Virtual Journal of Biological Physics Research -- November 1, 2009

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REVIEW ARTICLES

Invited Review Article: Review of centrifugal microfluidic and bio-optical disks
David D. Nolte
Review of Scientific Instruments   80, 101101 (2009) (22 pages)   
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What recent ribosome structures have revealed about the mechanism of translation
T. Martin Schmeing and V. Ramakrishnan
Nature   461, 1234-1242 (2009)   
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The DNA-damage response in human biology and disease
Stephen P. Jackson and Jiri Bartek
Nature   461, 1071-1078 (2009)   
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QUANTUM MECHANICAL DYNAMICS

Oscillator strength of the peptide bond ^* resonances at all relevant x-ray absorption edges
K. Kummer, V. N. Sivkov, D. V. Vyalikh, V. V. Maslyuk, A. Blüher, S. V. Nekipelov, T. Bredow, I. Mertig, M. Mertig, and S. L. Molodtsov
Physical Review B   80, 155433 (2009) (8 pages)   
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Lagrangian field theory of reaction-diffusion
C. Cherubini and S. Filippi
Physical Review E   80, 046117 (2009) (14 pages)   
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Automated calculation of anharmonic vibrational contributions to first hyperpolarizabilities: Quadratic response functions from vibrational configuration interaction wave functions
Mikkel Bo Hansen, Ove Christiansen, and Christof Hättig
The Journal of Chemical Physics   131, 154101 (2009) (16 pages)   
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Density-based energy decomposition analysis for intermolecular interactions with variationally determined intermediate state energies
Qin Wu, Paul W. Ayers, and Yingkai Zhang
The Journal of Chemical Physics   131, 164112 (2009) (8 pages)   
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Ab initio Path Integral Molecular Dynamics Based on Fragment Molecular Orbital Method
Takatoshi Fujita, Hirofumi Watanabe, and Shigenori Tanaka
Journal of the Physical Society of Japan   78, 104723 (2009) (7 pages)   
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PHYSICS OF WATER AND HYDROGEN-BONDED SOLVENTS

Quantum dynamical effects in liquid water: A semiclassical study on the diffusion and the infrared absorption spectrum
Jian Liu, William H. Miller, Francesco Paesani, Wei Zhang, and David A. Case
The Journal of Chemical Physics   131, 164509 (2009) (12 pages)   
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Theoretical study on effects of hydrogen bonding on the ring stretching modes of pyridine
An Yong Li, Hong Bo Ji, and Li Juan Cao
The Journal of Chemical Physics   131, 164305 (2009) (8 pages)   
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Ultrafast energy relaxation and anisotropy decay of the librational motion in liquid water: A molecular dynamics study
Takuma Yagasaki, Junichi Ono, and Shinji Saito
The Journal of Chemical Physics   131, 164511 (2009) (11 pages)   
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Concerted orientation induced unidirectional water transport through nanochannels
Rongzheng Wan, Hangjun Lu, Jinyuan Li, Jingdong Bao, Jun Hu, and Haiping Fang
Physical Chemistry Chemical Physics   11, 9898-9902 (2009)   
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Molecular dynamics simulations of polyamidoamine dendrimers and their complexes with linear poly(ethylene oxide) at different pH conditions: static properties and hydrogen bonding
I. Tanis and K. Karatasos
Physical Chemistry Chemical Physics   11, 10017-10028 (2009)   
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The conformational analysis and proton transfer of neuraminidase inhibitors: a theoretical study
Zhiwei Yang, Gang Yang, Yuangang Zu, Yujie Fu, and Lijun Zhou
Physical Chemistry Chemical Physics   11, 10035-10041 (2009)   
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Dewetting-Controlled Binding of Ligands to Hydrophobic Pockets
P. Setny, Z. Wang, L.-T. Cheng, B. Li, J. A. McCammon, and J. Dzubiella
Physical Review Letters   103, 187801 (2009) (4 pages)   
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Water-mediated signal multiplication with Y-shaped carbon nanotubes
Yusong Tu, Peng Xiu, Rongzheng Wan, Jun Hu, Ruhong Zhou, and Haiping Fang
Proceedings of the National Academy of Sciences of the United States of America   106, 18120-18124 (2009)   
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Ion-specific thermodynamics of multicomponent electrolytes: A hybrid HNC/MD approach
Luboš Vrbka, Mikael Lund, Immanuel Kalcher, Joachim Dzubiella, Roland R. Netz, and Werner Kunz
The Journal of Chemical Physics   131, 154109 (2009) (12 pages)   
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High level coupled cluster determination of the structure, frequencies, and heat of formation of water
David Feller and Kirk A. Peterson
The Journal of Chemical Physics   131, 154306 (2009) (10 pages)   
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An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions
Yuchun Lin, Andrij Baumketner, Shaozhong Deng, Zhenli Xu, Donald Jacobs, and Wei Cai
The Journal of Chemical Physics   131, 154103 (2009) (17 pages)   
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Ionic conductivity on a wetting surface
Brian Skinner, M. S. Loth, and B. I. Shklovksii
Physical Review E   80, 041925 (2009) (5 pages)   
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MEMBRANE BIOPHYSICS

Hydration of phospholipid interface: carbonyl–water hydrogen bond association
Victor Volkov, Yuji Takaoka, and Roberto Righini
Physical Chemistry Chemical Physics   11, 9979-9986 (2009)   
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Fluctuations of Ionic Current Through Lipid Bilayers at the Onset of Peptide Attacks and Pore Formation
G. C. Fadda, D. Lairez, and G. Zalczer
Physical Review Letters   103, 180601 (2009) (4 pages)   
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Reverse vesicles formed by hydrogen bonded arylamide-derived triammonium cyclophanes and hexaammonium capsule
Xiao-Na Xu, Lu Wang, and Zhan-Ting Li
Chemical Communications   2009, 6634-6636 (2009)   
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Rheology and phase behavior of dense casein micelle dispersions
A. Bouchoux, B. Debbou, G. Gésan-Guiziou, M.-H. Famelart, J.-L. Doublier, and B. Cabane
The Journal of Chemical Physics   131, 165106 (2009) (11 pages)   
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Structure of physical crystalline membranes within the self-consistent screening approximation
Doron Gazit
Physical Review E   80, 041117 (2009) (6 pages)   
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Mechanical properties of interacting lipopolysaccharide membranes from bacteria mutants studied by specular and off-specular neutron scattering
Emanuel Schneck, Rafael G. Oliveira, Florian Rehfeldt, Bruno Demé, Klaus Brandenburg, Ulrich Seydel, and Motomu Tanaka
Physical Review E   80, 041929 (2009) (9 pages)   
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Influence of laser parameters on nanoparticle-induced membrane permeabilization
Cuiping Yao, Xiaochao Qu, Zhenxi Zhang, Gereon Hüttmann, and Ramtin Rahmanzadeh
Journal of Biomedical Optics   14, 054034 (2009) (7 pages)   
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Non-entropic and reversible long-range deformation of an encapsulating bioelastomer
Ali Miserez, S. Scott Wasko, Christine F. Carpenter, and J. Herbert Waite
Nature Materials   8, 910-916 (2009)   
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Structure of an integrin IIb3 transmembrane-cytoplasmic heterocomplex provides insight into integrin activation
Jun Yang, Yan-Qing Ma, Richard C. Page, Saurav Misra, Edward F. Plow, and Jun Qin
Proceedings of the National Academy of Sciences of the United States of America   106, 17729-17734 (2009)   
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Fatty acid-cationic surfactant vesicles: counter-ion self-encapsulation
Daniel Kopetzki, Youlia Michina, Thomas Gustavsson, and David Carrière
Soft Matter   5, 4212-4218 (2009)   
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Observation of buried water molecules in phospholipid membranes by surface sum-frequency generation spectroscopy
Maria Sovago, Erik Vartiainen, and Mischa Bonn
The Journal of Chemical Physics   131, 161107 (2009) (4 pages)   
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Minimal membrane docking requirements revealed by reconstitution of Rab GTPase-dependent membrane fusion from purified components
Christopher Stroupe, Christopher M. Hickey, Joji Mima, Amy S. Burfeind, and William Wickner
Proceedings of the National Academy of Sciences of the United States of America   106, 17626-17633 (2009)   
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A secreted complement-control-related protein ensures acetylcholine receptor clustering
Marie Gendrel, Georgia Rapti, Janet E. Richmond, and Jean-Louis Bessereau
Nature   461, 992-996 (2009)   
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FUNDAMENTAL POLYMER STATICS/DYNAMICS

Phase coexistence and line tension in ternary lipid systems
T. Idema, J. M. J. van Leeuwen, and C. Storm
Physical Review E   80, 041924 (2009) (9 pages)   
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Semipermeable poly(ethylene glycol) films: the relationship between permeability and molecular structure of polymer chains
Robert Schlapak, Daren Caruana, David Armitage, and Stefan Howorka
Soft Matter   5, 4104-4112 (2009)   
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Entangled chain dynamics of polymer knots in extensional flow
Demosthenes Kivotides, S. Louise Wilkin, and Theo G. Theofanous
Physical Review E   80, 041808 (2009) (16 pages)   
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Implicit and explicit solvent models for the simulation of a single polymer chain in solution: Lattice Boltzmann versus Brownian dynamics
Tri T. Pham, Ulf D. Schiller, J. Ravi Prakash, and Burkhard Dünweg
The Journal of Chemical Physics   131, 164114 (2009) (11 pages)   
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The effect of interbranch spacing on structural and rheological properties of hyperbranched polymer melts
Tu C. Le, B. D. Todd, P. J. Daivis, and A. Uhlherr
The Journal of Chemical Physics   131, 164901 (2009) (12 pages)   
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Dilute gels with exceptional rigidity from self-assembling silk-collagen-like block copolymers
Aernout A. Martens, Jasper van der Gucht, Gerrit Eggink, Frits A. de Wolf, and Martien A. Cohen Stuart
Soft Matter   5, 4191-4197 (2009)   
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Global cross-over dynamics of single semiflexible polymers
M. Hinczewski and R. Netz
Europhysics Letters   88, 18001- (2009)   
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Self-assembly of polypeptides into left-handedly twisted fibril-like structures
Yan Mu and Yi Qin Gao
Physical Review E   80, 041927 (2009) (8 pages)   
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Protein–polysaccharide viscoelastic matrices: synergic effects of amylose on lysozyme physical gelation in aqueous dimethylsulfoxide
Willemberg A. Cruz and Elizabeth P. G. Arêas
Soft Matter   5, 4240-4249 (2009)   
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Reversible stress softening and stress recovery of cellulose networks
Fernando G. Torres, Omar P. Troncoso, Daniel Lopez, Cristian Grande, and Clara M. Gomez
Soft Matter   5, 4185-4190 (2009)   
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Controlled remodeling of a protein-polysaccharide mixed gel: examples of gelatin-hyaluronic acid mixtures
Julien Picard, Sebastien Giraudier, and Veronique Larreta-Garde
Soft Matter   5, 4198-4205 (2009)   
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Fibronectin forms the most extensible biological fibers displaying switchable force-exposed cryptic binding sites
Enrico Klotzsch, Michael L. Smith, Kristopher E. Kubow, Simon Muntwyler, William C. Little, Felix Beyeler, Delphine Gourdon, Bradley J. Nelson, and Viola Vogel
Proceedings of the National Academy of Sciences of the United States of America   106, 18267-18272 (2009)   
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Elastin-like polypeptides of different molecular weights show independent transition temperatures when mixed
Rosalie L. M. Teeuwen, Frits A. de Wolf, Han Zuilhof, and Jan C. M. van Hest
Soft Matter   5, 4305-4310 (2009)   
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Structure of high density fibrin networks probed with neutron scattering and rheology
Katie M. Weigandt, Danilo C. Pozzo, and Lionel Porcar
Soft Matter   5, 4321-4330 (2009)   
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PROTEIN CONFORMATIONAL DYNAMICS/FOLDING

Translational, rotational and internal dynamics of amyloid -peptides (A40 and A42) from molecular dynamics simulations
Ram Prasad Bora and Rajeev Prabhakar
The Journal of Chemical Physics   131, 155103 (2009) (11 pages)   
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Photoabsorption studies of neutral green fluorescent protein model chromophores in vacuo
J. Rajput, D. B. Rahbek, L. H. Andersen, T. Rocha-Rinza, O. Christiansen, K. B. Bravaya, A. V. Erokhin, A. V. Bochenkova, K. M. Solntsev, J. Dong, J. Kowalik, L. M. Tolbert, M. Åxman Petersen, and M. Brøndsted Nielsen
Physical Chemistry Chemical Physics   11, 9996-10002 (2009)   
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Folding simulations of gramicidin A into the -helix conformations: Simulated annealing molecular dynamics study
Takaharu Mori and Yuko Okamoto
The Journal of Chemical Physics   131, 165103 (2009) (6 pages)   
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Size, shape, and flexibility of proteins and DNA
Nidhi Rawat and Parbati Biswas
The Journal of Chemical Physics   131, 165104 (2009) (9 pages)   
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Solution structure of a paradigm ArsR family zinc sensor in the DNA-bound state
Alphonse I. Arunkumar, Gregory C. Campanello, and David P. Giedroc
Proceedings of the National Academy of Sciences of the United States of America   106, 18177-18182 (2009)   
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Multistart simulated annealing refinement of the crystal structure of the 70S ribosome
Andrei Korostelev, Martin Laurberg, and Harry F. Noller
Proceedings of the National Academy of Sciences of the United States of America   106, 18195-18200 (2009)   
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Hidden dynamic allostery in a PDZ domain
Chad M. Petit, Jun Zhang, Paul J. Sapienza, Ernesto J. Fuentes, and Andrew L. Lee
Proceedings of the National Academy of Sciences of the United States of America   106, 18249-18254 (2009)   
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Transient structural distortion of metal-free Cu/Zn superoxide dismutase triggers aberrant oligomerization
Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentsev, Mikael Oliveberg, and Mikael Akke
Proceedings of the National Academy of Sciences of the United States of America   106, 18273-18278 (2009)   
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Dual folding pathways of an / protein from all-atom ab initio folding simulations
Hongxing Lei, Zhi-Xiang Wang, Chun Wu, and Yong Duan
The Journal of Chemical Physics   131, 165105 (2009) (7 pages)   
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Structural imperatives impose diverse evolutionary constraints on helical membrane proteins
Amit Oberai, Nathan H. Joh, Frank K. Pettit, and James U. Bowie
Proceedings of the National Academy of Sciences of the United States of America   106, 17747-17750 (2009)   
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A gradient-directed Monte Carlo method for global optimization in a discrete space: Application to protein sequence design and folding
Xiangqian Hu, David N. Beratan, and Weitao Yang
The Journal of Chemical Physics   131, 154117 (2009) (8 pages)   
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Multiresolution phase extension of a trypsin inhibitor structure from 5  Å to 2  Å based on diffraction amplitudes alone
Xiangan Liu and Wu-Pei Su
Physical Review E   80, 047701 (2009) (4 pages)   
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Structural evolution of p53, p63, and p73: Implication for heterotetramer formation
Andreas C. Joerger, Sridharan Rajagopalan, Eviatar Natan, Dmitry B. Veprintsev, Carol V. Robinson, and Alan R. Fersht
Proceedings of the National Academy of Sciences of the United States of America   106, 17705-17710 (2009)   
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Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase
Kotaro Nakanishi, Luc Bonnefond, Satoshi Kimura, Tsutomu Suzuki, Ryuichiro Ishitani, and Osamu Nureki
Nature   461, 1144-1148 (2009)   
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Exploitation of binding energy for catalysis and design
Summer B. Thyme, Jordan Jarjour, Ryo Takeuchi, James J. Havranek, Justin Ashworth, Andrew M. Scharenberg, Barry L. Stoddard, and David Baker
Nature   461, 1300-1304 (2009)   
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DNA CONFORMATIONAL DYNAMICS

Discontinuities at the DNA supercoiling transition
Bryan C. Daniels, Scott Forth, Maxim Y. Sheinin, Michelle D. Wang, and James P. Sethna
Physical Review E   80, 040901 (2009) (4 pages)   
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Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging
Joost van Mameren, Peter Gross, Geraldine Farge, Pleuni Hooijman, Mauro Modesti, Maria Falkenberg, Gijs J. L. Wuite, and Erwin J. G. Peterman
Proceedings of the National Academy of Sciences of the United States of America   106, 18231-18236 (2009)   
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Thermodynamics of Intragenic Nucleosome Ordering
G. Chevereau, L. Palmeira, C. Thermes, A. Arneodo, and C. Vaillant
Physical Review Letters   103, 188103 (2009) (4 pages)   
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Hole mobility and transport mechanisms in -DNA
Mattias Jakobsson and Sven Stafström
The Journal of Chemical Physics   131, 155102 (2009) (7 pages)   
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Homology recognition funnel
Dominic Lee and Alexei A. Kornyshev
The Journal of Chemical Physics   131, 155104 (2009) (15 pages)   
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Equilibrium Properties and Force-Driven Unfolding Pathways of RNA Molecules
A. Imparato, A. Pelizzola, and M. Zamparo
Physical Review Letters   103, 188102 (2009) (4 pages)   
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Hydrophobic effects on multivalent-salt-induced self-condensation of DNA
Tomonari Sumi, Chiaki Suzuki, and Hideo Sekino
The Journal of Chemical Physics   131, 161103 (2009) (4 pages)   
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The role of DNA shape in protein–DNA recognition
Remo Rohs, Sean M. West, Alona Sosinsky, Peng Liu, Richard S. Mann, and Barry Honig
Nature   461, 1248-1253 (2009)   
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Predicted poxvirus FEN1-like nuclease required for homologous recombination, double-strand break repair and full-size genome formation
Tatiana G. Senkevich, Eugene V. Koonin, and Bernard Moss
Proceedings of the National Academy of Sciences of the United States of America   106, 17921-17926 (2009)   
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Peeling back the mystery of DNA overstretching
Mark C. Williams, Ioulia Rouzina, and Micah J. McCauley
Proceedings of the National Academy of Sciences of the United States of America   106, 18047-18048 (2009)   
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SSB protein diffusion on single-stranded DNA stimulates RecA filament formation
Rahul Roy, Alexander G. Kozlov, Timothy M. Lohman, and Taekjip Ha
Nature   461, 1092-1097 (2009)   
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SINGLE MOLECULE DYNAMICS

Force-velocity relations for multiple-molecular-motor transport
Ziqing Wang and Ming Li
Physical Review E   80, 041923 (2009) (4 pages)   
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Traffic by multiple species of molecular motors
Yan Chai, Stefan Klumpp, Melanie J. I. Müller, and Reinhard Lipowsky
Physical Review E   80, 041928 (2009) (9 pages)   
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Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations
Nobuyasu Koga, Tomoshi Kameda, Kei-ichi Okazaki, and Shoji Takada
Proceedings of the National Academy of Sciences of the United States of America   106, 18237-18242 (2009)   
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Mechanochemical model for myosin V
Erin M. Craig and Heiner Linke
Proceedings of the National Academy of Sciences of the United States of America   106, 18261-18266 (2009)   
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Continuous imaging of plasmon rulers in live cells reveals early-stage caspase-3 activation at the single-molecule level
Young-wook Jun, Sassan Sheikholeslami, Daniel R. Hostetter, Cheryl Tajon, Charles S. Craik, and A. Paul Alivisatos
Proceedings of the National Academy of Sciences of the United States of America   106, 17735-17740 (2009)   
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Strong field line shapes and photon statistics from a single molecule under anomalous noise
František Šanda
Physical Review E   80, 041132 (2009) (7 pages)   
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Manipulation of single DNA molecules by using optically projected images
Yen-Heng Lin, Chen-Min Chang, and Gwo-Bin Lee
Optics Express   17, 15318-15329 (2009)   
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Kinesin's step dissected with single-motor FRET
Sander Verbrugge, Zdenek Lansky, and Erwin J. G. Peterman
Proceedings of the National Academy of Sciences of the United States of America   106, 17741-17746 (2009)   
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INTERMOLECULAR INTERACTIONS

Self-assembly of cholesterol DNA at liquid crystal/aqueous interface and its application for DNA detection
Siok Lian Lai, Deny Hartono, and Kun-Lin Yang
Applied Physics Letters   95, 153702 (2009) (3 pages)   
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Thermodynamic basis of chiral recognition in a DNA aptamer
Po-Hsun Lin, Shau-Jhu Tong, Selva Roselin Louis, Yung Chang, and Wen-Yih Chen
Physical Chemistry Chemical Physics   11, 9744-9750 (2009)   
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Kirkwood–Buff theory of molecular and protein association, aggregation, and cellular crowding
Moon Bae Gee and Paul E. Smith
The Journal of Chemical Physics   131, 165101 (2009) (11 pages)   
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2D IR provides evidence for mobile water molecules in -amyloid fibrils
Yung Sam Kim, Liu Liu, Paul H. Axelsen, and Robin M. Hochstrasser
Proceedings of the National Academy of Sciences of the United States of America   106, 17751-17756 (2009)   
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Immobilization of catalase on electrospun nanofibrous membranes modified with bovine serum albumin or collagen: Coupling site-dependent activity and protein-dependent stability
Zhen-Gang Wang, Ling-Shu Wan, and Zhi-Kang Xu
Soft Matter   5, 4161-4168 (2009)   
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Spontaneous Imbibition Dynamics of an n-Alkane in Nanopores: Evidence of Meniscus Freezing and Monolayer Sticking
Simon Gruener and Patrick Huber
Physical Review Letters   103, 174501 (2009) (4 pages)   
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Intermolecular aurophilic interactions facilitate assembly of a complex rotaxane in solution
Ulrike E. I. Horvath, Jean M. McKenzie, Stephanie Cronje, Helgard G. Raubenheimer, and Leonard J. Barbour
Chemical Communications   2009, 6598-6600 (2009)   
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Microscopic density functional theory for dendrimers
Alexandr Malijevský
Physical Review E   80, 042801 (2009) (4 pages)   
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Diffusion and molecular binding in crowded vesicle solutions measured by fluorescence correlation spectroscopy
Hanna Engelke, Ingmar Dorn, and Joachim O. Rädler
Soft Matter   5, 4283-4289 (2009)   
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Electrostatically tuned DNA adsorption on like-charged colloids and resultant colloidal clustering
Lu Zhang and Yingxi Zhu
Soft Matter   5, 4290-4296 (2009)   
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Design of a -hairpin peptide-intercalator conjugate for simultaneous recognition of single stranded and double stranded regions of RNA
Lauren L. Cline and Marcey L. Waters
Organic and Biomolecular Chemistry   7, 4622-4630 (2009)   
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Design and x-ray crystal structures of high-potency nonsteroidal glucocorticoid agonists exploiting a novel binding site on the receptor
Keith Biggadike, Randy K. Bledsoe, Diane M. Coe, Tony W. J. Cooper, David House, Marie A. Iannone, Simon J. F. Macdonald, Kevin P. Madauss, Iain M. McLay, Tracy J. Shipley, Simon J. Taylor, Thuy B. Tran, Iain J. Uings, Victoria Weller, and Shawn P. Williams
Proceedings of the National Academy of Sciences of the United States of America   106, 18114-18119 (2009)   
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PHYSICAL STUDIES OF CELL MECHANICS

Rebuilding cytoskeleton roads: Active-transport-induced polarization of cells
R. J. Hawkins, O. Bénichou, M. Piel, and R. Voituriez
Physical Review E   80, 040903 (2009) (4 pages)   
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Why Do Red Blood Cells Have Asymmetric Shapes Even in a Symmetric Flow?
Badr Kaoui, George Biros, and Chaouqi Misbah
Physical Review Letters   103, 188101 (2009) (4 pages)   
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Mapping the mechanics and macromolecular organization of hyaluronan-rich cell coats
Heike Boehm, Tabea A. Mundinger, Christian H. J. Boehm, Valentin Hagel, Uwe Rauch, Joachim P. Spatz, and Jennifer E. Curtis
Soft Matter   5, 4331-4337 (2009)   
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Influence of cytoskeleton on nanoparticle migration in biological cells
A. Tarasenko and L. Jastrabik
Applied Physics Letters   95, 173705 (2009) (3 pages)   
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Single-cell response to stiffness exhibits muscle-like behavior
Démosthène Mitrossilis, Jonathan Fouchard, Axel Guiroy, Nicolas Desprat, Nicolas Rodriguez, Ben Fabry, and Atef Asnacios
Proceedings of the National Academy of Sciences of the United States of America   106, 18243-18248 (2009)   
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Live-Cell-Driven Insertion of a Nanoneedle
Takayuki Hoshino, Tomohiro Konno, Kazuhiko Ishihara, and Keisuke Morishima
Japanese Journal of Applied Physics   48, 107002 (2009) (6 pages)   
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Assembly of viruses and the pseudo-law of mass action
Alexander Yu. Morozov, Robijn F. Bruinsma, and Joseph Rudnick
The Journal of Chemical Physics   131, 155101 (2009) (17 pages)   
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Immune synapse formation determines interaction forces between T cells and antigen-presenting cells measured by atomic force microscopy
Babak H. Hosseini, Ilia Louban, Dominik Djandji, Guido H. Wabnitz, Janosch Deeg, Nadja Bulbuc, Yvonne Samstag, Matthias Gunzer, Joachim P. Spatz, and Günter J. Hämmerling
Proceedings of the National Academy of Sciences of the United States of America   106, 17852-17857 (2009)   
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Population distribution of wavefront aberrations in the peripheral human eye
Linda Lundström, Jörgen Gustafsson, and Peter Unsbo
Journal of the Optical Society of America A   26, 2192-2198 (2009)   
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Dielectric barrier discharge plasma treatment on E. coli: Influence of CH₄/N₂, O₂, N₂/O₂, N₂, and Ar gases
Abhijit Majumdar, Rajesh Kumar Singh, Gottfried J. Palm, and Rainer Hippler
Journal of Applied Physics   106, 084701 (2009) (5 pages)   
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Accurate simulation dynamics of microscopic filaments using “caterpillar” Oseen hydrodynamics
A. G. Bailey, C. P. Lowe, I. Pagonabarraga, and M. Cosentino Lagomarsino
Physical Review E   80, 046707 (2009) (8 pages)   
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INFORMATION TRANSFER IN BIOLOGICAL SYSTEMS

Spatiotemporal control of cell signalling using a light-switchable protein interaction
Anselm Levskaya, Orion D. Weiner, Wendell A. Lim, and Christopher A. Voigt
Nature   461, 997-1001 (2009)   
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Endosomes: A legitimate platform for the signaling train
Jane E. Murphy, Benjamin E. Padilla, Burcu Hasdemir, Graeme S. Cottrell, and Nigel W. Bunnett
Proceedings of the National Academy of Sciences of the United States of America   106, 17615-17622 (2009)   
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Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis
E. J. Sambriski, D. C. Schwartz, and J. J. de Pablo
Proceedings of the National Academy of Sciences of the United States of America   106, 18125-18130 (2009)   
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Age at first reproduction explains rate variation in the strepsirrhine molecular clock
C. Tsantes and M. E. Steiper
Proceedings of the National Academy of Sciences of the United States of America   106, 18165-18170 (2009)   
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Visual but not trigeminal mediation of magnetic compass information in a migratory bird
Manuela Zapka, Dominik Heyers, Christine M. Hein, Svenja Engels, Nils-Lasse Schneider, Jörg Hans, Simon Weiler, David Dreyer, Dmitry Kishkinev, J. Martin Wild, and Henrik Mouritsen
Nature   461, 1274-1277 (2009)   
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Optical control of zebrafish behavior with halorhodopsin
Aristides B. Arrenberg, Filippo Del Bene, and Herwig Baier
Proceedings of the National Academy of Sciences of the United States of America   106, 17968-17973 (2009)   
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MULTICELLULAR PHENOMENA

Noise and Synchronization in Pairs of Beating Eukaryotic Flagella
Raymond E. Goldstein, Marco Polin, and Idan Tuval
Physical Review Letters   103, 168103 (2009) (4 pages)   
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The adventures of Dicty, the Dictyostelium cell
Meghan Driscoll, Rael Kopace, Linjie Li, Colin McCann, John Watts, John T. Fourkas, and Wolfgang Losert
Chaos   19, 041110 (2009) (1 page)   
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Photometric measurements of red blood cell aggregation: light transmission versus light reflectance
Oguz K. Baskurt, Mehmet Uyuklu, Max R. Hardeman, and Herbert J. Meiselman
Journal of Biomedical Optics   14, 054044 (2009) (6 pages)   
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Bacillus subtilis spreads by surfing on waves of surfactant
Thomas E. Angelini, Marcus Roper, Roberto Kolter, David A. Weitz, and Michael P. Brenner
Proceedings of the National Academy of Sciences of the United States of America   106, 18109-18113 (2009)   
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Size Regulation in the Segmentation of Drosophila: Interacting Interfaces between Localized Domains of Gene Expression Ensure Robust Spatial Patterning
Sergei Vakulenko, Manu, John Reinitz, and Ovidiu Radulescu
Physical Review Letters   103, 168102 (2009) (4 pages)   
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Intracellular dynamics of hippocampal place cells during virtual navigation
Christopher D. Harvey, Forrest Collman, Daniel A. Dombeck, and David W. Tank
Nature   461, 941-946 (2009)   
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Three-dimensional model for the effective viscosity of bacterial suspensions
Brian M. Haines, Andrey Sokolov, Igor S. Aranson, Leonid Berlyand, and Dmitry A. Karpeev
Physical Review E   80, 041922 (2009) (7 pages)   
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BIOLOGICAL NETWORKS

Feed-forward inhibition as a buffer of the neuronal input-output relation
Michele Ferrante, Michele Migliore, and Giorgio A. Ascoli
Proceedings of the National Academy of Sciences of the United States of America   106, 18004-18009 (2009)   
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Ubiquitous “glassy” relaxation in catalytic reaction networks
Akinori Awazu and Kunihiko Kaneko
Physical Review E   80, 041931 (2009) (7 pages)   
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Regulation of cortical microcircuits by unitary GABA-mediated volume transmission
Szabolcs Oláh, Miklós Füle, Gergely Komlósi, Csaba Varga, Rita Báldi, Pál Barzó, and Gábor Tamás
Nature   461, 1278-1281 (2009)   
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Simple model for bursting dynamics of neurons
Anandamohan Ghosh, Dipanjan Roy, and Viktor K. Jirsa
Physical Review E   80, 041930 (2009) (5 pages)   
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Inhibition of protein kinase C signaling protects prefrontal cortex dendritic spines and cognition from the effects of chronic stress
Avis Brennan Hains, Mai Anh T. Vu, Paul K. Maciejewski, Christopher H. van Dyck, Melissa Gottron, and Amy F. T. Arnsten
Proceedings of the National Academy of Sciences of the United States of America   106, 17957-17962 (2009)   
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Layer-specific network oscillation and spatiotemporal receptive field in the visual cortex
Wenzhi Sun and Yang Dan
Proceedings of the National Academy of Sciences of the United States of America   106, 17986-17991 (2009)   
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Similarity index based on local paths for link prediction of complex networks
Linyuan Lü, Ci-Hang Jin, and Tao Zhou
Physical Review E   80, 046122 (2009) (9 pages)   
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Strong associations between microbe phenotypes and their network architecture
Soumen Roy and Vladimir Filkov
Physical Review E   80, 040902 (2009) (4 pages)   
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Control of Iron Homeostasis by an Iron-Regulated Ubiquitin Ligase
Ajay A. Vashisht, Kimberly B. Zumbrennen, Xinhua Huang, David N. Powers, Armando Durazo, Dahui Sun, Nimesh Bhaskaran, Anja Persson, Mathias Uhlen, Olle Sangfelt, Charles Spruck, Elizabeth A. Leibold, and James A. Wohlschlegel
Science   326, 718-721 (2009)   
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A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila
Kuniaki Saito, Sachi Inagaki, Toutai Mituyama, Yoshinori Kawamura, Yukiteru Ono, Eri Sakota, Hazuki Kotani, Kiyoshi Asai, Haruhiko Siomi, and Mikiko C. Siomi
Nature   461, 1296-1299 (2009)   
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Quantifying the Impact of Immune Escape on Transmission Dynamics of Influenza
Andrew W. Park, Janet M. Daly, Nicola S. Lewis, Derek J. Smith, James L. N. Wood, and Bryan T. Grenfell
Science   326, 726-728 (2009)   
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QUANTITATIVE GENOMICS

Pten in stromal fibroblasts suppresses mammary epithelial tumours
Anthony J. Trimboli, Carmen Z. Cantemir-Stone, Fu Li, Julie A. Wallace, Anand Merchant, Nicholas Creasap, John C. Thompson, Enrico Caserta, Hui Wang, Jean-Leon Chong, Shan Naidu, Guo Wei, Sudarshana M. Sharma, Julie A. Stephens, Soledad A. Fernandez, Metin N. Gurcan, Michael B. Weinstein, Sanford H. Barsky, Lisa Yee, Thomas J. Rosol, Paul C. Stromberg, Michael L. Robinson, Francois Pepin, Michael Hallett, Morag Park, Michael C. Ostrowski, and Gustavo Leone
Nature   461, 1084-1091 (2009)   
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Genome evolution and adaptation in a long-term experiment with Escherichia coli
Jeffrey E. Barrick, Dong Su Yu, Sung Ho Yoon, Haeyoung Jeong, Tae Kwang Oh, Dominique Schneider, Richard E. Lenski, and Jihyun F. Kim
Nature   461, 1243-1247 (2009)   
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Spectral solutions to stochastic models of gene expression with bursts and regulation
Andrew Mugler, Aleksandra M. Walczak, and Chris H. Wiggins
Physical Review E   80, 041921 (2009) (19 pages)   
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Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants
Jennifer S. Hawkins, Stephen R. Proulx, Ryan A. Rapp, and Jonathan F. Wendel
Proceedings of the National Academy of Sciences of the United States of America   106, 17811-17816 (2009)   
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Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids
Misook Ha, Jie Lu, Lu Tian, Vanitharani Ramachandran, Kristin D. Kasschau, Elisabeth J. Chapman, James C. Carrington, Xuemei Chen, Xiu-Jie Wang, and Z. Jeffrey Chen
Proceedings of the National Academy of Sciences of the United States of America   106, 17835-17840 (2009)   
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The transcription factors T-bet and GATA-3 control alternative pathways of T-cell differentiation through a shared set of target genes
Richard G. Jenner, Michael J. Townsend, Ian Jackson, Kaiming Sun, Russell D. Bouwman, Richard A. Young, Laurie H. Glimcher, and Graham M. Lord
Proceedings of the National Academy of Sciences of the United States of America   106, 17876-17881 (2009)   
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Immunologically silent cancer clone transmission from mother to offspring
Takeshi Isoda, Anthony M. Ford, Daisuke Tomizawa, Frederik W. van Delft, David Gonzalez De Castro, Norkio Mitsuiki, Joannah Score, Tomohiko Taki, Tomohiro Morio, Masatoshi Takagi, Hiroh Saji, Mel Greaves, and Shuki Mizutani
Proceedings of the National Academy of Sciences of the United States of America   106, 17882-17885 (2009)   
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Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli
Yoshitoshi Ogura, Tadasuke Ooka, Atsushi Iguchi, Hidehiro Toh, Md Asadulghani, Kenshiro Oshima, Toshio Kodama, Hiroyuki Abe, Keisuke Nakayama, Ken Kurokawa, Toru Tobe, Masahira Hattori, and Tetsuya Hayashi
Proceedings of the National Academy of Sciences of the United States of America   106, 17939-17944 (2009)   
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A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs
Wellington Muchero, Ndeye N. Diop, Prasanna R. Bhat, Raymond D. Fenton, Steve Wanamaker, Marti Pottorff, Sarah Hearne, Ndiaga Cisse, Christian Fatokun, Jeffrey D. Ehlers, Philip A. Roberts, and Timothy J. Close
Proceedings of the National Academy of Sciences of the United States of America   106, 18159-18164 (2009)   
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Site-specific recombination for the modification of transgenic strains of the Mediterranean fruit fly Ceratitis capitata
Marc F. Schetelig, Francesca Scolari, Alfred M. Handler, Sebastian Kittelmann, Giuliano Gasperi, and Ernst A. Wimmer
Proceedings of the National Academy of Sciences of the United States of America   106, 18171-18176 (2009)   
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Regulative recovery in the sea urchin embryo and the stabilizing role of fail-safe gene network wiring
Joel Smith and Eric H. Davidson
Proceedings of the National Academy of Sciences of the United States of America   106, 18291-18296 (2009)   
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Identifying genotype-dependent efficacy of single and combined PI3K- and MAPK-pathway inhibition in cancer
Martin L. Sos, Stefanie Fischer, Roland Ullrich, Martin Peifer, Johannes M. Heuckmann, Mirjam Koker, Stefanie Heynck, Isabel Stückrath, Jonathan Weiss, Florian Fischer, Kathrin Michel, Aviva Goel, Lucia Regales, Katerina A. Politi, Samanthi Perera, Matthäus Getlik, Lukas C. Heukamp, Sascha Ansén, Thomas Zander, Rameen Beroukhim, Hamid Kashkar, Kevan M. Shokat, William R. Sellers, Daniel Rauh, Christine Orr, Klaus P. Hoeflich, Lori Friedman, Kwok-Kin Wong, William Pao, and Roman K. Thomas
Proceedings of the National Academy of Sciences of the United States of America   106, 18351-18356 (2009)   
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Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones
David A. Walsh, Elena Zaikova, Charles G. Howes, Young C. Song, Jody J. Wright, Susannah G. Tringe, Philippe D. Tortell, and Steven J. Hallam
Science   326, 578-582 (2009)   
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Smoothened Mutation Confers Resistance to a Hedgehog Pathway Inhibitor in Medulloblastoma
Robert L. Yauch, Gerrit J. P. Dijkgraaf, Bruno Alicke, Thomas Januario, Christina P. Ahn, Thomas Holcomb, Kanan Pujara, Jeremy Stinson, Christopher A. Callahan, Tracy Tang, J. Fernando Bazan, Zhengyan Kan, Somasekar Seshagiri, Christine L. Hann, Stephen E. Gould, Jennifer A. Low, Charles M. Rudin, and Frederic J. de Sauvage
Science   326, 572-574 (2009)   
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A transcription switch toggled by noncoding RNAs
Fred Winston
Proceedings of the National Academy of Sciences of the United States of America   106, 18049-18050 (2009)   
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Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast
Stacie L. Bumgarner, Robin D. Dowell, Paula Grisafi, David K. Gifford, and Gerald R. Fink
Proceedings of the National Academy of Sciences of the United States of America   106, 18321-18326 (2009)   
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A wave of nascent transcription on activated human genes
Youichiro Wada, Yoshihiro Ohta, Meng Xu, Shuichi Tsutsumi, Takashi Minami, Kenji Inoue, Daisuke Komura, Jun'ichi Kitakami, Nobuhiko Oshida, Argyris Papantonis, Akashi Izumi, Mika Kobayashi, Hiroko Meguro, Yasuharu Kanki, Imari Mimura, Kazuki Yamamoto, Chikage Mataki, Takao Hamakubo, Katsuhiko Shirahige, Hiroyuki Aburatani, Hiroshi Kimura, Tatsuhiko Kodama, Peter R. Cook, and Sigeo Ihara
Proceedings of the National Academy of Sciences of the United States of America   106, 18357-18361 (2009)   
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Ribosomal DNA contributes to global chromatin regulation
Silvana Paredes and Keith A. Maggert
Proceedings of the National Academy of Sciences of the United States of America   106, 17829-17834 (2009)   
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Unexpected consequences of a sudden and massive transposon amplification on rice gene expression
Ken Naito, Feng Zhang, Takuji Tsukiyama, Hiroki Saito, C. Nathan Hancock, Aaron O. Richardson, Yutaka Okumoto, Takatoshi Tanisaka, and Susan R. Wessler
Nature   461, 1130-1134 (2009)   
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A transposon-induced epigenetic change leads to sex determination in melon
Antoine Martin, Christelle Troadec, Adnane Boualem, Mazen Rajab, Ronan Fernandez, Halima Morin, Michel Pitrat, Catherine Dogimont, and Abdelhafid Bendahmane
Nature   461, 1135-1138 (2009)   
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Epigenetic reversion of post-implantation epiblast to pluripotent embryonic stem cells
Siqin Bao, Fuchou Tang, Xihe Li, Katsuhiko Hayashi, Astrid Gillich, Kaiqin Lao, and M. Azim Surani
Nature   461, 1292-1295 (2009)   
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Fast catalytic and electrocatalytic oxidation of sodium borohydride on palladium nanoparticles and its application to ultrasensitive DNA detection
Jagotamoy Das, Heonjo Kim, Kyungmin Jo, Kang Hyun Park, Sangyong Jon, Kwangyeol Lee, and Haesik Yang
Chemical Communications   2009, 6394-6396 (2009)   
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Label-free aptamer-based sensor using abasic site-containing DNA and a nucleobase-specific fluorescent ligand
Zhiai Xu, Kotaro Morita, Yusuke Sato, Qing Dai, Seiichi Nishizawa, and Norio Teramae
Chemical Communications   2009, 6445-6447 (2009)   
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Site-selective scission of human genome by artificial restriction DNA cutter
Kenichiro Ito, Hitoshi Katada, Narumi Shigi, and Makoto Komiyama
Chemical Communications   2009, 6542-6544 (2009)   
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Homologous recombination in human cells using artificial restriction DNA cutter
Hitoshi Katada, Hsuan Jung Chen, Narumi Shigi, and Makoto Komiyama
Chemical Communications   2009, 6545-6547 (2009)   
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Transgenic songbirds offer an opportunity to develop a genetic model for vocal learning
R. J. Agate, B. B. Scott, B. Haripal, C. Lois, and F. Nottebohm
Proceedings of the National Academy of Sciences of the United States of America   106, 17963-17967 (2009)   
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STATISTICAL AND NONLINEAR PHYSICS

Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations
Daniel K. Shenfeld, Huafeng Xu, Michael P. Eastwood, Ron O. Dror, and David E. Shaw
Physical Review E   80, 046705 (2009) (4 pages)   
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Analytical results for bond percolation and k-core sizes on clustered networks
James P. Gleeson and Sergey Melnik
Physical Review E   80, 046121 (2009) (13 pages)   
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Isochronal sampling in non-Boltzmann Monte Carlo methods
Charlles R. A. Abreu
The Journal of Chemical Physics   131, 154113 (2009) (11 pages)   
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Error and efficiency of replica exchange molecular dynamics simulations
Edina Rosta and Gerhard Hummer
The Journal of Chemical Physics   131, 165102 (2009) (12 pages)   
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Using the minimum description length principle for global reconstruction of dynamic systems from noisy time series
Ya. I. Molkov, D. N. Mukhin, E. M. Loskutov, A. M. Feigin, and G. A. Fidelin
Physical Review E   80, 046207 (2009) (6 pages)   
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Dynamical formation of stable irregular transients in discontinuous map systems
Hailin Zou, Shuguang Guan, and C.-H. Lai
Physical Review E   80, 046214 (2009) (6 pages)   
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Accurate noise projection for reduced stochastic epidemic models
Eric Forgoston, Lora Billings, and Ira B. Schwartz
Chaos   19, 043110 (2009) (15 pages)   
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Viscoelastic subdiffusion: From anomalous to normal
Igor Goychuk
Physical Review E   80, 046125 (2009) (11 pages)   
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Topological phase transition in a RNA model in the de Gennes regime
Matías G. dell'Erba and Guillermo R. Zemba
Physical Review E   80, 041926 (2009) (7 pages)   
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WKB theory of epidemic fade-out in stochastic populations
Baruch Meerson and Pavel V. Sasorov
Physical Review E   80, 041130 (2009) (4 pages)   
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Residential segregation and cultural dissemination: An Axelrod-Schelling model
C. Gracia-Lázaro, L. F. Lafuerza, L. M. Floría, and Y. Moreno
Physical Review E   80, 046123 (2009) (5 pages)   
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Analysis and Monte Carlo simulations of a model for the spread of infectious diseases in heterogeneous metapopulations
David Juher, Jordi Ripoll, and Joan Saldaña
Physical Review E   80, 041920 (2009) (9 pages)   
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INSTRUMENTATION DEVELOPMENT

High-throughput in vivo screening of targeted molecular imaging agents
M. Karen J. Gagnon, Sven H. Hausner, Jan Marik, Craig K. Abbey, John F. Marshall, and Julie L. Sutcliffe
Proceedings of the National Academy of Sciences of the United States of America   106, 17904-17909 (2009)   
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A versatile liquid-core/liquid-twin-cladding waveguide micro flow cell fabricated by rapid prototyping
M. Rosenauer and M. J. Vellekoop
Applied Physics Letters   95, 163702 (2009) (3 pages)   
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Mesoporous zirconium oxide nanomaterials effectively enrich phosphopeptides for mass spectrometry-based phosphoproteomics
Cory A. Nelson, Jeannine R. Szczech, Qingge Xu, Mathew J. Lawrence, Song Jin, and Ying Ge
Chemical Communications   2009, 6607-6609 (2009)   
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SNP genotyping of unpurified PCR products by sandwich-type affinity electrophoresis on a microchip with programmed autonomous solution filling
Akira Inoue, Aishan Han, Kimiko Makino, Kazuo Hosokawa, and Mizuo Maeda
Lab on a Chip   9, 3297-3302 (2009)   
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Agarose microwell based neuronal micro-circuit arrays on microelectrode arrays for high throughput drug testing
Gyumin Kang, Ji-Hye Lee, Chang-Soo Lee, and Yoonkey Nam
Lab on a Chip   9, 3236-3242 (2009)   
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Development of Raman microspectroscopy for automated detection and imaging of basal cell carcinoma
Marta Larraona-Puy, Adrian Ghita, Alina Zoladek, William Perkins, Sandeep Varma, Iain H. Leach, Alexey A. Koloydenko, Hywel Williams, and Ioan Notingher
Journal of Biomedical Optics   14, 054031 (2009) (10 pages)   
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Repetition rate dependency of reactive oxygen species formation during femtosecond laser–based cell surgery
Judith Baumgart, Kai Kuetemeyer, Willem Bintig, Anaclet Ngezahayo, Wolfgang Ertmer, Holger Lubatschowski, and Alexander Heisterkamp
Journal of Biomedical Optics   14, 054040 (2009) (9 pages)   
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Microfluidic system with integrated electroosmotic pumps, concentration gradient generator and fish cell line (RTgill-W1)—towards water toxicity testing
Tomasz Glawdel, Caglar Elbuken, Lucy E. J. Lee, and Carolyn L. Ren
Lab on a Chip   9, 3243-3250 (2009)   
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Development of a diffraction imaging flow cytometer
Kenneth M. Jacobs, Jun Q. Lu, and Xin-Hua Hu
Optics Letters   34, 2985-2987 (2009)   
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Optical tweezers with millikelvin precision of temperature-controlled objectives and base-pair resolution
Mohammed Mahamdeh and Erik Schäffer
Optics Express   17, 17190-17199 (2009)   
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Novel fluorescence molecular imaging of chemotherapy-induced intestinal apoptosis
Galit Levin, Anat Shirvan, Hagit Grimberg, Ayelet Reshef, Merav Yogev-Falach, Avi Cohen, and Ilan Ziv
Journal of Biomedical Optics   14, 054019 (2009) (8 pages)   
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Study of cadmium-induced cytotoxicity using two-photon excitation endogenous fluorescence microscopy
Dong Li, Mildred S. Yang, Tao Lin, Wei Zheng, and Jianan Y. Qu
Journal of Biomedical Optics   14, 054028 (2009) (8 pages)   
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New method of estimating wavelength-dependent optical path length ratios for oxy- and deoxyhemoglobin measurement using near-infrared spectroscopy
Shinji Umeyama and Toru Yamada
Journal of Biomedical Optics   14, 054038 (2009) (6 pages)   
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Specific immobilization of influenza A virus on GaAs (001) surface
Valerie Duplan, Yannick Miron, Eric Frost, Michel Grandbois, and Jan J. Dubowski
Journal of Biomedical Optics   14, 054042 (2009) (6 pages)   
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Evans blue dye-enhanced capillary-resolution photoacoustic microscopy in vivo
Junjie Yao, Konstantin Maslov, Song Hu, and Lihong V. Wang
Journal of Biomedical Optics   14, 054049 (2009) (6 pages)   
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Characterization of single heat-activated Bacillus spores using laser tweezers ?Raman spectroscopy
Pengfei Zhang, Peter Setlow, and Yongqing Li
Optics Express   17, 16480-16491 (2009)   
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Late-fluorescence mammography assesses tumor capillary permeability and differentiates malignant from benign lesions
Axel Hagen, Dirk Grosenick, Rainer Macdonald, Herbert Rinneberg, Susen Burock, Peter Warnick, Alexander Poellinger, and Peter M. Schlag
Optics Express   17, 17016-17033 (2009)   
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Tracking lineages of single cells in lines using a microfluidic device
Amy C. Rowat, James C. Bird, Jeremy J. Agresti, Oliver J. Rando, and David A. Weitz
Proceedings of the National Academy of Sciences of the United States of America   106, 18149-18154 (2009)   
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Cerium oxide-chitosan based nanobiocomposite for food borne mycotoxin detection
Ajeet Kaushik, Pratima R. Solanki, M. K. Pandey, Sharif Ahmad, and Bansi D. Malhotra
Applied Physics Letters   95, 173703 (2009) (3 pages)   
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Automated segmentation of the macula by optical coherence tomography
Tapio Fabritius, Shuichi Makita, Masahiro Miura, Risto Myllylä, and Yoshiaki Yasuno
Optics Express   17, 15659-15669 (2009)   
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Dielectrophoretic field-flow method for separating particle populations in a chip with asymmetric electrodes
Ciprian Iliescu, Guillaume Tresset, and Guolin Xu
Biomicrofluidics   3, 044104 (2009) (10 pages)   
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Broadband reflectance spectroscopy for establishing a quantitative metric of vascular leak using the Miles assay
John McMurdy, Jonathan Reichner, Zara Mathews, Mary Markey, Sunny Intwala, and Gregory Crawford
Journal of Biomedical Optics   14, 054012 (2009) (6 pages)   
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Electrochemical Differentiation and TOF-SIMS Characterization of Thiol-Coated Gold Features for (Bio)chemical Sensor Applications
Michal Tencer, Heng-Yong Nie, and Pierre Berini
Journal of The Electrochemical Society   156, J386-J392 (2009)   
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A miniaturized fiber-coupled terahertz endoscope system
Young Bin Ji, Eui Su Lee, Sang-Hoon Kim, Joo-Hiuk Son, and Tae-In Jeon
Optics Express   17, 17082-17087 (2009)   
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Hard-X-Ray Phase-Difference Microscopy Using a Fresnel Zone Plate and a Transmission Grating
W. Yashiro, Y. Takeda, A. Takeuchi, Y. Suzuki, and A. Momose
Physical Review Letters   103, 180801 (2009) (4 pages)   
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Use of two-dimensional phase-only filters and compounding for speckle reduction and edge detection in ultrasonic B-scan images
P. M. Shankar
Applied Optics   48, 5589-5597 (2009)   
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A room temperature 19-channel magnetic field mapping device for cardiac signals
G. Bison, N. Castagna, A. Hofer, P. Knowles, J.-L. Schenker, M. Kasprzak, H. Saudan, and A. Weis
Applied Physics Letters   95, 173701 (2009) (3 pages)   
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Design and optimization of a double-enzyme glucose assay in microfluidic lab-on-a-chip
Yegermal Tesfaw Atalay, Daan Witters, Steven Vermeir, Nicolas Vergauwe, Pieter Verboven, Bart Nicolaï, and Jeroen Lammertyn
Biomicrofluidics   3, 044103 (2009) (14 pages)   
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Optical properties of dental restorative materials in the wavelength range 400  to  700  nm for the simulation of color perception
Moritz Friebel, Kirsten Povel, Hans-Joachim Cappius, Jürgen Helfmann, and Martina Meinke
Journal of Biomedical Optics   14, 054029 (2009) (7 pages)   
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Comparison of spectroscopically measured tissue alcohol concentration to blood and breath alcohol measurements
Trent D. Ridder, Benjamin J. Ver Steeg, and Bentley D. Laaksonen
Journal of Biomedical Optics   14, 054039 (2009) (11 pages)   
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Quantitative optical spectroscopy can identify long-term local tumor control in irradiated murine head and neck xenografts
Karthik Vishwanath, Daniel Klein, Kevin Chang, Thies Schroeder, Mark W. Dewhirst, and Nimmi Ramanujam
Journal of Biomedical Optics   14, 054051 (2009) (4 pages)   
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A source reconstruction algorithm based on adaptive hp-FEM for bioluminescence tomography
Runqiang Han, Jimin Liang, Xiaochao Qu, Yanbin Hou, Nunu Ren, Jingjing Mao, and Jie Tian
Optics Express   17, 14481-14494 (2009)   
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Chromophore concentrations, absorption and scattering properties of human skin in-vivo
Sheng-Hao Tseng, Paulo Bargo, Anthony Durkin, and Nikiforos Kollias
Optics Express   17, 14599-14617 (2009)   
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Ultra high-speed swept source OCT imaging of the anterior segment of human eye at 200 kHz with adjustable imaging range
Michalina Gora, Karol Karnowski, Maciej Szkulmowski, Bartlomiej J. Kaluzny, Robert Huber, Andrzej Kowalczyk, and Maciej Wojtkowski
Optics Express   17, 14880-14894 (2009)   
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Probabilistic atlas can improve reconstruction from optical imaging of the neonatal brain
Juha Heiskala, Mika Pollari, Marjo Metsäranta, P. Ellen Grant, and Ilkka Nissilä
Optics Express   17, 14977-14992 (2009)   
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Experimental evaluation of optimized ablation patterns for laser refractive surgery
Carlos Dorronsoro, Laura Remon, Jesús Merayo-Lloves, and Susana Marcos
Optics Express   17, 15292-15307 (2009)   
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Laser ultrasonic surface wave dispersion technique for non-destructive evaluation of human dental enamel
Hsiao-Chuan Wang, Simon Fleming, Yung-Chun Lee, Sue Law, Michael Swain, and Jing Xue
Optics Express   17, 15592-15607 (2009)   
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Ultra-fast multispectral optical imaging of cortical oxygenation, blood flow, and intracellular calcium dynamics
Matthew B. Bouchard, Brenda R. Chen, Sean A. Burgess, and Elizabeth M. C. Hillman
Optics Express   17, 15670-15678 (2009)   
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Seven-wavelength time-resolved optical mammography extending beyond 1000 nm for breast collagen quantification
Paola Taroni, Antonio Pifferi, Elena Salvagnini, Lorenzo Spinelli, Alessandro Torricelli, and Rinaldo Cubeddu
Optics Express   17, 15932-15946 (2009)   
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Three-dimensional combined photoacoustic and optical coherence microscopy for in vivo microcirculation studies
Li Li, Konstantin Maslov, Geng Ku, and Lihong V. Wang
Optics Express   17, 16450-16455 (2009)   
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Experimental bioluminescence tomography with fully parallel radiative-transfer-based reconstruction framework
Yujie Lu, Hidevaldo B. Machado, Ali Douraghy, David Stout, Harvey Herschman, and Arion F. Chatziioannou
Optics Express   17, 16681-16695 (2009)   
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1 mm ultrafast superconducting stripline molecule detector
N. Zen (全伸幸), A. Casaburi, S. Shiki (志岐成友), K. Suzuki (鈴木宏治), M. Ejrnaes, R. Cristiano, and M. Ohkubo (大久保雅隆)
Applied Physics Letters   95, 172508 (2009) (3 pages)   
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Experimental investigation of evanescence-based infrared biodetection technique for micro-total-analysis systems
Arvind Chandrasekaran and Muthukumaran Packirisamy
Journal of Biomedical Optics   14, 054050 (2009) (11 pages)   
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Enhancing DNA hybridization kinetics through constriction-based dielectrophoresis
Nathan Swami, Chia-Fu Chou, Venkatraman Ramamurthy, and Vasudha Chaurey
Lab on a Chip   9, 3212-3220 (2009)   
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Imaging chromophores with undetectable fluorescence by stimulated emission microscopy
Wei Min, Sijia Lu, Shasha Chong, Rahul Roy, Gary R. Holtom, and X. Sunney Xie
Nature   461, 1105-1109 (2009)   
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An experimental platform for systemic drug delivery to the retina
Matthew Campbell, Anh T. H. Nguyen, Anna-Sophia Kiang, Lawrence C. S. Tam, Oliviero L. Gobbo, Christian Kerskens, Sorcha Ni Dhubhghaill, Marian M. Humphries, G.-Jane Farrar, Paul F. Kenna, and Peter Humphries
Proceedings of the National Academy of Sciences of the United States of America   106, 17817-17822 (2009)   
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Connecting fabrication defects to fault models and SPICE simulations for DNA self-assembled nanoelectronics
V. Mao, V. Thusu, C. Dwyer, and K. Chakrabarty
IET Computers & Digital Techniques   3, 553-569 (2009)   
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Femtosecond Laser Processing of Agarose Gel Surrounding Protein Crystals for Development of an Automated Crystal Capturing System
Shigeru Sugiyama, Hitoshi Hasenaka, Mika Hirose, Noriko Shimizu, Tomoya Kitatani, Yoshinori Takahashi, Hiroaki Adachi, Kazufumi Takano, Satoshi Murakami, Tsuyoshi Inoue, Yusuke Mori, and Hiroyoshi Matsumura
Japanese Journal of Applied Physics   48, 105502 (2009) (5 pages)   
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Pt metallization of laser transformed medical grade silicone rubber: Last step toward a miniaturized nerve electrode fabrication process
C. Dupas-Bruzek, P. Dréan, and D. Derozier
Journal of Applied Physics   106, 074913 (2009) (5 pages)   
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High-throughput confinement and detection of single DNA molecules in aqueous microdroplets
Monpichar Srisa-Art, Andrew J. deMello, and Joshua B. Edel
Chemical Communications   2009, 6548-6550 (2009)   
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Detection of DNA using bioactive paper strips
M. Monsur Ali, Sergio D. Aguirre, Yaqin Xu, Carlos D. M. Filipe, Robert Pelton, and Yingfu Li