Virtual Journal of Biological Physics Research -- April 15, 2012

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REVIEW ARTICLES

Integrating Genomes
D. R. Zerbino, B. Paten, and D. Haussler
Science   336, 179-182 (2012)   
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Using Gene Expression Noise to Understand Gene Regulation
Brian Munsky, Gregor Neuert, and Alexander van Oudenaarden
Science   336, 183-187 (2012)   
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Cell Polarity: Quantitative Modeling as a Tool in Cell Biology
Alex Mogilner, Jun Allard, and Roy Wollman
Science   336, 175-179 (2012)   
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Computational Approaches to Developmental Patterning
Luis G. Morelli, Koichiro Uriu, Sal Ares, and Andrew C. Oates
Science   336, 187-191 (2012)   
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Emerging fungal threats to animal, plant and ecosystem health
Matthew C. Fisher, Daniel. A. Henk, Cheryl J. Briggs, John S. Brownstein, Lawrence C. Madoff, Sarah L. McCraw, and Sarah J. Gurr
Nature   484, 186-194 (2012)   
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QUANTUM MECHANICAL DYNAMICS

Fluorescent nanohybrids: quantum dots coupled to polymer recombinant protein conjugates for the recognition of biological hazards
Herman Sander Mansur and Alexandra Ancelmo Piscitelli Mansur
Journal of Materials Chemistry   22, 9006-9018 (2012)   
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A combined quantum mechanics/molecular mechanics study of the one- and two-photon absorption in the green fluorescent protein
Arnfinn Hykkerud Steindal, Jógvan Magnus Haugaard Olsen, Kenneth Ruud, Luca Frediani, and Jacob Kongsted
Physical Chemistry Chemical Physics   14, 5440-5451 (2012)   
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Modeling and computations of the intramolecular electron transfer process in the two-heme protein cytochrome c₄
Renat R. Nazmutdinov, Michael D. Bronshtein, Tamara T. Zinkicheva, Qijin Chi, Jingdong Zhang, and Jens Ulstrup
Physical Chemistry Chemical Physics   14, 5953-5965 (2012)   
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Quantum limits for the magnetic sensitivity of a chemical compass
Jianming Cai, Filippo Caruso, and Martin B. Plenio
Physical Review A   85, 040304 (2012) (5 pages)   
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Quantum dynamics in continuum for proton transport—Generalized correlation
Duan Chen and Guo-Wei Wei
The Journal of Chemical Physics   136, 134109 (2012) (16 pages)   
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Quantum effects in biological electron transfer
Aurélien de la Lande, Nathan S. Babcock, Jan Řezáč, Bernard Lévy, Barry C. Sanders, and Dennis R. Salahub
Physical Chemistry Chemical Physics   14, 5902-5918 (2012)   
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Effects of DNA nucleotide adsorption on the conductance of graphene nanoribbons from first principles
Eun-Cheol Lee
Applied Physics Letters   100, 153117 (2012) (4 pages)   
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Coherent cavity networks with complete connectivity
Elica Kyoseva, Almut Beige, and Leong Kwek
New Journal of Physics   14, 23023- (2012)   
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A resonance mechanism of efficient energy transfer mediated by Fenna-Matthews-Olson complex
Robert Alicki and Wiesaw Miklaszewski
The Journal of Chemical Physics   136, 134103 (2012) (5 pages)   
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PHYSICS OF WATER AND HYDROGEN-BONDED SOLVENTS

X-ray emission from pure and dilute H₂O and D₂O in a liquid microjet: Hydrogen bonds and nuclear dynamics
Kathrin M. Lange, Mikhail Soldatov, Ronny Golnak, Malte Gotz, Nicholas Engel, René Könnecke, Jan-Erik Rubensson, and Emad F. Aziz
Physical Review B   85, 155104 (2012) (6 pages)   
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Ion exclusion and electrokinetic effects resulting from electro-osmotic flow of salt solutions in charged silica nanopores
Neil R. Haria and Christian D. Lorenz
Physical Chemistry Chemical Physics   14, 5935-5944 (2012)   
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Exploring the inter-molecular interactions in amyloid- protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations
Fu-Feng Liu, Zhen Liu, Shu Bai, Xiao-Yan Dong, and Yan Sun
The Journal of Chemical Physics   136, 145101 (2012) (8 pages)   
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Strength of hydrogen bonds of water depends on local environment
Matej Huš and Tomaz Urbic
The Journal of Chemical Physics   136, 144305 (2012) (7 pages)   
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Structured water in polyelectrolyte dendrimers: Understanding small angle neutron scattering results through atomistic simulation
Bin Wu, Boutheïna Kerkeni, Takeshi Egami, Changwoo Do, Yun Liu, Yongmei Wang, Lionel Porcar, Kunlun Hong, Sean C. Smith, Emily L. Liu, Gregory S. Smith, and Wei-Ren Chen
The Journal of Chemical Physics   136, 144901 (2012) (9 pages)   
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Monoacylglycerols as transmembrane Cl^- anion transporters
Soheila Bahmanjah, Ning Zhang, and Jeffery T. Davis
Chemical Communications   48, 4432-4434 (2012)   
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Structural destabilization of chignolin under the influence of oscillating electric fields
Loukas G. Astrakas, Christos Gousias, and Margaret Tzaphlidou
Journal of Applied Physics   111, 074702 (2012) (8 pages)   
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Self-assembling PVA-F127 thermosensitive nanocarriers with highly sensitive magnetically-triggered drug release for epilepsy therapy in vivo
Hsin-Yang Huang, Shang-Hsiu Hu, Chih-Shang Chian, San-Yuan Chen, Hsin-Yi Lai, and You-Yin Chen
Journal of Materials Chemistry   22, 8566-8573 (2012)   
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Structural basis of ultraviolet-B perception by UVR8
Di Wu, Qi Hu, Zhen Yan, Wen Chen, Chuangye Yan, Xi Huang, Jing Zhang, Panyu Yang, Haiteng Deng, Jiawei Wang, XingWang Deng, and Yigong Shi
Nature   484, 214-219 (2012)   
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Chemistry in solution: recent techniques and applications using soft X-ray spectroscopy
Kathrin M. Lange, Alexander Kothe, and Emad F. Aziz
Physical Chemistry Chemical Physics   14, 5331-5338 (2012)   
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Vibrations and hydrogen bonding in porphycene
Sylwester Gawinkowski, ukasz Walewski, Alexander Vdovin, Alkwin Slenczka, Stephane Rols, Mark R. Johnson, Bogdan Lesyng, and Jacek Waluk
Physical Chemistry Chemical Physics   14, 5489-5503 (2012)   
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The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
Anna Kuffel and Jan Zielkiewicz
Physical Chemistry Chemical Physics   14, 5561-5569 (2012)   
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Energetics of ligand binding to the DNA minor groove
Viktor V. Kostjukov, Adrian A. Hernandez Santiago, Fernando Rojas Rodriguez, Salvador Rosas Castilla, John A. Parkinson, and Maxim P. Evstigneev
Physical Chemistry Chemical Physics   14, 5588-5600 (2012)   
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Detailed insight into the hydrogen bonding interactions in acetone–methanol mixtures. A molecular dynamics simulation and Voronoi polyhedra analysis study
Abdenacer Idrissi, Kamil Polok, W. Gadomski, Ivan Vyalov, Alexander Agapov, M. Kiselev, Mohamed Barj, and Pál Jedlovszky
Physical Chemistry Chemical Physics   14, 5979-5987 (2012)   
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Internal nonlinear dynamics of a short lattice DNA model in terms of propagating kink-antikink solitons
M. Vanitha and M. Daniel
Physical Review E   85, 041911 (2012) (12 pages)   
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Response of polymer molecules embedded in a nanodroplet to collisions with a wall
Si Neng Sun and Herbert M. Urbassek
Soft Matter   8, 4707-4715 (2012)   
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A simulation study of the self-assembly of coarse-grained skin lipids
K. R. Hadley and C. McCabe
Soft Matter   8, 4802-4814 (2012)   
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A comparison of the value of viscosity for several water models using Poiseuille flow in a nano-channel
A. P. Markesteijn, Remco Hartkamp, S. Luding, and J. Westerweel
The Journal of Chemical Physics   136, 134104 (2012) (8 pages)   
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Variational calculation of quantum mechanical/molecular mechanical free energy with electronic polarization of solvent
Hiroshi Nakano and Takeshi Yamamoto
The Journal of Chemical Physics   136, 134107 (2012) (17 pages)   
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First-principles calculation of thermodynamic stability of acids and bases under pH environment: A microscopic pH theory
Yong-Hyun Kim, Kwiseon Kim, and S. B. Zhang
The Journal of Chemical Physics   136, 134112 (2012) (4 pages)   
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A phenomenological approach to modeling chemical dynamics in nonlinear and two-dimensional spectroscopy
Krupa Ramasesha, Luigi De Marco, Andrew D. Horning, Aritra Mandal, and Andrei Tokmakoff
The Journal of Chemical Physics   136, 134507 (2012) (11 pages)   
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Solvent effect on the folding dynamics and structure of E6-associated protein characterized from ab initio protein folding simulations
Zhijun Xu, Raudah Lazim, Tiedong Sun, Ye Mei, and Dawei Zhang
The Journal of Chemical Physics   136, 135102 (2012) (6 pages)   
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Coupled-monomers in molecular assemblies: Theory and application to the water tetramer, pentamer, and ring hexamer
Yimin Wang and Joel M. Bowman
The Journal of Chemical Physics   136, 144113 (2012) (9 pages)   
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Auger spectrum of a water molecule after single and double core ionization
L. Inhester, C. F. Burmeister, G. Groenhof, and H. Grubmüller
The Journal of Chemical Physics   136, 144304 (2012) (12 pages)   
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An orbital and electron density analysis of weak interactions in ethanol-water, methanol-water, ethanol and methanol small clusters
Sol M. Mejía, Elizabeth Flórez, and Fanor Mondragón
The Journal of Chemical Physics   136, 144306 (2012) (8 pages)   
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Nuclear dynamics and spectator effects in resonant inelastic soft x-ray scattering of gas-phase water molecules
Lothar Weinhardt, Andreas Benkert, Frank Meyer, Monika Blum, Regan G. Wilks, Wanli Yang, Marcus Bär, Friedrich Reinert, and Clemens Heske
The Journal of Chemical Physics   136, 144311 (2012) (6 pages)   
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MEMBRANE BIOPHYSICS

Chemical and biological decontamination functions of nanofibrous membranes
Jing Zhu, Qazaleh Bahramian, Philip Gibson, Heidi Schreuder-Gibson, and Gang Sun
Journal of Materials Chemistry   22, 8532-8540 (2012)   
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Structure of components of an intercellular channel complex in sporulating Bacillus subtilis
Vladimir M. Levdikov, Elena V. Blagova, Amanda McFeat, Mark J. Fogg, Keith S. Wilson, and Anthony J. Wilkinson
Proceedings of the National Academy of Sciences of the United States of America   109, 5441-5445 (2012)   
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Self-assembled architectures with multiple aqueous compartments
Hans-Peter M. de Hoog, Madhavan Nallani, and Nikodem Tomczak
Soft Matter   8, 4551-4560 (2012)   
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Texture defects in lipid membrane domains
Jes Dreier, Jonathan Brewer, and Adam Cohen Simonsen
Soft Matter   8, 4894-4904 (2012)   
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Slow growth of the Rayleigh-Plateau instability in aqueous two phase systems
Sam D. Geschiere, Iwona Ziemecka, Volkert van Steijn, Ger J. M. Koper, Jan H. van Esch, and Michiel T. Kreutzer
Biomicrofluidics   6, 022007 (2012) (11 pages)   
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High pressure effect on phase transition behavior of lipid bilayers
Kan Lai, Biao Wang, Yong Zhang, and Yongwei Zhang
Physical Chemistry Chemical Physics   14, 5744-5752 (2012)   
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TWIK1, a unique background channel with variable ion selectivity
Franck C. Chatelain, Delphine Bichet, Dominique Douguet, Sylvain Feliciangeli, Saïd Bendahhou, Markus Reichold, Richard Warth, Jacques Barhanin, and Florian Lesage
Proceedings of the National Academy of Sciences of the United States of America   109, 5499-5504 (2012)   
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X-Ray propagation imaging of a lipid bilayer in solution
André Beerlink, Shashi Thutupalli, Michael Mell, Matthias Bartels, Peter Cloetens, Stephan Herminghaus, and Tim Salditt
Soft Matter   8, 4594-4600 (2012)   
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Effect of channel mutations on the uptake and release of the retinal ligand in opsin
Ronny Piechnick, Eglof Ritter, Peter W. Hildebrand, Oliver P. Ernst, Patrick Scheerer, Klaus Peter Hofmann, and Martin Heck
Proceedings of the National Academy of Sciences of the United States of America   109, 5247-5252 (2012)   
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Mechanism of Voltage Gating in Potassium Channels
Morten . Jensen, Vishwanath Jogini, David W. Borhani, Abba E. Leffler, Ron O. Dror, and David E. Shaw
Science   336, 229-233 (2012)   
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FUNDAMENTAL POLYMER STATICS/DYNAMICS

MichaelisMenten dynamics of a polymer chain out of a dichotomous ATP-based motor
Alessandro Fiasconaro, Juan Mazo, and Fernando Falo
New Journal of Physics   14, 23004- (2012)   
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High-pressure effect on the dynamics of solvated peptides
Ricky B. Nellas, Mary M. Glover, Donald Hamelberg, and Tongye Shen
The Journal of Chemical Physics   136, 145103 (2012) (9 pages)   
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Folding kinetics of a polymer
Štěpán Žička, David Quigley, and Michael P. Allen
Physical Chemistry Chemical Physics   14, 6044-6053 (2012)   
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A highly coarse-grained model to simulate entangled polymer melts
You-Liang Zhu, Hong Liu, and Zhong-Yuan Lu
The Journal of Chemical Physics   136, 144903 (2012) (7 pages)   
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Correlations between mechanical, structural, and dynamical properties of polymer nanocomposites
Aki Kutvonen, Giulia Rossi, and Tapio Ala-Nissila
Physical Review E   85, 041803 (2012) (6 pages)   
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Effective interactions between grafted nanoparticles in a polymer matrix
Dong Meng, Sanat K. Kumar, J. Matthew D. Lane, and Gary S. Grest
Soft Matter   8, 5002-5010 (2012)   
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Computer simulation of linkage of two ring chains
Zhimin Xiong, Charles C. Han, and Qi Liao
The Journal of Chemical Physics   136, 134902 (2012) (9 pages)   
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Forced translocation of a polymer: Dynamical scaling versus molecular dynamics simulation
J. L. A. Dubbeldam, V. G. Rostiashvili, A. Milchev, and T. A. Vilgis
Physical Review E   85, 041801 (2012) (12 pages)   
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Lattice stretching bistability and dynamic heterogeneity
P. L. Christiansen, A. V. Savin, and A. V. Zolotaryuk
Physical Review E   85, 046601 (2012) (11 pages)   
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Nucleation of colloids and macromolecules: Does the nucleation pathway matter?
James F. Lutsko
The Journal of Chemical Physics   136, 134502 (2012) (7 pages)   
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Sheet-like assemblies of spherical particles with point-symmetrical patches
Ethayaraja Mani, Eduardo Sanz, Soumyajit Roy, Marjolein Dijkstra, Jan Groenewold, and Willem K. Kegel
The Journal of Chemical Physics   136, 144706 (2012) (5 pages)   
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Biopolymer elasticity: Mechanics and thermal fluctuations
Supurna Sinha and Joseph Samuel
Physical Review E   85, 041802 (2012) (11 pages)   
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PROTEIN CONFORMATIONAL DYNAMICS/FOLDING

Formation of embryoid bodies using dielectrophoresis
Sneha Agarwal, Anil Sebastian, Lesley M. Forrester, and Gerard H. Markx
Biomicrofluidics   6, 024101 (2012) (11 pages)   
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Locating binding poses in protein-ligand systems using reconnaissance metadynamics
Pär Söderhjelm, Gareth A. Tribello, and Michele Parrinello
Proceedings of the National Academy of Sciences of the United States of America   109, 5170-5175 (2012)   
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Using sketch-map coordinates to analyze and bias molecular dynamics simulations
Gareth A. Tribello, Michele Ceriotti, and Michele Parrinello
Proceedings of the National Academy of Sciences of the United States of America   109, 5196-5201 (2012)   
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Direct observation of multiple misfolding pathways in a single prion protein molecule
Hao Yu, Xia Liu, Krishna Neupane, Amar Nath Gupta, Angela M. Brigley, Allison Solanki, Iveta Sosova, and Michael T. Woodside
Proceedings of the National Academy of Sciences of the United States of America   109, 5283-5288 (2012)   
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Riboswitch control of Rho-dependent transcription termination
Kerry Hollands, Sergey Proshkin, Svetlana Sklyarova, Vitaly Epshtein, Alexander Mironov, Evgeny Nudler, and Eduardo A. Groisman
Proceedings of the National Academy of Sciences of the United States of America   109, 5376-5381 (2012)   
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Structure of the basal components of a bacterial transporter
Jeffrey Meisner, Tatsuya Maehigashi, Ingemar André, Christine M. Dunham, and Charles P. Moran
Proceedings of the National Academy of Sciences of the United States of America   109, 5446-5451 (2012)   
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Fast relaxation and elasticity-related properties of trehalose-glycerol mixtures
Devin Averett, Marcus T. Cicerone, Jack F. Douglas, and Juan J. de Pablo
Soft Matter   8, 4936-4945 (2012)   
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Theory of binless multi-state free energy estimation with applications to protein-ligand binding
Zhiqiang Tan, Emilio Gallicchio, Mauro Lapelosa, and Ronald M. Levy
The Journal of Chemical Physics   136, 144102 (2012) (14 pages)   
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DNA CONFORMATIONAL DYNAMICS

The geometrical origin of the strain-twist coupling in double helices
Kasper Olsen and Jakob Bohr
AIP Advances   1, 012108 (2011) (7 pages)   
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An effective model of DNA like helicoidal structure: with length fluctuation nonlinearity
Y. M. Tseytlin
AIP Advances   1, 012116 (2011) (6 pages)   
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Automated forward and reverse ratcheting of DNA in a nanopore at 5- precision
Gerald M Cherf, Kate R Lieberman, Hytham Rashid, Christopher E Lam, Kevin Karplus, and Mark Akeson
Nature Biotechnology   30, 344-348 (2012)   
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Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase
Elizabeth A Manrao, Ian M Derrington, Andrew H Laszlo, Kyle W Langford, Matthew K Hopper, Nathaniel Gillgren, Mikhail Pavlenok, Michael Niederweis, and Jens H Gundlach
Nature Biotechnology   30, 349-353 (2012)   
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DNA with amphiphilic counterions: tuning colloidal DNA with cyclodextrin
Azat Bilalov, Jonas Carlstedt, Elena Krivtsova, Björn Lindman, and Ulf Olsson
Soft Matter   8, 4988-4994 (2012)   
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SINGLE MOLECULE DYNAMICS

Event distributions of polymer translocation
R. P. Linna and K. Kaski
Physical Review E   85, 041910 (2012) (7 pages)   
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Two independent switches regulate cytoplasmic dynein's processivity and directionality
Wilhelm J. Walter, Michael P. Koonce, Bernhard Brenner, and Walter Steffen
Proceedings of the National Academy of Sciences of the United States of America   109, 5289-5293 (2012)   
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INTERMOLECULAR INTERACTIONS

Polarization switching and patterning in self-assembled peptide tubular structures
Igor Bdikin, Vladimir Bystrov, Ivonne Delgadillo, José Gracio, Svitlana Kopyl, Maciej Wojtas, Elena Mishina, Alexander Sigov, and Andrei L. Kholkin
Journal of Applied Physics   111, 074104 (2012) (7 pages)   
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Glycoconjugate-functionalized carbon nanotubes in biomedicine
Narasimha Murthy Bandaru and Nicolas Hans Voelcker
Journal of Materials Chemistry   22, 8748-8758 (2012)   
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Surface adhered poly(vinyl alcohol) physical hydrogels as tools for rational design of intelligent biointerfaces
Bettina E. B. Jensen, Marie-Helene Alves, Betina Fejerskov, Brigitte Städler, and Alexander N. Zelikin
Soft Matter   8, 4624-4633 (2012)   
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Influence of adsorbed polyelectrolytes on pore size distribution of a water-swollen biomaterial
Niko Aarne, Eero Kontturi, and Janne Laine
Soft Matter   8, 4739-4748 (2012)   
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Mastered proteolysis of gelatin gel can control delivery kinetics of entrapped large molecules
Marie-Cécile Klak, Julien Picard, Sébastien Giraudier, and Véronique Larreta-Garde
Soft Matter   8, 4749-4754 (2012)   
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Well-defined hydroxyapatite–polycation nanohybrids via surface-initiated atom transfer radical polymerization for biomedical applications
Q. Cai, Y. Zhu, J. Q. He, Z. H. Wang, Fabing Su, F. J. Xu, X. P. Yang, and W. T. Yang
Journal of Materials Chemistry   22, 9358-9367 (2012)   
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Self-assembly mechanisms of silk protein nanostructures on two-dimensional surfaces
Nicholas E. Kurland, Joydip Kundu, Shilpa Pal, Subhas C. Kundu, and Vamsi K. Yadavalli
Soft Matter   8, 4952-4959 (2012)   
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PHYSICAL STUDIES OF CELL MECHANICS

Tensegrity and motor-driven effective interactions in a model cytoskeleton
Shenshen Wang and Peter G. Wolynes
The Journal of Chemical Physics   136, 145102 (2012) (18 pages)   
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Long-distance correlations of rhinovirus capsid dynamics contribute to uncoating and antiviral activity
Amitava Roy and Carol Beth Post
Proceedings of the National Academy of Sciences of the United States of America   109, 5271-5276 (2012)   
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Development of a theoretical model describing sonoporation activity of cells exposed to ultrasound in the presence of contrast agents
Monica M. Forbes and William D. O'Brien, Jr.
The Journal of the Acoustical Society of America   131, 2723-2729 (2012)   
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A method for tensile tests of biological tissues at the mesoscale
Thierry Savin, Amy E. Shyer, and L. Mahadevan
Journal of Applied Physics   111, 074704 (2012) (6 pages)   
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Effect of erythrocytes oscillations on dielectric properties of human diabetic-blood
S. Abdalla
AIP Advances   1, 012104 (2011) (11 pages)   
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Bioactive silica–poly(-glutamic acid) hybrids for bone regeneration: effect of covalent coupling on dissolution and mechanical properties and fabrication of porous scaffolds
G. Poologasundarampillai, B. Yu, O. Tsigkou, E. Valliant, S. Yue, P. D. Lee, R. W. Hamilton, M. M. Stevens, T. Kasuga, and J. R. Jones
Soft Matter   8, 4822-4832 (2012)   
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MAP and kinesin-dependent nuclear positioning is required for skeletal muscle function
Thomas Metzger, Vincent Gache, Mu Xu, Bruno Cadot, Eric S. Folker, Brian E. Richardson, Edgar R. Gomes, and Mary K. Baylies
Nature   484, 120-124 (2012)   
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Nanoscale imaging of the bone cell network with synchrotron X-ray tomography: optimization of acquisition setup
Alexandra Pacureanu, Max Langer, Elodie Boller, Paul Tafforeau, and Françoise Peyrin
Medical Physics   39, 2229-2238 (2012)   
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Requirements for contractility in disordered cytoskeletal bundles
Martin Lenz, Margaret Gardel, and Aaron Dinner
New Journal of Physics   14, 33037- (2012)   
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Pathway switching in templated virus-like particle assembly
Irina Tsvetkova, Chao Chen, Subinoy Rana, C. Cheng Kao, Vincent M. Rotello, and Bogdan Dragnea
Soft Matter   8, 4570-4576 (2012)   
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INFORMATION TRANSFER IN BIOLOGICAL SYSTEMS

Carotenoid oxidation products are stress signals that mediate gene responses to singlet oxygen in plants
Fanny Ramel, Simona Birtic, Christian Ginies, Ludivine Soubigou-Taconnat, Christian Triantaphylidès, and Michel Havaux
Proceedings of the National Academy of Sciences of the United States of America   109, 5535-5540 (2012)   
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Experimental assessment of the contribution of electrodynamic interactions to long-distance recruitment of biomolecular partners: Theoretical basis
Jordane Preto, Elena Floriani, Ilaria Nardecchia, Pierre Ferrier, and Marco Pettini
Physical Review E   85, 041904 (2012) (12 pages)   
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Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair
Gregory T. Kapp, Sen Liu, Amelie Stein, Derek T. Wong, Attila Reményi, Brian J. Yeh, James S. Fraser, Jack Taunton, Wendell A. Lim, and Tanja Kortemme
Proceedings of the National Academy of Sciences of the United States of America   109, 5277-5282 (2012)   
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Designing orthogonal signaling pathways: How to fit in with the surroundings
John Karanicolas
Proceedings of the National Academy of Sciences of the United States of America   109, 5140-5141 (2012)   
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Structure of the mitotic checkpoint complex
William C. H. Chao, Kiran Kulkarni, Ziguo Zhang, Eric H. Kong, and David Barford
Nature   484, 208-213 (2012)   
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Structure of TIGIT immunoreceptor bound to poliovirus receptor reveals a cell–cell adhesion and signaling mechanism that requires cis-trans receptor clustering
Katharina F. Stengel, Kristin Harden-Bowles, Xin Yu, Lionel Rouge, Jianping Yin, Laëtitia Comps-Agrar, Christian Wiesmann, J. Fernando Bazan, Dan L. Eaton, and Jane L. Grogan
Proceedings of the National Academy of Sciences of the United States of America   109, 5399-5404 (2012)   
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Adaptation at the output of the chemotaxis signalling pathway
Junhua Yuan, Richard W. Branch, Basarab G. Hosu, and Howard C. Berg
Nature   484, 233-236 (2012)   
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A new understanding of the decoding principle on the ribosome
Natalia Demeshkina, Lasse Jenner, Eric Westhof, Marat Yusupov, and Gulnara Yusupova
Nature   484, 256-259 (2012)   
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MULTICELLULAR PHENOMENA

Critical Behavior and Axis Defining Symmetry Breaking in Hydra Embryonic Development
Andrea Gamba, Mario Nicodemi, Jordi Soriano, and Albrecht Ott
Physical Review Letters   108, 158103 (2012) (5 pages)   
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A numerical analysis of multicellular environment for modeling tissue electroporation
M. Essone Mezeme, G. Pucihar, M. Pavlin, C. Brosseau, and D. Miklavčič
Applied Physics Letters   100, 143701 (2012) (4 pages)   
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Scale-Invariant Correlations in Dynamic Bacterial Clusters
Xiao Chen, Xu Dong, Avraham Be'er, Harry L. Swinney, and H. P. Zhang
Physical Review Letters   108, 148101 (2012) (5 pages)   
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Method for physiologic phenotype characterization at the single-cell level in non-interacting and interacting cells
Laimonas Kelbauskas, Shashanka P. Ashili, Jeff Houkal, Dean Smith, Aida Mohammadreza, Kristen B. Lee, Jessica Forrester, Ashok Kumar, Yasser H. Anis, Thomas G. Paulson, Cody A. Youngbull, Yanqing Tian, Mark R. Holl, Roger H. Johnson, and Deirdre R. Meldrum
Journal of Biomedical Optics   17, 037008 (2012) (12 pages)   
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Competitive Brownian and Lévy walkers
E. Heinsalu, E. Hernández-García, and C. López
Physical Review E   85, 041105 (2012) (10 pages)   
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Cluster identification based on correlations
L. S. Schulman
Physical Review E   85, 041114 (2012) (6 pages)   
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Quantitative correlation between light depolarization and transport albedo of various porcine tissues
Sanaz Alali, Manzoor Ahmad, Anthony Kim, Nasit Vurgun, Michael F. G. Wood, and I. Alex Vitkin
Journal of Biomedical Optics   17, 045004 (2012) (8 pages)   
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Wetting transitions of cellular aggregates induced by substrate rigidity
Stéphane Douezan, Julien Dumond, and Françoise Brochard-Wyart
Soft Matter   8, 4577-4582 (2012)   
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BIOLOGICAL NETWORKS

Neuronal avalanches of a self-organized neural network with active-neuron-dominant structure
Xiumin Li and Michael Small
Chaos   22, 023104 (2012) (10 pages)   
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Unbiased degree-preserving randomization of directed binary networks
E. S. Roberts and A. C. C. Coolen
Physical Review E   85, 046103 (2012) (13 pages)   
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Tunable oscillations in the Purkinje neuron
Ze'ev R. Abrams, Ajithkumar Warrier, Yuan Wang, Dirk Trauner, and Xiang Zhang
Physical Review E   85, 041905 (2012) (9 pages)   
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Analytical framework for recurrence network analysis of time series
Jonathan F. Donges, Jobst Heitzig, Reik V. Donner, and Jürgen Kurths
Physical Review E   85, 046105 (2012) (16 pages)   
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Neutral theory of chemical reaction networks
Sang Lee, Sebastian Bernhardsson, Petter Holme, Beom Kim, and Petter Minnhagen
New Journal of Physics   14, 33032- (2012)   
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Bistability and Spatiotemporal Irregularity in Neuronal Networks with Nonlinear Synaptic Transmission
Gianluigi Mongillo, David Hansel, and Carl van Vreeswijk
Physical Review Letters   108, 158101 (2012) (5 pages)   
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Coordination of the transcriptome and metabolome by the circadian clock
Kristin L. Eckel-Mahan, Vishal R. Patel, Robert P. Mohney, Katie S. Vignola, Pierre Baldi, and Paolo Sassone-Corsi
Proceedings of the National Academy of Sciences of the United States of America   109, 5541-5546 (2012)   
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Mapping the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator
W. Huang, P. Prez-Garca, A. Pokhilko, A. J. Millar, I. Antoshechkin, J. L. Riechmann, and P. Mas
Science   336, 75-79 (2012)   
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Choice-specific sequences in parietal cortex during a virtual-navigation decision task
Christopher D. Harvey, Philip Coen, and David W. Tank
Nature   484, 62-68 (2012)   
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QUANTITATIVE GENOMICS

Emergence of robustness against noise: A structural phase transition in evolved models of gene regulatory networks
Tiago P. Peixoto
Physical Review E   85, 041908 (2012) (12 pages)   
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Stochastic stability of genetic regulatory networks with a finite set delay characterization
Wenbing Zhang, Yang Tang, Jian-an Fang, and Xiaotai Wu
Chaos   22, 023106 (2012) (12 pages)   
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Population Genomics of Early Events in the Ecological Differentiation of Bacteria
B. Jesse Shapiro, Jonathan Friedman, Otto X. Cordero, Sarah P. Preheim, Sonia C. Timberlake, Gitta Szab, Martin F. Polz, and Eric J. Alm
Science   336, 48-51 (2012)   
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DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes
Ofir Hakim, Wolfgang Resch, Arito Yamane, Isaac Klein, Kyong-Rim Kieffer-Kwon, Mila Jankovic, Thiago Oliveira, Anne Bothmer, Ty C. Voss, Camilo Ansarah-Sobrinho, Ewy Mathe, Genqing Liang, Jesse Cobell, Hirotaka Nakahashi, Davide F. Robbiani, Andre Nussenzweig, Gordon L. Hager, Michel C. Nussenzweig, and Rafael Casellas
Nature   484, 69-74 (2012)   
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Genome-wide proteinDNA binding dynamics suggest a molecular clutch for transcription factor function
Colin R. Lickwar, Florian Mueller, Sean E. Hanlon, James G. McNally, and Jason D. Lieb
Nature   484, 251-255 (2012)   
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Optimizing information flow in small genetic networks. III. A self-interacting gene
Gašper Tkačik, Aleksandra M. Walczak, and William Bialek
Physical Review E   85, 041903 (2012) (16 pages)   
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Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds
Jie Lu, Changqing Zhang, David C. Baulcombe, and Z. Jeffrey Chen
Proceedings of the National Academy of Sciences of the United States of America   109, 5529-5534 (2012)   
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Extrachromosomal MicroDNAs and Chromosomal Microdeletions in Normal Tissues
Yoshiyuki Shibata, Pankaj Kumar, Ryan Layer, Smaranda Willcox, Jeffrey R. Gagan, Jack D. Griffith, and Anindya Dutta
Science   336, 82-86 (2012)   
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A Fine-Scale Chimpanzee Genetic Map from Population Sequencing
Adam Auton, Adi Fledel-Alon, Susanne Pfeifer, Oliver Venn, Laure Sgurel, Teresa Street, Ellen M. Leffler, Rory Bowden, Ivy Aneas, John Broxholme, Peter Humburg, Zamin Iqbal, Gerton Lunter, Julian Maller, Ryan D. Hernandez, Cord Melton, Aarti Venkat, Marcelo A. Nobrega, Ronald Bontrop, Simon Myers, Peter Donnelly, Molly Przeworski, and Gil McVean
Science   336, 193-198 (2012)   
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CANCER PHYSICS

Paclitaxel-loaded tocopheryl succinate-conjugated chitosan oligosaccharide nanoparticles for synergistic chemotherapy
Youhua Tao, Jianfeng Han, and Huanyu Dou
Journal of Materials Chemistry   22, 8930-8937 (2012)   
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Tumor-binding prodrug micelles of polymer–drug conjugates for anticancer therapy in HeLa cells
Bokyung Jung, Yong-Cheol Jeong, Jun-Hong Min, Jung-Eun Kim, Yoon-Jae Song, Jung-Ki Park, Jung-Hwan Park, and Jong-Duk Kim
Journal of Materials Chemistry   22, 9385-9394 (2012)   
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Comparative analysis of nonlinear dimensionality reduction techniques for breast MRI segmentation
Alireza Akhbardeh and Michael A. Jacobs
Medical Physics   39, 2275-2289 (2012)   
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Multiphoton microscopy and microspectroscopy for diagnostics of inflammatory and neoplastic lung
Ina Pavlova, Kelly R. Hume, Stephanie A. Yazinski, James Flanders, Teresa L. Southard, Robert S. Weiss, and Watt W. Webb
Journal of Biomedical Optics   17, 036014 (2012) (9 pages)   
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Notch-dependent VEGFR3 upregulation allows angiogenesis without VEGFVEGFR2 signalling
Rui Benedito, Susana F. Rocha, Marina Woeste, Martin Zamykal, Freddy Radtke, Oriol Casanovas, Antonio Duarte, Bronislaw Pytowski, and Ralf H. Adams
Nature   484, 110-114 (2012)   
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Monitoring of tumor response to cisplatin by subsurface fluorescence molecular tomography
Fei Liu, Xu Cao, Wei He, Jinping Song, Zhongquan Dai, Bin Zhang, Jianwen Luo, Yinghui Li, and Jing Bai
Journal of Biomedical Optics   17, 040504 (2012) (3 pages)   
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Atg7 Modulates p53 Activity to Regulate Cell Cycle and Survival During Metabolic Stress
In Hye Lee, Yoshichika Kawai, Maria M. Fergusson, Ilsa I. Rovira, Alexander J. R. Bishop, Noboru Motoyama, Liu Cao, and Toren Finkel
Science   336, 225-228 (2012)   
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Dense PEG layers for efficient immunotargeting of nanoparticles to cancer cells
Benjamin Thierry and Hans J. Griesser
Journal of Materials Chemistry   22, 8810-8819 (2012)   
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Mixed lineage kinase domain-like is a key receptor interacting protein 3 downstream component of TNF-induced necrosis
Jie Zhao, Siriporn Jitkaew, Zhenyu Cai, Swati Choksi, Qiuning Li, Ji Luo, and Zheng-Gang Liu
Proceedings of the National Academy of Sciences of the United States of America   109, 5322-5327 (2012)   
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EVOLUTION PHYSICS

Protein misinteraction avoidance causes highly expressed proteins to evolve slowly
Jian-Rong Yang, Ben-Yang Liao, Shi-Mei Zhuang, and Jianzhi Zhang
Proceedings of the National Academy of Sciences of the United States of America   109, E831-E840 (2012)   
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The genomic basis of adaptive evolution in threespine sticklebacks
Felicity C. Jones et al. (Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team) and Jen Baldwin, Toby Bloom, David B. Jaffe, Robert Nicol, Jane Wilkinson, Eric S. Lander, Federica Di Palma, Kerstin Lindblad-Toh, and David M. Kingsley
Nature   484, 55-61 (2012)   
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Stochastic differential equations for evolutionary dynamics with demographic noise and mutations
Arne Traulsen, Jens Christian Claussen, and Christoph Hauert
Physical Review E   85, 041901 (2012) (8 pages)   
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Evolutionary Dynamics of Restriction Site Avoidance
Long Qian and Edo Kussell
Physical Review Letters   108, 158105 (2012) (5 pages)   
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Vertebrate time-tree elucidates the biogeographic pattern of a major biotic change around the K–T boundary in Madagascar
Angelica Crottini, Ole Madsen, Celine Poux, Axel Strauss, David R. Vieites, and Miguel Vences
Proceedings of the National Academy of Sciences of the United States of America   109, 5358-5363 (2012)   
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Emergence of Fairness in Repeated Group Interactions
S. Van Segbroeck, J. M. Pacheco, T. Lenaerts, and F. C. Santos
Physical Review Letters   108, 158104 (2012) (5 pages)   
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Topological analysis of complexity in multiagent systems
Nicole Abaid, Erik Bollt, and Maurizio Porfiri
Physical Review E   85, 041907 (2012) (9 pages)   
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Accelerating consensus on coevolving networks: The effect of committed individuals
P. Singh, S. Sreenivasan, B. K. Szymanski, and G. Korniss
Physical Review E   85, 046104 (2012) (8 pages)   
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Effect of space in the game “war of attrition”
Philip Gerlee and Torbjörn Lundh
Physical Review E   85, 041115 (2012) (6 pages)   
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Origin of first cells at terrestrial, anoxic geothermal fields
Armen Y. Mulkidjanian, Andrew Yu. Bychkov, Daria V. Dibrova, Michael Y. Galperin, and Eugene V. Koonin
Proceedings of the National Academy of Sciences of the United States of America   109, E821-E830 (2012)   
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STATISTICAL AND NONLINEAR PHYSICS

A universal model for mobility and migration patterns
Filippo Simini, Marta C. Gonzlez, Amos Maritan, and Albert-Lszl Barabsi
Nature   484, 96-100 (2012)   
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Non-Brownian dynamics and strategy of amoeboid cell locomotion
Shin I. Nishimura, Masahiro Ueda, and Masaki Sasai
Physical Review E   85, 041909 (2012) (8 pages)   
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Reaction-diffusion master equation in the microscopic limit
Stefan Hellander, Andreas Hellander, and Linda Petzold
Physical Review E   85, 042901 (2012) (5 pages)   
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Adiabatically slow and adiabatically fast driven ratchets
V. M. Rozenbaum, Yu. A. Makhnovskii, I. V. Shapochkina, S.-Y. Sheu, D.-Y. Yang, and S. H. Lin
Physical Review E   85, 041116 (2012) (5 pages)   
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Footprint traversal by adenosine-triphosphate-dependent chromatin remodeler motor
Ashok Garai, Jesrael Mani, and Debashish Chowdhury
Physical Review E   85, 041902 (2012) (9 pages)   
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Langevin dynamics simulation of polymer-assisted virus-like assembly
J. P. Mahalik and M. Muthukumar
The Journal of Chemical Physics   136, 135101 (2012) (13 pages)   
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Stochastic dynamics of phase singularities under ventricular fibrillation in 2D Beeler-Reuter model
Akio Suzuki and Hidetoshi Konno
AIP Advances   1, 032103 (2011) (13 pages)   
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Hydrodynamic synchronization of nonlinear oscillators at low Reynolds number
M. Leoni and T. B. Liverpool
Physical Review E   85, 040901 (2012) (4 pages)   
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Testing for time-localized coherence in bivariate data
L. W. Sheppard, A. Stefanovska, and P. V. E. McClintock
Physical Review E   85, 046205 (2012) (16 pages)   
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Noise-sustained fluctuations in stochastic dynamics with a delay
Paolo D'Odorico, Francesco Laio, and Luca Ridolfi
Physical Review E   85, 041106 (2012) (6 pages)   
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Time-varying linear and nonlinear parametric model for Granger causality analysis
Yang Li, Hua-Liang Wei, Steve A. Billings, and Xiao-Feng Liao
Physical Review E   85, 041906 (2012) (8 pages)   
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Oscillation death in asymmetrically delay-coupled oscillators
Wei Zou, Yang Tang, Lixiang Li, and Jürgen Kurths
Physical Review E   85, 046206 (2012) (6 pages)   
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Improved delay-leaping simulation algorithm for biochemical reaction systems with delays
Na Yi, Gang Zhuang, Liang Da, and Yifei Wang
The Journal of Chemical Physics   136, 144108 (2012) (4 pages)   
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INSTRUMENTATION DEVELOPMENT

Biocompatible and functionalizable polyphosphate nanogel with a branched structure
You-Yong Yuan, Jin-Zhi Du, Wen-Jing Song, Feng Wang, Xian-Zhu Yang, Meng-Hua Xiong, and Jun Wang
Journal of Materials Chemistry   22, 9322-9329 (2012)   
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Conjugated polyelectrolyte complexes with single-walled carbon nanotubes for amperometric detection of glucose with inherent anti-interference properties
Xin Pang, Patigul Imin, Igor Zhitomirsky, and Alex Adronov
Journal of Materials Chemistry   22, 9147-9154 (2012)   
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Using feature vectors to detect frog calls in wireless sensor networks
Benjamin Croker and Navinda Kottege
The Journal of the Acoustical Society of America   131, EL400-EL405 (2012)   
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Development of formaldehyde-free agar/gelatin microcapsules containing berberine HCl and gallic acid and their topical and oral applications
Pik-Ling Lam, Kenneth Ka-Ho Lee, Stanton Hon-Lung Kok, Gregory Yin-Ming Cheng, Xiao-Ming Tao, Desmond Kwok-Po Hau, Marcus Chun-Wah Yuen, Kim-Hung Lam, Roberto Gambari, Chung-Hin Chui, and Raymond Siu-Ming Wong
Soft Matter   8, 5027-5037 (2012)   
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A microfluidic platform for controlled biochemical stimulation of twin neuronal networks
Emilia Biffi, Francesco Piraino, Alessandra Pedrocchi, Gianfranco B. Fiore, Giancarlo Ferrigno, Alberto Redaelli, Andrea Menegon, and Marco Rasponi
Biomicrofluidics   6, 024106 (2012) (10 pages)   
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Physics of ultra-high bioproductivity in algal photobioreactors
Efrat Greenwald, Jeffrey M. Gordon, and Yair Zarmi
Applied Physics Letters   100, 143703 (2012) (4 pages)   
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Hollow YPO₄:Eu³⁺ microspheres: synthesis, characterisation and luminescent properties
Hongfang Jiu, Yuehua Fu, Lixin Zhang, Yixin Sun, Yuanzhong Wang, and Tao Han
Micro & Nano Letters   7, 287-291 (2012)   
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Fluorescence microscopy for simultaneous observation of 3D orientation and movement and its application to quantum rod-tagged myosin V
Masashi Ohmachi, Yasunori Komori, Atsuko H. Iwane, Fumihiko Fujii, Takashi Jin, and Toshio Yanagida
Proceedings of the National Academy of Sciences of the United States of America   109, 5294-5298 (2012)   
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Rapid crystallization from acoustically levitated droplets
Hui-Ling Cao, Da-Chuan Yin, Yun-Zhu Guo, Xiao-Liang Ma, Jin He, Wei-Hong Guo, Xu-Zhuo Xie, and Bo-Ru Zhou
The Journal of the Acoustical Society of America   131, 3164-3172 (2012)   
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Covalent attachment of a specific site of a protein molecule on a carbon nanotube tip
Hiroyuki Maruyama, Shige H. Yoshimura, Satoshi Ohno, Kazuya Nishikawa, and Yoshikazu Nakayama
Journal of Applied Physics   111, 074701 (2012) (4 pages)   
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A controlled biochemical release device with embedded nanofluidic channels
Haifeng Yang, Wei Hong, and Liang Dong
Applied Physics Letters   100, 153510 (2012) (4 pages)   
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Linear conversion of pressure into concentration, rapid switching of concentration, and generation of linear ramps of concentration in a microfluidic device
Micha Adler and Alex Groisman
Biomicrofluidics   6, 024109 (2012) (16 pages)   
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Fluorescent graphene oxide composites synthesis and its biocompatibility study
Guoqiang Xie, Ju Cheng, Yifan Li, Pinxian Xi, Fengjuan Chen, Hongyan Liu, Fengping Hou, Yanjun Shi, Liang Huang, Zhihong Xu, Decheng Bai, and Zhengzhi Zeng
Journal of Materials Chemistry   22, 9308-9314 (2012)   
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Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination
Reto Fiolka, Lin Shao, E. Hesper Rego, Michael W. Davidson, and Mats G. L. Gustafsson
Proceedings of the National Academy of Sciences of the United States of America   109, 5311-5315 (2012)   
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Gold nanoparticle wire and integrated wire array for electronic detection of chemical and biological molecules
J. J. Diao and Qing Cao
AIP Advances   1, 012115 (2011) (5 pages)   
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Stereoscopic full aperture imaging in nuclear medicine
Sergio G. Strocovsky and Dino Otero
AIP Advances   1, 022121 (2011) (18 pages)   
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Supercontinuum ultra wide range confocal microscope for reflectance spectroscopy of living matter and material science surfaces
Stefano Selci, Francesca R. Bertani, and Luisa Ferrari
AIP Advances   1, 032143 (2011) (11 pages)   
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Two-Dimensional X-Ray Beam Phase Sensing
Sébastien Bérujon, Eric Ziegler, Roberto Cerbino, and Luca Peverini
Physical Review Letters   108, 158102 (2012) (5 pages)   
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Functionalized electrospun nanofibers as bioseparators in microfluidic systems
Lauren Matlock-Colangelo, Daehwan Cho, Christine L. Pitner, Margaret W. Frey, and Antje J. Baeumner
Lab on a Chip   12, 1696-1701 (2012)   
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A thermal study of cellular motility by optical time-resolved correlation
F. J. Sierra-Valdez, A. J. Cisneros-Mejorado, D. P. Sánchez Herrera, and J. C. Ruiz-Suárez
Review of Scientific Instruments   83, 044302 (2012) (4 pages)   
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Note: Multiplexed multiple-tau auto- and cross-correlators on a single field programmable gate array
G. Mocsár, B. Kreith, J. Buchholz, J. W. Krieger, J. Langowski, and G. Vámosi
Review of Scientific Instruments   83, 046101 (2012) (3 pages)   
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Performance and scaling effects in a multilayer microfluidic extracorporeal lung oxygenation device
Tatiana Kniazeva, Alla A. Epshteyn, James C. Hsiao, Ernest S. Kim, Vijaya B. Kolachalama, Joseph L. Charest, and Jeffrey T. Borenstein
Lab on a Chip   12, 1686-1695 (2012)   
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Micro-patterned porous substrates for cell-based assays
Fanny Evenou, Jean-Marc Di Meglio, Benoit Ladoux, and Pascal Hersen
Lab on a Chip   12, 1717-1722 (2012)   
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Cantilever deflection associated with hybridization of monomolecular DNA film
Yue Zhao, Baskar Ganapathysubramanian, and Pranav Shrotriya
Journal of Applied Physics   111, 074310 (2012) (9 pages)   
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Correlations between ultrasonic guided wave velocities and bone properties in bovine tibia in vitro
Kang Il Lee and Suk Wang Yoon
The Journal of the Acoustical Society of America   131, EL375-EL381 (2012)   
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Fano resonance in two-intersecting nanorings: Multiple layers of plasmon hybridizations
Hailong Liu, Xijun Wu, Bing Li, Chenxi Xu, Guangbiao Zhang, and Longjiang Zheng
Applied Physics Letters   100, 153114 (2012) (4 pages)   
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Electrokinetic effects on detection time of nanowire biosensor
Yaling Liu, Qingjiang Guo, Shunqiang Wang, and Walter Hu
Applied Physics Letters   100, 153502 (2012) (4 pages)   
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The double-helix microscope super-resolves extended biological structures by localizing single blinking molecules in three dimensions with nanoscale precision
Hsiao-lu D. Lee, Steffen J. Sahl, Matthew D. Lew, and W. E. Moerner
Applied Physics Letters   100, 153701 (2012) (3 pages)   
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Proposal for tunnel-field-effect-transistor as ultra-sensitive and label-free biosensors
Deblina Sarkar and Kaustav Banerjee
Applied Physics Letters   100, 143108 (2012) (4 pages)   
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Vibrational frequencies of anti-diabetic drug studied by terahertz time-domain spectroscopy
S. Q. Du, H. Li, L. Xie, L. Chen, Y. Peng, Y. M. Zhu, H. Li, P. Dong, and J. T. Wang
Applied Physics Letters   100, 143702 (2012) (4 pages)   
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Pico calorimeter for detection of heat produced in an individual brown fat cell
Naoki Inomata, Masaya Toda, Masaaki Sato, Akihiko Ishijima, and Takahito Ono
Applied Physics Letters   100, 154104 (2012) (4 pages)   
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Handheld magnetic sensor for measurement of tension
K. Singal and R. Rajamani
Applied Physics Letters   100, 154105 (2012) (5 pages)   
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Calcium carbonate polymorph control using droplet-based microfluidics
Alexandra Yashina, Fiona Meldrum, and Andrew deMello
Biomicrofluidics   6, 022001 (2012) (10 pages)   
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CO₂ dissolution in water using long serpentine microchannels
Thomas Cubaud, Martin Sauzade, and Ruopeng Sun
Biomicrofluidics   6, 022002 (2012) (9 pages)   
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Tuning bubbly structures in microchannels
Sharon M. Vuong and Shelley L. Anna
Biomicrofluidics   6, 022004 (2012) (18 pages)   
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Tunable spatial heterogeneity in structure and composition within aqueous microfluidic droplets
Su Hui Sophia Lee, Pengzhi Wang, Swee Kun Yap, T. Alan Hatton, and Saif A. Khan
Biomicrofluidics   6, 022005 (2012) (8 pages)   
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Field-free particle focusing in microfluidic plugs
G. K. Kurup and Amar S. Basu
Biomicrofluidics   6, 022008 (2012) (10 pages)   
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New rationale for large metazoan embryo manipulations on chip-based devices
Khashayar Khoshmanesh, Jin Akagi, Chris J. Hall, Kathryn E. Crosier, Philip S. Crosier, Jonathan M. Cooper, and Donald Wlodkowic
Biomicrofluidics   6, 024102 (2012) (14 pages)   
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Novel on-demand droplet generation for selective fluid sample extraction
Robert Lin, Jeffery S. Fisher, Melinda G. Simon, and Abraham P. Lee
Biomicrofluidics   6, 024103 (2012) (10 pages)   
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Dielectrophoretic differentiation of mouse ovarian surface epithelial cells, macrophages, and fibroblasts using contactless dielectrophoresis
Alireza Salmanzadeh, Harsha Kittur, Michael B. Sano, Paul C. Roberts, Eva M. Schmelz, and Rafael V. Davalos
Biomicrofluidics   6, 024104 (2012) (13 pages)   
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High-performance microfluidic rectifier based on sudden expansion channel with embedded block structure
Chien-Hsiung Tsai, Che-Hsin Lin, Lung-Ming Fu, and Hui-Chun Chen
Biomicrofluidics   6, 024108 (2012) (9 pages)   
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Microstripes for transport and separation of magnetic particles
Marco Donolato, Bjarke Thomas Dalslet, and Mikkel Fougt Hansen
Biomicrofluidics   6, 024110 (2012) (6 pages)   
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Covalently immobilized biomolecule gradient on hydrogel surface using a gradient generating microfluidic device for a quantitative mesenchymal stem cell study
Zongbin Liu, Lidan Xiao, Baojian Xu, Yu Zhang, Arthur FT Mak, Yi Li, Wing-yin Man, and Mo Yang
Biomicrofluidics   6, 024111 (2012) (12 pages)   
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The microwave sensing of DNA hybridization using carbon nanotubes decorated with gold nanoislands
Alina Cismaru, Mircea Dragoman, Antonio Radoi, A. Dinescu, and Daniela Dragoman
Journal of Applied Physics   111, 076106 (2012) (3 pages)   
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Error analysis of ratiometric imaging of extracellular pH in a window chamber model
Yuxiang Lin, Tzu-Yu Wu, and Arthur F. Gmitro
Journal of Biomedical Optics   17, 046004 (2012) (6 pages)   
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Squeeze-chip: a finger-controlled microfluidic flow network device and its application to biochemical assays
Wentao Li, Tao Chen, Zitian Chen, Peng Fei, Zhilong Yu, Yuhong Pang, and Yanyi Huang
Lab on a Chip   12, 1587-1590 (2012)   
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Possible use of a Cooper-pair box for low-dose electron microscopy
Hiroshi Okamoto
Physical Review A   85, 043810 (2012) (13 pages)   
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A new device for performing reference point indentation without a reference probe
Daniel Bridges, Connor Randall, and Paul K. Hansma
Review of Scientific Instruments   83, 044301 (2012) (8 pages)   
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Continuous-waveform constant-current isolated physiological stimulator
Mark R. Holcomb, Jack M. Devine, Rene Harder, and Veniamin Y. Sidorov
Review of Scientific Instruments   83, 044303 (2012) (6 pages)   
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A three-lead, programmable, and microcontroller-based electrocardiogram generator with frequency domain characteristics of heart rate variability
Ying-Chieh Wei, Ying-Yu Wei, Kai-Hsiung Chang, and Ming-Shing Young
Review of Scientific Instruments   83, 045109 (2012) (7 pages)   
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Development of a microbial high-throughput screening instrument based on elastic light scatter patterns
Euiwon Bae, Valery Patsekin, Bartek Rajwa, Arun K. Bhunia, Cheryl Holdman, V. Jo Davisson, E. Daniel Hirleman, and J. Paul Robinson
Review of Scientific Instruments   83, 044304 (2012) (10 pages)   
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Anisotropic light scattering of individual sickle red blood cells
Youngchan Kim, John M. Higgins, Ramachandra R. Dasari, Subra Suresh, and YongKeun Park
Journal of Biomedical Optics   17, 040501 (2012) (3 pages)   
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Ultrafast Rotary PCR system for multiple influenza viral RNA detection
Jae Hwan Jung, Seok Jin Choi, Byung Hyun Park, Young Ki Choi, and Tae Seok Seo
Lab on a Chip   12, 1598-1600 (2012)   
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On-bead expression of recombinant proteins in an agarose gel matrix coated on a glass slide
Kyung-Ho Lee, Ka-Young Lee, Ju-Young Byun, Byung-Gee Kim, and Dong-Myung Kim
Lab on a Chip   12, 1605-1610 (2012)   
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A miniaturized and integrated gel post platform for multiparameter PCR detection of herpes simplex viruses from raw genital swabs
Dammika P. Manage, Jana Lauzon, Alexey Atrazhev, Yuen C. Morrissey, Ann L. Edwards, Alexander J. Stickel, H. John Crabtree, Kanti Pabbaraju, George Zahariadis, Stephanie K. Yanow, and Linda M. Pilarski
Lab on a Chip   12, 1664-1671 (2012)   
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Spectral analysis of fundamental signal and noise performances in photoconductors for mammography
Ho Kyung Kim, Chang Hwy Lim, Jesse Tanguay, Seungman Yun, and Ian A. Cunningham
Medical Physics   39, 2478-2490 (2012)   
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Inhibiting protein biofouling using graphene oxide in droplet-based microfluidic microsystems
Guillaume Perry, Vincent Thomy, Manash R. Das, Yannick Coffinier, and Rabah Boukherroub
Lab on a Chip   12, 1601-1604 (2012)   
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Determination of single cell surface protein expression using a tagless microfluidic method
Rajan Kumar, Sri HariKrishna Vellanki, Robin Smith, and Robert Wieder
Lab on a Chip   12, 1646-1655 (2012)   
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Direct Electrochemistry and Electrocatalysis of Hemoglobin Immobilized on the Functionalized Graphene-Carbon Nanotube Composite Film
Minzhi Wang and Jianbin Zheng
Journal of The Electrochemical Society   159, F150-F156 (2012)   
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High-throughput genotoxicity assay identifies antioxidants as inducers of DNA damage response and cell death
Jennifer T. Fox, Srilatha Sakamuru, Ruili Huang, Nedelina Teneva, Steven O. Simmons, Menghang Xia, Raymond R. Tice, Christopher P. Austin, and Kyungjae Myung
Proceedings of the National Academy of Sciences of the United States of America   109, 5423-5428 (2012)   
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Optical trapping force reduction and manipulation of nanoporous beads
Tao Wang, Fan Jiang, Stefan Oehrlein, Erliang Zeng, Ryan Kershner, and Franco Cerrina
Applied Physics Letters   100, 153702 (2012) (3 pages)   
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MISCELLANEOUS

Construction and operation of a microrobot based on magnetotactic bacteria in a microfluidic chip
Qiufeng Ma, Changyou Chen, Shufeng Wei, Chuanfang Chen, Long-Fei Wu, and Tao Song
Biomicrofluidics   6, 024107 (2012) (12 pages)   
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