Bibliografic database on Semiconductors, Heterostructures and Biophysics

1988 - 2008 year

• Model for Stretching and Unfolding the Giant Multidomain Muscle Protein Using Single-Molecule Force Spectroscopy
  Douglas B. Staple, Stephen H. Payne, Andrew L. Reddin, and Hans Jürgen Kreuzer
  Phys. Rev. Lett. 101, 248301 (2008)
• Length of Time
  Edward H. Feng and Gavin E. Crooks
  Phys. Rev. Lett. 101, 090602 (2008)
• Impact of Loop Statistics on the Thermodynamics of RNA Folding
  Thomas R. Einert, Paul Näger, Henri Orland, and Roland R. Netz
  Phys. Rev. Lett. 101, 048103 (2008)
• Radial Distribution of RNA Genomes Packaged inside Spherical Viruses
  Se Il Lee and Toan T. Nguyen
  Phys. Rev. Lett. 100, 198102 (2008)
• Melting of Branched RNA Molecules
  Ralf Bundschuh and Robijn Bruinsma
  Phys. Rev. Lett. 100, 148101 (2008)
• Effects of Spatial Competition on the Diversity of a Quasispecies
  Jacobo Aguirre and Susanna C. Manrubia
  Phys. Rev. Lett. 100, 038106 (2008)
• Reversibility, Heat Dissipation, and the Importance of the Thermal Environment in Stochastic Models of Nonequilibrium Steady States
  R. A. Blythe
  Phys. Rev. Lett. 100, 010601 (2008)
• Force-induced misfolding in RNA
  M. Manosas, I. Junier, and F. Ritort
  Phys. Rev. E 78, 061925 (2008)
• Nonspecific interactions in spontaneous assembly of empty versus functional single-stranded RNA viruses
  Antonio Šiber and Rudolf Podgornik
  Phys. Rev. E 78, 051915 (2008)
• Model of human immunodeficiency virus budding and self-assembly: Role of the cell membrane
  Rui Zhang and Toan T. Nguyen
  Phys. Rev. E 78, 051903 (2008)
• Experiments and simulation models of a basic computation element of an autonomous molecular computing system
  Masahiro Takinoue, Daisuke Kiga, Koh-ichiroh Shohda, and Akira Suyama
  Phys. Rev. E 78, 041921 (2008)
• Modeling background intensity in DNA microarrays
  K. M. Kroll, G. T. Barkema, and E. Carlon
  Phys. Rev. E 77, 061915 (2008)
• Two-state model for helicase translocation and unwinding of nucleic acids
  Ashok Garai, Debashish Chowdhury, and M. D. Betterton
  Phys. Rev. E 77, 061910 (2008)
• Interacting RNA polymerase motors on a DNA track: Effects of traffic congestion and intrinsic noise on RNA synthesis
  Tripti Tripathi and Debashish Chowdhury
  Phys. Rev. E 77, 011921 (2008)
• Observation of a dynamic crossover in RNA hydration water which triggers a dynamic transition in the biopolymer
  Xiang-qiang Chu, Emiliano Fratini, Piero Baglioni, Antonio Faraone, and Sow-Hsin Chen
  Phys. Rev. E 77, 011908 (2008)
• Stretching of Homopolymeric RNA Reveals Single-Stranded Helices and Base-Stacking
  Yeonee Seol, Gary M. Skinner, Koen Visscher, Arnaud Buhot, and Avraham Halperin
  Phys. Rev. Lett. 98, 158103 (2007)
• Systematic Field Theory of the RNA Glass Transition
  Francois David and Kay Jörg Wiese
  Phys. Rev. Lett. 98, 128102 (2007)
• Resonant Channel Coupling in Electron Scattering by Pyrazine
  Carl Winstead and Vincent McKoy
  Phys. Rev. Lett. 98, 113201 (2007)
• Soft elasticity of RNA gels and negative Poisson ratio
  Amir Ahsan, Joseph Rudnick, and Robijn Bruinsma
  Phys. Rev. E 76, 061910 (2007)
• Universal power law behaviors in genomic sequences and evolutionary models
  Loredana Martignetti and Michele Caselle
  Phys. Rev. E 76, 021902 (2007)
• RNA folding in the presence of counterions
  Yevgeni Sh. Mamasakhlisov, Shura Hayryan, V. F. Morozov, and Chin-Kun Hu
  Phys. Rev. E 75, 061907 (2007)
• Kinetics of viral self-assembly: Role of the single-stranded RNA antenna
  Tao Hu and B. I. Shklovskii
  Phys. Rev. E 75, 051901 (2007)
• Necklace-cloverleaf transition in associating RNA -like diblock copolymers
  M. V. Tamm and S. K. Nechaev
  Phys. Rev. E 75, 031904 (2007)
• Freezing transition of the random bond RNA model: Statistical properties of the pairing weights
  Cécile Monthus and Thomas Garel
  Phys. Rev. E 75, 031103 (2007)
• RNA secondary structure design
  Bernd Burghardt and Alexander K. Hartmann
  Phys. Rev. E 75, 021920 (2007)
• Traffic of interacting ribosomes: Effects of single-machine mechanochemistry on protein synthesis
  Aakash Basu and Debashish Chowdhury
  Phys. Rev. E 75, 021902 (2007)
• RNA Condensation and the Wetting Transition
  Toan T. Nguyen and Robijn F. Bruinsma
  Phys. Rev. Lett. 97, 108102 (2006)
• Freezing of Random RNA
  Michael Lässig and Kay Jörg Wiese
  Phys. Rev. Lett. 96, 228101 (2006)
• Force-Dependent Fragility in RNA Hairpins
  M. Manosas, D. Collin, and F. Ritort
  Phys. Rev. Lett. 96, 218301 (2006)
• Physical Nature of Bacterial Cytoplasm
  Ido Golding and Edward C. Cox
  Phys. Rev. Lett. 96, 098102 (2006)
• Model for Folding and Aggregation in RNA Secondary Structures
  Vishwesha Guttal and Ralf Bundschuh
  Phys. Rev. Lett. 96, 018105 (2006)
• RNA -like polymer model: Exact calculation on the Bethe lattice
  M. Pretti
  Phys. Rev. E 74, 051803 (2006)
• Analytical theory of the nonequilibrium spatial distribution of RNA polymerase translocations
  Hyung-June Woo
  Phys. Rev. E 74, 011907 (2006)
• Comment on
  E. Carlon, T. Heim, J. Klein Wolterink, and G. T. Barkema
  Phys. Rev. E 73, 063901 (2006)
• Monte Carlo simulations of polyelectrolytes inside viral capsids
  Daniel George Angelescu, Robijn Bruinsma, and Per Linse
  Phys. Rev. E 73, 041921 (2006)
• Topology of pseudoknotted homopolymers
  Graziano Vernizzi, Paolo Ribeca, Henri Orland, and A. Zee
  Phys. Rev. E 73, 031902 (2006)
• Electron spectroscopy in proton collisions with dry gas-phase uracil base
  Patrick Moretto-Capelle and Arnaud Le Padellec
  Phys. Rev. A 74, 062705 (2006)
• All in the RNA family
  Beverly L Davidson
  Nature Biotechnology 24, 951 (2006)
• A genetic strategy to treat sickle cell anemia by coregulating globin transgene expression and RNA interference
  Selda Samakoglu, Leszek Lisowski, Tulin Budak-Alpdogan, Yelena Usachenko, Santina Acuto, Rosalba Di Marzo, Aurelio Maggio, Ping Zhu, John F. Tisdale, Isabelle Rivière and Michel Sadelain
  Nature Biotechnology 24, 89 (2006)
• Short hairpin RNA
  Shuanglin Xiang, Johannes Fruehauf and Chiang J Li
  Nature Biotechnology 24, 697 (2006)
• RNA synthetic biology
  Farren J Isaacs, Daniel J Dwyer and James J Collins
  Nature Biotechnology 24, 545 (2006)
• RNA interference below the immune radar
  Mouldy Sioud
  Nature Biotechnology 24, 521 (2006)
• Corrigendum: All in the RNA family
  Beverly L. Davidson
  Nature Biotechnology 24, 1170 (2006)
• Evaluation of external RNA controls for the assessment of microarray performance
  Weida Tong, Anne Bergstrom Lucas, Richard Shippy, Xiaohui Fan, Hong Fang, Huixiao Hong, Michael S Orr, Tzu-Ming Chu, Xu Guo, Patrick J Collins, Yongming Andrew Sun, Sue-Jane Wang, Wenjun Bao, Russell D Wolfinger, Svetlana Shchegrova, Lei Guo, Janet A Warrington and Leming Shi
  Nature Biotechnology 24, 1132 (2006)
• Using RNA sample titrations to assess microarray platform performance and normalization techniques
  Richard Shippy, Stephanie Fulmer-Smentek, Roderick V Jensen, Wendell D Jones, Paul K Wolber, Charles D Johnson, P Scott Pine, Cecilie Boysen, Xu Guo, Eugene Chudin, Yongming Andrew Sun, James C Willey, Jean Thierry-Mieg, Danielle Thierry-Mieg, Robert A Setterquist, Mike Wilson, Anne Bergstrom Lucas, Natalia Novoradovskaya, Adam Papallo, Yaron Turpaz, Shawn C Baker, Janet A Warrington, Leming Shi and Damir Herman
  Nature Biotechnology 24, 1123 (2006)
• Detection and identification of IHN and ISA viruses by isothermal DNA amplification in microcapillary tubes
  Erik L. McCarthy, Teressa J. Egeler, Lee E. Bickerstaff, Mauricio Pereira da Cunha and Paul J. Millard
  Anal. Bioanal. Chem. 386, 1975 (2006)
• Optimization of DNA-tagged dye-encapsulating liposomes for lateral-flow assays based on sandwich hybridization
  Katie A. Edwards and Antje J. Baeumner
  Anal. Bioanal. Chem. 386, 1335 (2006)
• Mass spectrometric identification and characterization of antimony complexes with ribose-containing biomolecules and an RNA oligomer
  Helle Rüsz Hansen and Spiros A. Pergantis
  Anal. Bioanal. Chem. 385, 821 (2006)
• Optimization of DNA-tagged liposomes for use in microtiter plate analyses
  Katie A. Edwards and Antje J. Baeumner
  Anal. Bioanal. Chem. 385, 1613 (2006)
• Persistence Length Changes Dramatically as RNA Folds
  G. Caliskan, C. Hyeon, U. Perez-Salas, R. M. Briber, S. A. Woodson, and D. Thirumalai
  Phys. Rev. Lett. 95, 268303 (2005)
• Coupled Dynamics of RNA Folding and Nanopore Translocation
  Ralf Bundschuh and Ulrich Gerland
  Phys. Rev. Lett. 95, 208104 (2005)
• Model for Codon Position Bias in RNA Editing
  Tsunglin Liu and Ralf Bundschuh
  Phys. Rev. Lett. 95, 088101 (2005)
• Enumeration of RNA Structures by Matrix Models
  Graziano Vernizzi, Henri Orland, and A. Zee
  Phys. Rev. Lett. 94, 168103 (2005)
• Unravelling the Mechanism of RNA-Polymerase Forward Motion by Using Mechanical Force
  P. Thomen, P. J. Lopez, and F. Heslot
  Phys. Rev. Lett. 94, 128102 (2005)
• Icosahedral Packing of RNA Viral Genomes
  Joseph Rudnick and Robijn Bruinsma
  Phys. Rev. Lett. 94, 038101 (2005)
• Quantification of the differences between quenched and annealed averaging for RNA secondary structures
  Tsunglin Liu and Ralf Bundschuh
  Phys. Rev. E 72, 061905 (2005)
• Core genetic module: The mixed feedback loop
  Paul François and Vincent Hakim
  Phys. Rev. E 72, 031908 (2005)
• Steepest descent calculation of RNA pseudoknots
  M. Pillsbury, Henri Orland, and A. Zee
  Phys. Rev. E 72, 011911 (2005)
• Electrostatics and the assembly of an RNA virus
  P. van der Schoot and R. Bruinsma
  Phys. Rev. E 71, 061928 (2005)
• Dynamics of molecular motors with finite processivity on heterogeneous tracks
  Yariv Kafri, David K. Lubensky, and David R. Nelson
  Phys. Rev. E 71, 041906 (2005)
• Dependence of RNA secondary structure on the energy model
  Bernd Burghardt and Alexander K. Hartmann
  Phys. Rev. E 71, 021913 (2005)
• Theoretical treatment of charge-transfer processes induced by collision of Cq+ ions with uracil
  M. C. Bacchus-Montabonel, M. Łabuda, Y. S. Tergiman, and J. E. Sienkiewicz
  Phys. Rev. A 72, 052706 (2005)
• Clustered Bottlenecks in mRNA Translation and Protein Synthesis
  Tom Chou and Greg Lakatos
  Phys. Rev. Lett. 93, 198101 (2004)
• Elastic Properties of a Single-Stranded Charged Homopolymeric Ribonucleotide
  Yeonee Seol, Gary M. Skinner, and Koen Visscher
  Phys. Rev. Lett. 93, 118102 (2004)
• Disorder and nonconservation in a driven diffusive system
  M. R. Evans, T. Hanney, and Y. Kafri
  Phys. Rev. E 70, 066124 (2004)
• Importance of DNA repair in tumor suppression
  Yisroel Brumer and Eugene I. Shakhnovich
  Phys. Rev. E 70, 061912 (2004)
• Base-sequence-dependent sliding of proteins on DNA
  M. Barbi, C. Place, V. Popkov, and M. Salerno
  Phys. Rev. E 70, 041901 (2004)
• Unfolding single RNA molecules by mechanical force: A stochastic kinetic method
  Fei Liu and Zhong-can Ou-Yang
  Phys. Rev. E 70, 040901 (2004)
• Analytical description of finite size effects for RNA secondary structures
  Tsunglin Liu and Ralf Bundschuh
  Phys. Rev. E 69, 061912 (2004)
• Thermodynamic modeling of donor splice site recognition in pre-mRNA
  Jeffrey A. Garland and Daniel P. Aalberts
  Phys. Rev. E 69, 041903 (2004)
• Transcription rate of RNA polymerase under rotary torque
  H. Kiryu
  Phys. Rev. E 69, 041902 (2004)
• RNA Denaturation: Excluded Volume, Pseudoknots, and Transition Scenarios
  M. Baiesi, E. Orlandini, and A. L. Stella
  Phys. Rev. Lett. 91, 198102 (2003)
• Statistical mechanics of RNA folding: A lattice approach
  P. Leoni and C. Vanderzande
  Phys. Rev. E 68, 051904 (2003)
• Statistical mechanics of RNA folding: Importance of alphabet size
  Ranjan Mukhopadhyay, Eldon Emberly, Chao Tang, and Ned S. Wingreen
  Phys. Rev. E 68, 041904 (2003)
• Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays
  Felix Naef and Marcelo O. Magnasco
  Phys. Rev. E 68, 011906 (2003)
• Statistical physics of RNA folding
  M. Müller
  Phys. Rev. E 67, 021914 (2003)
• Configurational entropy and mechanical properties of cross-linked polymer chains: Implications for protein and RNA folding
  Dmitrii E. Makarov and Gregory J. Rodin
  Phys. Rev. E 66, 011908 (2002)
• Tightness of slip-linked polymer chains
  Ralf Metzler, Andreas Hanke, Paul G. Dommersnes, Yacov Kantor, and Mehran Kardar
  Phys. Rev. E 65, 061103 (2002)
• Ensemble-based control of evolutionary optimization algorithms
  Axel Reimann and Werner Ebeling
  Phys. Rev. E 65, 046106 (2002)
• Zero-temperature properties of RNA secondary structures
  Enzo Marinari, Andrea Pagnani, and Federico Ricci-Tersenghi
  Phys. Rev. E 65, 041919 (2002)
• DNA hybridization to mismatched templates: A chip study
  Felix Naef, Daniel A. Lim, Nila Patil, and Marcelo Magnasco
  Phys. Rev. E 65, 040902 (2002)
• Single molecule statistics and the polynucleotide unzipping transition
  David K. Lubensky and David R. Nelson
  Phys. Rev. E 65, 031917 (2002)
• Statistical mechanics of secondary structures formed by random RNA sequences
  R. Bundschuh and T. Hwa
  Phys. Rev. E 65, 031903 (2002)
• Stretch-Induced Hairpin-Coil Transitions in Designed Polynucleotide Chains
  Haijun Zhou, Yang Zhang, and Zhong-Can Ou-Yang
  Phys. Rev. Lett. 86, 356 (2001)
• Hairpin Formation and Elongation of Biomolecules
  Andrea Montanari and Marc Mézard
  Phys. Rev. Lett. 86, 2178 (2001)
• Comment on "Glassy Transition in a Disordered Model for the RNA Secondary Structure"
  A. K. Hartmann
  Phys. Rev. Lett. 86, 1382 (2001)
• Removal of DNA-bound proteins by DNA twisting
  Abhijit Sarkar and John F. Marko
  Phys. Rev. E 64, 061909 (2001)
• Thermodynamics of local DNA openings
  Tomasz Lipniacki
  Phys. Rev. E 64, 051919 (2001)
• Field theory for a reaction-diffusion model of quasispecies dynamics
  Romualdo Pastor-Satorras and Ricard V. Solé
  Phys. Rev. E 64, 051909 (2001)
• Phylogenetic Study of the Spatial Distribution of Protein-Coding and Control Segments in DNA Chains
  Nestor N. Oiwa and Carla Goldman
  Phys. Rev. Lett. 85, 2396 (2000)
• Glassy Transition in a Disordered Model for the RNA Secondary Structure
  A. Pagnani, G. Parisi, and F. Ricci-Tersenghi
  Phys. Rev. Lett. 84, 2026 (2000)
• Base opening in RNA and DNA duplexes: Implication for RNA stability
  Y. Z. Chen, V. Mohan, and R. H. Griffey
  Phys. Rev. E 61, 5640 (2000)
• RNA Secondary Structure Formation: A Solvable Model of Heteropolymer Folding
  R. Bundschuh and T. Hwa
  Phys. Rev. Lett. 83, 1479 (1999)
• Chemically driven traveling waves in DNA
  Tomasz Lipniacki
  Phys. Rev. E 60, 7253 (1999)
• Energy-level statistics in the fine conformational resolution of RNA folding dynamics
  Ariel Fernández, Teresita Burastero, Rodolfo Salthú, and Ana Tablar
  Phys. Rev. E 60, 5888 (1999)
• Statistical mechanics of protein sequences
  T. Gregory Dewey
  Phys. Rev. E 60, 4652 (1999)
• Discretized torsional dynamics and the folding of an RNA chain
  Ariel Fernández, Rodolfo Salthú, and Hernán Cendra
  Phys. Rev. E 60, 2105 (1999)
• Selection-mutation process of RNA viruses
  Amal Aafif and Juan Lin
  Phys. Rev. E 57, 2471 (1998)
• Atomic-force-microscopy studies of phase separations in macromolecular systems
  Yu. G. Kuznetsov, A. J. Malkin, and A. McPherson
  Phys. Rev. B 58, 6097 (1998)
• Adiabatic ansatz in RNA folding dynamics
  Ariel Fernández, Gustavo A. Appignanesi, and Ruben A. Montani
  Phys. Rev. E 56, 927 (1997)
• Overlaps between RNA Secondary Structures
  Paul G. Higgs
  Phys. Rev. Lett. 76, 704 (1996)
• RNA Virus Evolution via a Fitness-Space Model
  Lev S. Tsimring, Herbert Levine, and David A. Kessler
  Phys. Rev. Lett. 76, 4440 (1996)
• Erratum: Folding RNA with the minimal loss of entropy
  Ariel Fernández, Hugo Arias, and Diego Guerín
  Phys. Rev. E 54, 1005 (1996)
• Folding RNA with the minimal loss of entropy
  Ariel Fernández, Hugo Arias, and Diego Guerín
  Phys. Rev. E 52, R1299 (1995)
• Describing RNA sequential folding by dynamic coarse graining of the extended conformation space
  Ariel Fernández
  Phys. Rev. E 50, R2435 (1994)
• Near-neighbor effects in cooperative modified self-consistent phonon approximation melting in DNA
  Y. Z. Chen and E. W. Prohofsky
  Phys. Rev. E 49, 873 (1994)
• Nonlinear effects and thermal expansion as expressed in self-consistent phonon calculations on the temperature dependence of a phase change: Application to the B to Z conformation change in DNA
  Y. Z. Chen and E. W. Prohofsky
  Phys. Rev. E 49, 3444 (1994)
• Simulating an exploration of RNA conformation space with an appropriate parallel-updating strategy
  Ariel Fernández
  Phys. Rev. E 48, 3107 (1993)
• Dynamics of an A-DNA homopolymer crystal with sodium ions: A Green-function approach
  L. Chern and E. W. Prohofsky
  Phys. Rev. E 47, 4483 (1993)
• RNA folding and combinatory landscapes
  Walter Fontana
  Phys. Rev. E 47, 2083 (1993)
• Localization of strain in the RNA backbone and its functional implication
  Ariel Fernández and Herschel Rabitz
  Phys. Rev. Lett. 69, 546 (1992)
• Computation of the fraction of RNA sequences that fold sequentially into a unique free-energy minimum
  Ariel Fernández
  Phys. Rev. A 46, R4524 (1992)
• Folding pathway leading to the most stable conformation of a random RNA chain
  Ariel Fernández
  Phys. Rev. A 45, R8348 (1992)
• Global fractal dimension of human DNA sequences treated as pseudorandom walks
  Cheryl L. Berthelsen, James A. Glazier, and Mark H. Skolnick
  Phys. Rev. A 45, 8902 (1992)
• Excluded-volume effects on the stacking of RNA base pairs
  Ariel Fernández
  Phys. Rev. A 44, R7910 (1991)
• Sequence dependence of low-frequency Raman-active modes in nucleic acids
  Glenn Edwards and Changle Liu
  Phys. Rev. A 44, 2709 (1991)
• Fluctuations and resulting competing pathways in RNA folding: The activation of splicing
  Ariel Fernández
  Phys. Rev. A 43, 1138 (1991)
• Random energy model for the kinetics of RNA folding
  Ariel Fernández
  Phys. Rev. Lett. 65, 2259 (1990)
• Glassy kinetic barriers between conformational substates in RNA
  Ariel Fernández
  Phys. Rev. Lett. 64, 2328 (1990)
• Activation-energy landscape for metastable RNA folding
  Ariel Fernández and Eugene I. Shakhnovich
  Phys. Rev. A 42, 3657 (1990)
• Dynamics of layered adenine molecules
  P. Martel, V. Frank, and M. Hennion
  Phys. Rev. A 41, 7006 (1990)
• Solitons hiding in DNA and their possible significance in RNA transcription
  E. W. Prohofsky
  Phys. Rev. A 38, 1538 (1988)