome a dual cellular barrier to actin assembly imposed by profilin and capping protein. These observations define a new function for APC and support an emerging view of collaboration between distinct actin assembly-promoting factors with complementary activities.

2010_okada_jrnl.pdf
Narayana S, Sato Y. Compact miniature high-resolution thermometer. IEEE Transactions on Applied Superconductivity 2010;20:2402. 2010_sato_ieee.pdf
Narayana S, Sato Y. Direct observation of dynamical bifurcation in a superfluid Josephson junction. Phys Rev Lett 2010;105(20):205302.Abstract

We report a direct observation of dynamical bifurcation between two plasma oscillation states of a superfluid Josephson junction. We excite the superfluid plasma resonance into a nonlinear regime by driving below the natural plasma frequency and observe a clear transition between two dynamical states. We also demonstrate bifurcation by changing the potential well with temperature variations.

2010_narayana_prl.pdf
Barry E, Dogic Z. Entropy driven self-assembly of nonamphiphilic colloidal membranes. Proc Natl Acad Sci U S A 2010;107(23):10348-53.Abstract

We demonstrate that homogeneous monodisperse rods in the presence of attractive interactions assemble into equilibrium 2D fluid-like membranes composed of a one-rod length thick monolayer of aligned rods. Unique features of our system allow us to simultaneously investigate properties of these membranes at both continuum and molecular lengthscales. Analysis of thermal fluctuations at continuum lengthscales yields the membranes' lateral compressibility and bending rigidity and demonstrates that the properties of colloidal membranes are comparable to those of traditional lipid bilayers. Fluctuations at molecular lengthscales, in which single rods protrude from the membrane surface, are directly measured by comparing the positions of individual fluorescently labeled rods within a membrane to that of the membrane's continuum conformation. As two membranes approach each other in suspension, protrusion fluctuations are suppressed leading to effective repulsive interactions. Motivated by these observations, we propose an entropic mechanism that explains the stability of colloidal membranes and offers a general design principle for the self-assembly of 2D nanostructured materials from rod-like molecules.

2010_dogic_pnas.pdf
Sato Y. Fiske-amplified superfluid interferometry. Physical Review B 2010;81:172502. 2010_sato_pr.pdf
Fischer P, Ghosh A, Premasiri WR, Ziegler LD. Nanostructured Plasmonic Surfaces for Surface Enhanced Raman Scattering   of Bacteria. XXII International Conference on Raman Spectroscopy 2010;1267:994-995.
Pinto N, Cox DD. An Evaluation of the Invariance Properties of a Biologically-Inspired System for Unconstrained Face Recognition. ICST Conference on Biologically Inspired Network, Information, and Computing Systems 2010;
Sriram V, Tsoi K, Luk W, Cox DD. A Design-Space Exploration of Biologically-Inspired Visual Object Recognition Algorithms Using CPUs, GPUs and FPGAs. Many-Core and Reconfigurable Supercomputing 2010; 2010_sriram_.pdf
Halvorsen K, Wong WP. Massively parallel single-molecule manipulation using centrifugal force. Biophys J 2010;98(11):L53-5.Abstract

Precise manipulation of single molecules has already led to remarkable insights in physics, chemistry, biology, and medicine. However, widespread adoption of single-molecule techniques has been impeded by equipment cost and the laborious nature of making measurements one molecule at a time. We have solved these issues by developing an approach that enables massively parallel single-molecule force measurements using centrifugal force. This approach is realized in an instrument that we call the centrifuge force microscope in which objects in an orbiting sample are subjected to a calibration-free, macroscopically uniform force-field while their micro-to-nanoscopic motions are observed. We demonstrate high-throughput single-molecule force spectroscopy with this technique by performing thousands of rupture experiments in parallel, characterizing force-dependent unbinding kinetics of an antibody-antigen pair in minutes rather than days. Additionally, we verify the force accuracy of the instrument by measuring the well-established DNA overstretching transition at 66 +/- 3 pN. With significant benefits in efficiency, cost, simplicity, and versatility, single-molecule centrifugation has the potential to expand single-molecule experimentation to a wider range of researchers and experimental systems.

2010_halvorsen_jrnl.pdf
Fischer P, Salam A. Molecular QED of coherent and incoherent sum-frequency and second-harmonic generation in chiral liquids in the presence of a static electric field. Molecular Physics 2010;108(14):1857-1868. 2010_fischer_mp.pdf
Cheng D, Halvorsen K, Wong WP. Note: High-precision microsphere sorting using velocity sedimentation. Rev Sci Instrum 2010;81(2):026106.Abstract

Monodisperse populations of microspheres are desirable for a variety of research and industrial applications, but many desirable sizes and materials can be difficult to synthesize and have limited commercial availability. In this paper, we present an effective, straightforward, and low cost method for sorting polydisperse microspheres into many separate monodisperse samples. The basic approach is to use velocity sedimentation through a density gradient in a long vertical column, followed by carefully targeted extraction. We demonstrate this technique by reducing the coefficient of variation of melamine microspheres from 13% to 1%-4% and glass microspheres from 35% to 3%-8%. This simple and inexpensive method can be used to sort microspheres of many sizes and materials, and is easily scalable, opening the possibility of cheap, monodisperse microspheres.

2010_cheng_apl.pdf
Zoccolan D, Graham BJ, Cox DD. A self-calibrating, camera-based eye tracker for the recording of rodent eye movements. Front Neurosci 2010;4:193.Abstract

Much of neurophysiology and vision science relies on careful measurement of a human or animal subject's gaze direction. Video-based eye trackers have emerged as an especially popular option for gaze tracking, because they are easy to use and are completely non-invasive. However, video eye trackers typically require a calibration procedure in which the subject must look at a series of points at known gaze angles. While it is possible to rely on innate orienting behaviors for calibration in some non-human species, other species, such as rodents, do not reliably saccade to visual targets, making this form of calibration impossible. To overcome this problem, we developed a fully automated infrared video eye-tracking system that is able to quickly and accurately calibrate itself without requiring co-operation from the subject. This technique relies on the optical geometry of the cornea and uses computer-controlled motorized stages to rapidly estimate the geometry of the eye relative to the camera. The accuracy and precision of our system was carefully measured using an artificial eye, and its capability to monitor the gaze of rodents was verified by tracking spontaneous saccades and evoked oculomotor reflexes in head-fixed rats (in both cases, we obtained measurements that are consistent with those found in the literature). Overall, given its fully automated nature and its intrinsic robustness against operator errors, we believe that our eye-tracking system enhances the utility of existing approaches to gaze-tracking in rodents and represents a valid tool for rodent vision studies.

2010_graham_frontiers_in_neuroscience.pdf
2009
de Bivort BL, Perlstein EO, Kunes S, Schreiber SL. Amino acid metabolic origin as an evolutionary influence on protein sequence in yeast. J Mol Evol 2009;68:490-7.Abstract

The metabolic cycle of Saccharomyces cerevisiae consists of alternating oxidative (respiration) and reductive (glycolysis) energy-yielding reactions. The intracellular concentrations of amino acid precursors generated by these reactions oscillate accordingly, attaining maximal concentration during the middle of their respective yeast metabolic cycle phases. Typically, the amino acids themselves are most abundant at the end of their precursor's phase. We show that this metabolic cycling has likely biased the amino acid composition of proteins across the S. cerevisiae genome. In particular, we observed that the metabolic source of amino acids is the single most important source of variation in the amino acid compositions of functionally related proteins and that this signal appears only in (facultative) organisms using both oxidative and reductive metabolism. Periodically expressed proteins are enriched for amino acids generated in the preceding phase of the metabolic cycle. Proteins expressed during the oxidative phase contain more glycolysis-derived amino acids, whereas proteins expressed during the reductive phase contain more respiration-derived amino acids. Rare amino acids (e.g., tryptophan) are greatly overrepresented or underrepresented, relative to the proteomic average, in periodically expressed proteins, whereas common amino acids vary by a few percent. Genome-wide, we infer that 20,000 to 60,000 residues have been modified by this previously unappreciated pressure. This trend is strongest in ancient proteins, suggesting that oscillating endogenous amino acid availability exerted genome-wide selective pressure on protein sequences across evolutionary time.

2009_de_bivort_j_mol_evol.pdf
de Bivort BL, Guo H-FF, Zhong Y. Notch signaling is required for activity-dependent synaptic plasticity at the Drosophila neuromuscular junction. J Neurogenet 2009;23:395-404.Abstract

The cell-surface-signaling protein Notch, is required for numerous developmental processes and typically specifies which of two adjacent cells will adopt a non-neuronal developmental fate. It has recently been implicated in long-term memory formation in mammals and Drosophila. Here, we investigated whether activity-dependent synaptic plasticity at the neuromuscular junctions (NMJs) of third instar Drosophila larvae depends on Notch signaling. The length and number of axonal branches and number of presynaptic sites (boutons) in NMJ vary with the level of synaptic activity, so we increased activity at the NMJ by two complementary methods: increasing the chronic growth temperature of third instar larvae from 18 to 28 degrees C and using the double-mutant ether-a-gogo,Shaker (eagSh), both of which increase NMJ size and bouton count. Animals homozygous for the functionally null, temperature-sensitive Notch alleles, N(ts1) and N(ts2), displayed no activity-dependent increase in NMJ complexity when reared at the restrictive temperature. Dominant-negative Notch transgenic expression also blocked activity-dependent plasticity. Ectopic expression of wild-type Notch and constitutively active truncated Notch transgenes also reduced activity-dependent plasticity, suggesting that there is a "happy medium" level of Notch activity in mediating NMJ outgrowth. Last, we show that endogenous Notch is primarily expressed in the presynaptic cell bodies where its expression level is positively correlated with motor neuron activity.

2009_de_bivort_jrnl.pdf
Clouse R, de Bivort BL, Giribet G. A phylogenetic analysis for the South-east Asian mite harvestman family Stylocellidae (Opiliones : Cyphophthalmi) - a combined analysis using morphometric and molecular data. Invertebrate Systematics 2009;23:515-529. 2009_clouse_csiro.pdf
Bar-Yam Y, Harmon D, de Bivort B. Systems biology. Attractors and democratic dynamics. Science 2009;323:1016-7. 2009_bar-yam_perpectives.pdf

Pages