Virtual Journal of Biological Physics Research -- February 15, 2010

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QUANTUM MECHANICAL DYNAMICS

Polypeptides in alpha-helix conformation perform as diodes
Dahiyana Cristancho and Jorge M. Seminario
The Journal of Chemical Physics   132, 065102 (2010) (5 pages)   
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Coherently wired light-harvesting in photosynthetic marine algae at ambient temperature
Elisabetta Collini, Cathy Y. Wong, Krystyna E. Wilk, Paul M. G. Curmi, Paul Brumer, and Gregory D. Scholes
Nature   463, 644-647 (2010)   
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PHYSICS OF WATER AND HYDROGEN-BONDED SOLVENTS

Heat transfer in protein–water interfaces
Anders Lervik, Fernando Bresme, Signe Kjelstrup, Dick Bedeaux, and J. Miguel Rubi
Physical Chemistry Chemical Physics   12, 1610-1617 (2010)   
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Collisional cooling investigation of THz rotational transitions of water
Michael J. Dick, Brian J. Drouin, and John C. Pearson
Physical Review A   81, 022706 (2010) (12 pages)   
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Long-distance correlations in molecular orientations of liquid water and shape-dependent hydrophobic force
J. Maruthi Pradeep Kanth, Satyavani Vemparala, and Ramesh Anishetty
Physical Review E   81, 021201 (2010) (10 pages)   
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Low-Frequency Modes of Aqueous Alkali Halide Solutions: Glimpsing the Hydrogen Bonding Vibration
Ismael A. Heisler and Stephen R. Meech
Science   327, 857-860 (2010)   
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The single donator-single acceptor hydrogen bonding structure in water probed by Raman spectroscopy
Qiang Sun
The Journal of Chemical Physics   132, 054507 (2010) (4 pages)   
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Dynamics of water at the nanoscale hydrophobic confinement
Niharendu Choudhury
The Journal of Chemical Physics   132, 064505 (2010) (5 pages)   
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A hydrogen bonding motif for forming extended assemblies
Jiahui Zhang, Xiangxiang Wu, Kazuhiro Yamato, Futao Liu, Tianyi Su, Chong Zheng, Lan He, and Bing Gong
Chemical Communications   46, 1062-1064 (2010)   
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Ultrafast energy transfer between water molecules
T. Jahnke, H. Sann, T. Havermeier, K. Kreidi, C. Stuck, M. Meckel, M. Schöffler, N. Neumann, R. Wallauer, S. Voss, A. Czasch, O. Jagutzki, A. Malakzadeh, F. Afaneh, Th. Weber, H. Schmidt-Böcking, and R. Dörner
Nature Physics   6, 139-142 (2010)   
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Terahertz response of dipolar impurities in polar liquids: On anomalous dielectric absorption of protein solutions
Dmitry V. Matyushov
Physical Review E   81, 021914 (2010) (11 pages)   
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MEMBRANE BIOPHYSICS

Interplay between micelle formation and waterlike phase transitions
G. Heinzelmann, W. Figueiredo, and M. Girardi
The Journal of Chemical Physics   132, 064905 (2010) (8 pages)   
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Cholic acid micelles—controlling the size of the aqueous cavity by PEGylation
F. Despa, J. T. Luo, J. Li, Y. Duan, and K. S. Lam
Physical Chemistry Chemical Physics   12, 1589-1594 (2010)   
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Abnormal dispersion of refractive index of purple membranes in an aqueous medium
Alexandar Metodiev Zhivkov
Applied Optics   49, 272-274 (2010)   
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Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers
Sarah D. Cady, Klaus Schmidt-Rohr, Jun Wang, Cinque S. Soto, William F. DeGrado, and Mei Hong
Nature   463, 689-692 (2010)   
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Thermal noise due to surface-charge effects within the Debye layer of endogenous structures in dendrites
Roman R. Poznanski
Physical Review E   81, 021902 (2010) (11 pages)   
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Polarizability of red blood cells with an anisotropic membrane
José Luis Sebastián, Sagrario Muñoz, Miguel Sancho, Genoveva Martínez, and Karan V. I. S. Kaler
Physical Review E   81, 022901 (2010) (4 pages)   
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Alcohol solubility in a lipid bilayer: Efficient grand-canonical simulation of an interfacially active molecule
Jocelyn M. Rodgers, Michael Webb, and Berend Smit
The Journal of Chemical Physics   132, 064107 (2010) (10 pages)   
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Overcharging below the nanoscale: Multivalent cations reverse the ion selectivity of a biological channel
Elena García-Giménez, Antonio Alcaraz, and Vicente M. Aguilella
Physical Review E   81, 021912 (2010) (7 pages)   
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Rational design of cationic lipids for siRNA delivery
Sean C Semple, Akin Akinc, Jianxin Chen, Ammen P Sandhu, Barbara L Mui, Connie K Cho, Dinah W Y Sah, Derrick Stebbing, Erin J Crosley, Ed Yaworski, Ismail M Hafez, J Robert Dorkin, June Qin, Kieu Lam, Kallanthottathil G Rajeev, Kim F Wong, Lloyd B Jeffs, Lubomir Nechev, Merete L Eisenhardt, Muthusamy Jayaraman, Mikameh Kazem, Martin A Maier, Masuna Srinivasulu, Michael J Weinstein, Qingmin Chen, Rene Alvarez, Scott A Barros, Soma De, Sandra K Klimuk, Todd Borland, Verbena Kosovrasti, William L Cantley, Ying K Tam, Muthiah Manoharan, Marco A Ciufolini, Mark A Tracy, Antonin de Fougerolles, Ian MacLachlan, Pieter R Cullis, Thomas D Madden, and Michael J Hope
Nature Biotechnology   28, 172-176 (2010)   
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FUNDAMENTAL POLYMER STATICS/DYNAMICS

Molecular dynamics study of the effects of chain properties on the order formation dynamics of self-assembled monolayers of long-chain molecules
Toshiaki Miura and Masuhiro Mikami
Physical Review E   81, 021801 (2010) (11 pages)   
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Lateral organization of complex lipid mixtures from multiscale modeling
Paul W. Tumaneng, Sagar A. Pandit, Guijun Zhao, and H. L. Scott
The Journal of Chemical Physics   132, 065104 (2010) (10 pages)   
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Thermodynamic stability of soft-core Lennard-Jones fluids and their mixtures
D. M. Heyes
The Journal of Chemical Physics   132, 064504 (2010) (8 pages)   
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Sequence dependent self-assembly of -peptides: Insights from a coarse-grained model
Jagannath Mondal, Bong June Sung, and Arun Yethiraj
The Journal of Chemical Physics   132, 065103 (2010) (7 pages)   
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Analytical theory of finite-size effects in mechanical desorption of a polymer chain
A. M. Skvortsov, L. I. Klushin, G. J. Fleer, and F. A. M. Leermakers
The Journal of Chemical Physics   132, 064110 (2010) (15 pages)   
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PROTEIN CONFORMATIONAL DYNAMICS/FOLDING

Effects of side-chain packing on the formation of secondary structures in protein folding
Satoshi Yasuda, Takashi Yoshidome, Hiraku Oshima, Ryota Kodama, Yuichi Harano, and Masahiro Kinoshita
The Journal of Chemical Physics   132, 065105 (2010) (10 pages)   
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Patterns of protein unfolding and protein aggregation in ionic liquids
Diana Constatinescu, Christian Herrmann, and Hermann Weingärtner
Physical Chemistry Chemical Physics   12, 1756-1763 (2010)   
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Nucleation process in the folding of a domain-swapped dimer
Zhiqiang Yan, Jun Wang, Yujie Zhang, Meng Qin, and Wei Wang
Physical Review E   81, 021910 (2010) (8 pages)   
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Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein
Jocelyne Vreede, Jarek Juraszek, and Peter G. Bolhuis
Proceedings of the National Academy of Sciences of the United States of America   107, 2397-2402 (2010)   
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Interpolation schemes for peptide rearrangements
Marianne S. Bauer, Birgit Strodel, Szilard N. Fejer, Elena F. Koslover, and David J. Wales
The Journal of Chemical Physics   132, 054101 (2010) (9 pages)   
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Experimental evidence for a frustrated energy landscape in a three-helix-bundle protein family
Beth G. Wensley, Sarah Batey, Fleur A. C. Bone, Zheng Ming Chan, Nuala R. Tumelty, Annette Steward, Lee Gyan Kwa, Alessandro Borgia, and Jane Clarke
Nature   463, 685-688 (2010)   
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X-Ray absorption spectroscopy quantitative analysis of biomimetic copper(ii) complexes with tridentate nitrogen ligands mimicking the tris(imidazole) array of protein centres
Elena Borghi and Luigi Casella
Physical Chemistry Chemical Physics   12, 1525-1534 (2010)   
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Helix propensities of conformationally restricted amino acids. Non-natural substitutes for helix breaking proline and helix forming alanine
Miriam Alías, Sara Ayuso-Tejedor, Juan Fernández-Recio, Carlos Cativiela, and Javier Sancho
Organic and Biomolecular Chemistry   8, 788-792 (2010)   
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A new model for mapping the peptide backbone: predicting proton chemical shifts in proteins
José Luis Barneto, Martín Avalos, Reyes Babiano, Pedro Cintas, José Luis Jiménez, and Juan Carlos Palacios
Organic and Biomolecular Chemistry   8, 857-863 (2010)   
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DNA CONFORMATIONAL DYNAMICS

Highly selective separation of DNA fragments using optically directed transport
Avital Braiman, Fedor Rudakov, and Thomas Thundat
Applied Physics Letters   96, 053701 (2010) (3 pages)   
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Analytical method to determine the orientation of rigid spin labels in DNA
Andriy Marko, Dominik Margraf, Pavol Cekan, Snorri Th. Sigurdsson, Olav Schiemann, and Thomas F. Prisner
Physical Review E   81, 021911 (2010) (9 pages)   
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How double-stranded DNA breathing enhances its flexibility and instability on short length scales
O-chul Lee, Jae-Hyung Jeon, and Wokyung Sung
Physical Review E   81, 021906 (2010) (4 pages)   
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How stiff is DNA?
Guohui Zheng, Luke Czapla, A. R. Srinivasan, and Wilma K. Olson
Physical Chemistry Chemical Physics   12, 1399-1406 (2010)   
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Cleavage pattern of DNA caused by endonuclease: Theoretical modeling and experimental verification
Shio Inagaki, Li Liu, Masahiro Takinoue, and Kenichi Yoshikawa
Applied Physics Letters   96, 063701 (2010) (3 pages)   
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Multiple native states reveal persistent ruggedness of an RNA folding landscape
Sergey V. Solomatin, Max Greenfeld, Steven Chu, and Daniel Herschlag
Nature   463, 681-684 (2010)   
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SINGLE MOLECULE DYNAMICS

Formation and dissociation of M₁ muscarinic receptor dimers seen by total internal reflection fluorescence imaging of single molecules
Jonathan A. Hern, Asma H. Baig, Gregory I. Mashanov, Berry Birdsall, John E. T. Corrie, Sebastian Lazareno, Justin E. Molloy, and Nigel J. M. Birdsall
Proceedings of the National Academy of Sciences of the United States of America   107, 2693-2698 (2010)   
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INTERMOLECULAR INTERACTIONS

Parallel tempering Monte Carlo simulations of lysozyme orientation on charged surfaces
Yun Xie, Jian Zhou, and Shaoyi Jiang
The Journal of Chemical Physics   132, 065101 (2010) (8 pages)   
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Laser selective cutting of biological tissues by impulsive heat deposition through ultrafast? vibrational excitations
Kresimir Franjic, Michael L. Cowan, Darren Kraemer, and R. J. Dwayne Miller
Optics Express   17, 22937-22959 (2009)   
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Treecode algorithm for pairwise electrostatic interactions with solvent-solute polarization
Zhenli Xu
Physical Review E   81, 020902 (2010) (4 pages)   
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Site-selective immobilisation of functional enzymes on to polystyrene nanoparticles
Lu Shin Wong, Krzysztof Okrasa, and Jason Micklefield
Organic and Biomolecular Chemistry   8, 782-787 (2010)   
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A simple strategy to realize biomimetic surfaces with controlled anisotropic wetting
Dong Wu, Qi-Dai Chen, Jia Yao, Yong-Chao Guan, Jian-Nan Wang, Li-Gang Niu, Hong-Hua Fang, and Hong-Bo Sun
Applied Physics Letters   96, 053704 (2010) (3 pages)   
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PHYSICAL STUDIES OF CELL MECHANICS

Axon Extension Occurs Independently of Centrosomal Microtubule Nucleation
Michael Stiess, Nicola Maghelli, Lukas C. Kapitein, Susana Gomis-Rth, Michaela Wilsch-Bruninger, Casper C. Hoogenraad, Iva M. Tolić-Nrrelykke, and Frank Bradke
Science   327, 704-707 (2010)   
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PR65, the HEAT-repeat scaffold of phosphatase PP2A, is an elastic connector that links force and catalysis
Alison Grinthal, Ivana Adamovic, Beth Weiner, Martin Karplus, and Nancy Kleckner
Proceedings of the National Academy of Sciences of the United States of America   107, 2467-2472 (2010)   
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Statics and dynamics of the wormlike bundle model
Claus Heussinger, Felix Schüller, and Erwin Frey
Physical Review E   81, 021904 (2010) (15 pages)   
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Origins of Elasticity in Intermediate Filament Networks
Yi-Chia Lin, Norman Y. Yao, Chase P. Broedersz, Harald Herrmann, Fred C. MacKintosh, and David A. Weitz
Physical Review Letters   104, 058101 (2010) (4 pages)   
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Cryo-EM Model of the Bullet-Shaped Vesicular Stomatitis Virus
Peng Ge, Jun Tsao, Stan Schein, Todd J. Green, Ming Luo, and Z. Hong Zhou
Science   327, 689-693 (2010)   
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Survival of the Aligned: Ordering of the Plant Cortical Microtubule Array
Simon H. Tindemans, Rhoda J. Hawkins, and Bela M. Mulder
Physical Review Letters   104, 058103 (2010) (4 pages)   
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INFORMATION TRANSFER IN BIOLOGICAL SYSTEMS

Influence of inhibitory synaptic kinetics on the interaural time difference sensitivity in a linear model of binaural coincidence detection
Christian Leibold
The Journal of the Acoustical Society of America   127, 931-942 (2010)   
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Spatio-temporal correlations can drastically change the response of a MAPK pathway
Koichi Takahashi, Sorin Tănase-Nicola, and Pieter Rein ten Wolde
Proceedings of the National Academy of Sciences of the United States of America   107, 2473-2478 (2010)   
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Nucleation dynamics in two-dimensional cylindrical Ising models and chemotaxis
C. Bosia, M. Caselle, and D. Corá
Physical Review E   81, 021907 (2010) (9 pages)   
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Increased accuracy of ligand sensing by receptor internalization
Gerardo Aquino and Robert G. Endres
Physical Review E   81, 021909 (2010) (9 pages)   
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Evolution of Boolean networks under selection for a robust response to external inputs yields an extensive neutral space
Agnes Szejka and Barbara Drossel
Physical Review E   81, 021908 (2010) (9 pages)   
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MULTICELLULAR PHENOMENA

Arabidopsis synaptotagmin SYTA regulates endocytosis and virus movement protein cell-to-cell transport
Jennifer D. Lewis and Sondra G. Lazarowitz
Proceedings of the National Academy of Sciences of the United States of America   107, 2491-2496 (2010)   
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Coordination of plant cell division and expansion in a simple morphogenetic system
Lionel Dupuy, Jonathan Mackenzie, and Jim Haseloff
Proceedings of the National Academy of Sciences of the United States of America   107, 2711-2716 (2010)   
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Orbital Motion of Spiral Waves in Excitable Media
V. N. Biktashev, D. Barkley, and I. V. Biktasheva
Physical Review Letters   104, 058302 (2010) (4 pages)   
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Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities
Vincent J. Denef, Linda H. Kalnejais, Ryan S. Mueller, Paul Wilmes, Brett J. Baker, Brian C. Thomas, Nathan C. VerBerkmoes, Robert L. Hettich, and Jillian F. Banfield
Proceedings of the National Academy of Sciences of the United States of America   107, 2383-2390 (2010)   
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Linear dielectric response of clustered living cells
Titus Sandu, Daniel Vrinceanu, and Eugen Gheorghiu
Physical Review E   81, 021913 (2010) (11 pages)   
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BIOLOGICAL NETWORKS

Synchronized chaos in networks of simple units
F. Bauer, F. Atay, and J. Jost
Europhysics Letters   89, 20002- (2010)   
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Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana
Insuk Lee, Bindu Ambaru, Pranjali Thakkar, Edward M Marcotte, and Seung Y Rhee
Nature Biotechnology   28, 149-156 (2010)   
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Conversion of graded to binary response in an activator-repressor system
Rajesh Karmakar
Physical Review E   81, 021905 (2010) (7 pages)   
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Better synchronizability in generalized adaptive networks
Jun-Fang Zhu, Ming Zhao, Wenwu Yu, Changsong Zhou, and Bing-Hong Wang
Physical Review E   81, 026201 (2010) (6 pages)   
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Dynamics of coupled adaptive elements: Bursting and intermittent oscillations generated by frustration in networks
Masayo Inoue and Kunihiko Kaneko
Physical Review E   81, 026203 (2010) (14 pages)   
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Amplitude death in nonlinear oscillators with nonlinear coupling
Awadhesh Prasad, Mukeshwar Dhamala, Bhim Mani Adhikari, and Ramakrishna Ramaswamy
Physical Review E   81, 027201 (2010) (4 pages)   
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Correlations and Synchrony in Threshold Neuron Models
Tatjana Tchumatchenko, Aleksey Malyshev, Theo Geisel, Maxim Volgushev, and Fred Wolf
Physical Review Letters   104, 058102 (2010) (4 pages)   
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Depolarization Induced Suppression of Excitation and the Emergence of Ultraslow Rhythms in Neural Networks
J. Hlinka and S. Coombes
Physical Review Letters   104, 068101 (2010) (4 pages)   
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Switch of encoding characteristics in single neurons by subthreshold and suprathreshold stimuli
Toshiaki Omori, Toru Aonishi, and Masato Okada
Physical Review E   81, 021901 (2010) (9 pages)   
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Synthetic design of strong promoters
Michael R. Schlabach, Jimmy K. Hu, Mamie Li, and Stephen J. Elledge
Proceedings of the National Academy of Sciences of the United States of America   107, 2538-2543 (2010)   
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The circadian output gene takeout is regulated by Pdp1
Juliana Benito, Valbona Hoxha, Chamala Lama, Anna A. Lazareva, Jean-François Ferveur, Paul E. Hardin, and Brigitte Dauwalder
Proceedings of the National Academy of Sciences of the United States of America   107, 2544-2549 (2010)   
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Repulsion of Superinfecting Virions: A Mechanism for Rapid Virus Spread
Virginie Doceul, Michael Hollinshead, Lonneke van der Linden, and Geoffrey L. Smith
Science   327, 873-876 (2010)   
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QUANTITATIVE GENOMICS

Hierarchical multifractal representation of symbolic sequences and application to human chromosomes
A. Provata and P. Katsaloulis
Physical Review E   81, 026102 (2010) (8 pages)   
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Drive Against Hotspot Motifs in Primates Implicates the PRDM9 Gene in Meiotic Recombination
Simon Myers, Rory Bowden, Afidalina Tumian, Ronald E. Bontrop, Colin Freeman, Tammie S. MacFie, Gil McVean, and Peter Donnelly
Science   327, 876-879 (2010)   
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Hsp90 prevents phenotypic variation by suppressing the mutagenic activity of transposons
Valeria Specchia, Lucia Piacentini, Patrizia Tritto, Laura Fanti, Rosalba D'Alessandro, Gioacchino Palumbo, Sergio Pimpinelli, and Maria P. Bozzetti
Nature   463, 662-665 (2010)   
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Abundance of Ribosomal RNA Gene Copies Maintains Genome Integrity
Satoru Ide, Takaaki Miyazaki, Hisaji Maki, and Takehiko Kobayashi
Science   327, 693-696 (2010)   
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Prdm9 Controls Activation of Mammalian Recombination Hotspots
Emil D. Parvanov, Petko M. Petkov, and Kenneth Paigen
Science   327, 835 (2010)   
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PRDM9 Is a Major Determinant of Meiotic Recombination Hotspots in Humans and Mice
F. Baudat, J. Buard, C. Grey, A. Fledel-Alon, C. Ober, M. Przeworski, G. Coop, and B. de Massy
Science   327, 836-840 (2010)   
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CANCER PHYSICS

Rescue of paclitaxel sensitivity by repression of Prohibitin1 in drug-resistant cancer cells
Nish Patel, Sabarni K. Chatterjee, Vladimir Vrbanac, Ivy Chung, Chunyao Jenny Mu, Rachelle R. Olsen, Carol Waghorne, and Bruce R. Zetter
Proceedings of the National Academy of Sciences of the United States of America   107, 2503-2508 (2010)   
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HUNK suppresses metastasis of basal type breast cancers by disrupting the interaction between PP2A and cofilin-1
Miguel Quintela-Fandino, Enrico Arpaia, Dirk Brenner, Theo Goh, Faith Au Yeung, Heiko Blaser, Roumiana Alexandrova, Evan F. Lind, Mike W. Tusche, Andrew Wakeham, Pamela S. Ohashi, and Tak W. Mak
Proceedings of the National Academy of Sciences of the United States of America   107, 2622-2627 (2010)   
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Genetic inactivation of AKT1, AKT2, and PDPK1 in human colorectal cancer cells clarifies their roles in tumor growth regulation
Kajsa Ericson, Christine Gan, Ian Cheong, Carlo Rago, Yardena Samuels, Victor E. Velculescu, Kenneth W. Kinzler, David L. Huso, Bert Vogelstein, and Nickolas Papadopoulos
Proceedings of the National Academy of Sciences of the United States of America   107, 2598-2603 (2010)   
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Role of DAB2IP in modulating epithelial-to-mesenchymal transition and prostate cancer metastasis
Daxing Xie, Crystal Gore, Jun Liu, Rey-Chen Pong, Ralph Mason, Guiyang Hao, Michael Long, Wareef Kabbani, Luyang Yu, Haifeng Zhang, Hong Chen, Xiankai Sun, David A. Boothman, Wang Min, and Jer-Tsong Hsieh
Proceedings of the National Academy of Sciences of the United States of America   107, 2485-2490 (2010)   
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EVOLUTION PHYSICS

Evolutionary Dynamics of Complex Networks of HIV Drug-Resistant Strains: The Case of San Francisco
Robert J. Smith?, Justin T. Okano, James S. Kahn, Erin N. Bodine, and Sally Blower
Science   327, 697-701 (2010)   
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Darwinian Evolution of Prions in Cell Culture
Jiali Li, Shawn Browning, Sukhvir P. Mahal, Anja M. Oelschlegel, and Charles Weissmann
Science   327, 869-872 (2010)   
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Fairness emergence from zero-intelligence agents
Wen-Qi Duan and H. Eugene Stanley
Physical Review E   81, 026104 (2010) (6 pages)   
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STATISTICAL AND NONLINEAR PHYSICS

Experimental evidence of strong anomalous diffusion in living cells
Naama Gal and Daphne Weihs
Physical Review E   81, 020903 (2010) (4 pages)   
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Biased motion and molecular motor properties of bipedal spiders
Laleh Samii, Heiner Linke, Martin J. Zuckermann, and Nancy R. Forde
Physical Review E   81, 021106 (2010) (11 pages)   
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Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories
John S. Perkyns, Gillian C. Lynch, Jesse J. Howard, and B. Montgomery Pettitt
The Journal of Chemical Physics   132, 064106 (2010) (13 pages)   
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AQUASOL: An efficient solver for the dipolar Poisson–Boltzmann–Langevin equation
Patrice Koehl and Marc Delarue
The Journal of Chemical Physics   132, 064101 (2010) (16 pages)   
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Fractional Brownian motion and motion governed by the fractional Langevin equation in confined geometries
Jae-Hyung Jeon and Ralf Metzler
Physical Review E   81, 021103 (2010) (11 pages)   
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Effects of Interparticle Attractions on Colloidal Sedimentation
A. Moncho-Jordá, A. A. Louis, and J. T. Padding
Physical Review Letters   104, 068301 (2010) (4 pages)   
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Fluctuation-Induced Interaction between Randomly Charged Dielectrics
Ali Naji, David S. Dean, Jalal Sarabadani, Ron R. Horgan, and Rudolf Podgornik
Physical Review Letters   104, 060601 (2010) (4 pages)   
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Extinction of metastable stochastic populations
Michael Assaf and Baruch Meerson
Physical Review E   81, 021116 (2010) (18 pages)   
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Erratum: Dissipative stochastic mechanics for capturing neuronal dynamics under the influence of ion channel noise: Formalism using a special membrane [Phys. Rev. E 76, 041918 (2007)]
Marifi Güler
Physical Review E   81, 029902 (2010) (1 page)   
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Implicitly causality enforced solution of multidimensional transient photon transport equation
Chintha C. Handapangoda and Malin Premaratne
Optics Express   17, 23423-23442 (2009)   
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INSTRUMENTATION DEVELOPMENT

Design considerations for surface plasmon resonance based detection of human blood group in near infrared
Anuj K. Sharma, Rajan Jha, and Himansu S. Pattanaik
Journal of Applied Physics   107, 034701 (2010) (7 pages)   
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Charge pumping technique to analyze the effect of intrinsically retained charges and extrinsically trapped charges in biomolecules by use of a nanogap embedded biotransistor
Sungho Kim, Jae-Hyuk Ahn, Tae Jung Park, Sang Yup Lee, and Yang-Kyu Choi
Applied Physics Letters   96, 053702 (2010) (3 pages)   
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Enhanced photoacoustic stability of gold nanorods by silica matrix confinement
Leng-Chun Chen, Chen-Wei Wei, Jeffrey S. Souris, Shih-Hsun Cheng, Chin-Tu Chen, Chung-Shi Yang, Pai-Chi Li, and Leu-Wei Lo
Journal of Biomedical Optics   15, 016010 (2010) (6 pages)   
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Infrared differential-absorption Mueller matrix spectroscopy and neural network-based data fusion for biological aerosol standoff detection
Arthur H. Carrieri, Jack Copper, David J. Owens, Erik S. Roese, Jerold R. Bottiger, Robert D. Everly, II, and Kevin C. Hung
Applied Optics   49, 382-393 (2010)   
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Scanning protocols dedicated to smart velocity ranging in Spectral OCT
Ireneusz Grulkowski, Iwona Gorczynska, Maciej Szkulmowski, Daniel Szlag, Anna Szkulmowska, Rainer A. Leitgeb, Andrzej Kowalczyk, and Maciej Wojtkowski
Optics Express   17, 23736-23754 (2009)   
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Limiting factors to the OCT axial resolution?for in-vivo imaging of human and rodent retina in the 1060nm wavelength range
Sepideh Hariri, Alireza A. Moayed, Aphrodite Dracopolos, Chulho Hyun, Shelley Boyd, and Kostadinka Bizheva
Optics Express   17, 24304-24316 (2009)   
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Worm chips: Microtools for C. elegans biology
Nikos Chronis
Lab on a Chip   10, 432-437 (2009)   
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Optical monitoring of oxygen tension in cortical microvessels with confocal microscopy
Mohammad A. Yaseen, Vivek J. Srinivasan, Sava Sakadžić, Weicheng Wu, Svetlana Ruvinskaya, Sergei A. Vinogradov, and David A. Boas
Optics Express   17, 22341-22350 (2009)   
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Noninvasive monitoring of tissue hemoglobin using UV-VIS diffuse reflectance spectroscopy: a pilot study
Janelle E. Bender, Allan B. Shang, Eugene W. Moretti, Bing Yu, Lisa M. Richards, and Nirmala Ramanujam
Optics Express   17, 23396-23409 (2009)   
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Ultrasound characterization of red blood cell aggregation with intervening attenuating tissue-mimicking phantoms
Emilie Franceschini, François T. H. Yu, François Destrempes, and Guy Cloutier
The Journal of the Acoustical Society of America   127, 1104-1115 (2010)   
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An optical imaging method to monitor stem cell migration in a model of immune-mediated arthritis
Elizabeth J. Sutton, Sophie E. Boddington, Alexander J. Nedopil, Tobias D. Henning, Stavros G. Demos, Rick Baehner, Barbara Sennino, Ying Lu, and Heike E. Daldrup-Link
Optics Express   17, 24403-24413 (2009)   
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Optical fiber laser induced fluorescence spectroscopy as a citrus canker diagnostic
E. C. Lins, J. Belasque, Jr., and L. G. Marcassa
Applied Optics   49, 663-667 (2010)   
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In vivo real-time recording of UV-induced changes in the autofluorescence of a melanin-containing fungus using a micro-spectrofluorimeter and a low-cost webcam
V. Raimondi, G. Agati, G. Cecchi, I. Gomoiu, D. Lognoli, and L. Palombi
Optics Express   17, 22735-22746 (2009)   
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A mesh-free approach to acoustic scattering from multiple spheres nested inside a large sphere by using diagonal translation operators
Andrew J. Hesford, Jeffrey P. Astheimer, Leslie F. Greengard, and Robert C. Waag
The Journal of the Acoustical Society of America   127, 850-861 (2010)   
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Biological signal monitor device
Yoshinobu Watanabe
The Journal of the Acoustical Society of America   127, 1180 (2010)   
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Design and validation of a clinical instrument for spectral diagnosis of cutaneous malignancy
Narasimhan Rajaram, Timothy J. Aramil, Kelvin Lee, Jason S. Reichenberg, Tri H. Nguyen, and James W. Tunnell
Applied Optics   49, 142-152 (2010)   
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Noise and stray light characterization of a compact CCD spectrophotometer used in biomedical applications
George Zonios
Applied Optics   49, 163-169 (2010)   
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Optical design of a variable view imaging system with the combination of a telecentric scanner and double wedge prisms
Xiaodong Tao, Hyungsuck Cho, and Farrokh Janabi-Sharifi
Applied Optics   49, 239-246 (2010)   
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Dual-mode operation of flexible piezoelectric polymer diaphragm for intracranial pressure measurement
Chunyan Li, Pei-Ming Wu, Lori A. Shutter, and Raj K. Narayan
Applied Physics Letters   96, 053502 (2010) (3 pages)   
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A contour-mode film bulk acoustic resonator of high quality factor in a liquid environment for biosensing applications
Wencheng Xu, Seokheun Choi, and Junseok Chae
Applied Physics Letters   96, 053703 (2010) (3 pages)   
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Enhancement of biosensing performance in a droplet-based bioreactor by in situ microstreaming
Olivier Ducloux, Elisabeth Galopin, Farzam Zoueshtiagh, Alain Merlen, and Vincent Thomy
Biomicrofluidics   4, 011102 (2010) (5 pages)   
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Numerical investigation of flow-through immunoassay in a microchannel
A Sinha, R Ganguly, and I K. Puri
Journal of Applied Physics   107, 034907 (2010) (6 pages)   
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Application of intravital microscopy in studies of tumor microcirculation
Sarah Jane Lunt, Colin Gray, Constantino Carlos Reyes-Aldasoro, Stephen J. Matcher, and Gillian M. Tozer
Journal of Biomedical Optics   15, 011113 (2010) (14 pages)   
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Advanced statistical techniques applied to comprehensive FTIR spectra on human colonic tissues
A. Zwielly, S. Mordechai, I. Sinielnikov, A. Salman, E. Bogomolny, and S. Argov
Medical Physics   37, 1047-1055 (2010)   
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Analysis of fast full angle fluorescence diffuse optical tomography with beam-forming illumination
Daifa Wang, Xin Liu, and Jing Bai
Optics Express   17, 21376-21395 (2009)   
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Multispectral optoacoustic tomography (MSOT) scanner for whole-body small animal imaging
Rui Ma, Adrian Taruttis, Vasilis Ntziachristos, and Daniel Razansky
Optics Express   17, 21414-21426 (2009)   
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Retinal imaging with polarization-sensitive optical coherence tomography and adaptive optics
Barry Cense, Weihua Gao, Jeffrey M. Brown, Steven M. Jones, Ravi S. Jonnal, Mircea Mujat, B. Hyle Park, Johannes F. de Boer, and Donald T. Miller
Optics Express   17, 21634-21651 (2009)   
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Adaptive improved element free Galerkin method for quasi- or multi-spectral bioluminescence tomography
Chenghu Qin, Jie Tian, Xin Yang, Jinchao Feng, Kai Liu, Junting Liu, Guorui Yan, Shouping Zhu, and Min Xu
Optics Express   17, 21925-21934 (2009)   
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High throughput transmission optical projection tomography using low cost graphics processing unit
Claudio Vinegoni, Lyuba Fexon, Paolo Fumene Feruglio, Misha Pivovarov, Jose-Luiz Figueiredo, Matthias Nahrendorf, Antonio Pozzo, Andrea Sbarbati, and Ralph Weissleder
Optics Express   17, 22320-22332 (2009)   
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Design of a high-sensor count fibre optic manometry catheter for in-vivo colonic diagnostics
John W. Arkwright, Ian D. Underhill, Simon A. Maunder, Neil Blenman, Michal M. Szczesniak, Lukasz Wiklendt, Ian J. Cook, David Z. Lubowski, and Phil G. Dinning
Optics Express   17, 22423-22431 (2009)   
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Polarization maintaining fiber based ultra-high resolution spectral domain polarization sensitive optical coherence tomography
Erich Götzinger, Bernhard Baumann, Michael Pircher, and Christoph K. Hitzenberger
Optics Express   17, 22704-22717 (2009)   
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Design and optimization of a novel surface plasmon resonance biosensor based on Otto configuration
E. K. Akowuah, T. Gorman, and S. Haxha
Optics Express   17, 23511-23521 (2009)   
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Intra-retinal layer segmentation in optical coherence tomography images
Akshaya Mishra, Alexander Wong, Kostadinka Bizheva, and David A. Clausi
Optics Express   17, 23719-23728 (2009)   
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Dynamic micro-bead arrays using optical tweezers combined with intelligent control techniques
Yoshio Tanaka, Hiroyuki Kawada, Shogo Tsutsui, Mitsuru Ishikawa, and Hiroyuki Kitajima
Optics Express   17, 24102-24111 (2009)   
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Spectroscopic measurements with dispersion encoded full range frequency domain optical coherence tomography in single- and multilayered non- scattering phantoms
Boris Hermann, Bernd Hofer, Christoph Meier, and Wolfgang Drexler
Optics Express   17, 24162-24174 (2009)   
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Bio-Nano ECRIS: An electron cyclotron resonance ion source for new materials production
T. Uchida, H. Minezaki, K. Tanaka, M. Muramatsu, T. Asaji, Y. Kato, A. Kitagawa, S. Biri, and Y. Yoshida
Review of Scientific Instruments   81, 02A306 (2010) (3 pages)   
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Progress in ion source injector development at the ion beam therapy center (Heidelberg Ion Beam Therapy Center)
T. Winkelmann, R. Cee, T. Haberer, B. Naas, and A. Peters
Review of Scientific Instruments   81, 02A311 (2010) (3 pages)   
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Quantitative test for sensory hand symptoms based on mechanoreceptor-specific vibrotactile thresholds
Anthony J. Brammer, Paivi Sutinen, Sourish Das, Ilmari Pyykkö, Esko Toppila, and Jukka Starck
The Journal of the Acoustical Society of America   127, 1146-1155 (2010)   
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Surface-enhanced plasmon resonance detection of nanoparticle-conjugated DNA hybridization
Seyoung Moon, Dong Jun Kim, Kyujung Kim, Donghyun Kim, Hosub Lee, Kangtaek Lee, and Seungjoo Haam
Applied Optics   49, 484-491 (2010)   
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Relative capacities of time-gated versus continuous-wave imaging to localize tissue embedded vessels with increasing depth
Nimit L. Patel, Zi-Jing Lin, Yajuvendra Rathore, Edward H. Livingston, Hanli Liu, and George Alexandrakis
Journal of Biomedical Optics   15, 016015 (2010) (9 pages)   
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Lipid-modified conjugated polymer nanoparticles for cell imaging and transfection
Xuli Feng, Yanli Tang, Xinrui Duan, Libing Liu, and Shu Wang
Journal of Materials Chemistry   20, 1312-1316 (2010)   
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The extraction of liquid, protein molecules and yeast cells from paper through surface acoustic wave atomization
Aisha Qi, Leslie Yeo, James Friend, and Jenny Ho
Lab on a Chip   10, 470-476 (2009)   
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A microchip fabricated with a vapor-diffusion self-assembled-monolayer method to transport droplets across superhydrophobic to hydrophilic surfaces
Yu-Hsuan Lai, Jing-Tang Yang, and Dar-Bin Shieh
Lab on a Chip   10, 499-504 (2009)   
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Microfluidic isolation and transcriptome analysis of serum microvesicles
Chihchen Chen, Johan Skog, Chia-Hsien Hsu, Ryan T. Lessard, Leonora Balaj, Thomas Wurdinger, Bob S. Carter, Xandra O. Breakefield, Mehmet Toner, and Daniel Irimia
Lab on a Chip   10, 505-511 (2009)   
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In vivo dynamic optical coherence elastography using a ring actuator
Brendan F. Kennedy, Timothy R. Hillman, Robert A. McLaughlin, Bryden C. Quirk, and David D. Sampson
Optics Express   17, 21762-21772 (2009)   
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Combined photoacoustic and ultrasound biomicroscopy
Tyler Harrison, Janaka C. Ranasinghesagara, Huihong Lu, Kory Mathewson, Andrew Walsh, and Roger J. Zemp
Optics Express   17, 22041-22046 (2009)   
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Measuring directionality of the retinal reflection with a Shack-Hartmann wavefront sensor
Weihua Gao, Ravi S. Jonnal, Barry Cense, Omer P. Kocaoglu, Qiang Wang, and Donald T. Miller
Optics Express   17, 23085-23097 (2009)   
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Facile fabrication and biological application of tin-rich indium tin oxide nanorods
Nitin Kumar, Omkar Parajuli, Man Feng, Jian Xu, and Jong-in Hahm
Applied Physics Letters   96, 053705 (2010) (3 pages)   
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Enhanced photothermal therapy assisted with gold nanorods using a radially polarized beam
Hong Kang, Baohua Jia, Jingliang Li, Dru Morrish, and Min Gu
Applied Physics Letters   96, 063702 (2010) (3 pages)   
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