Bibliografic database on Semiconductors, Heterostructures and Biophysics

Enzymes

• Exact Solution of a Model DNA-Inversion Genetic Switch with Orientational Control
  Paolo Visco, Rosalind J. Allen, and Martin R. Evans
  Phys. Rev. Lett. 101, 118104 (2008)
• Prediction of Binding Sites in Receptor-Ligand Complexes with the Gaussian Network Model
  Turkan Haliloglu, Emek Seyrek, and Burak Erman
  Phys. Rev. Lett. 100, 228102 (2008)
• Decay times in turnover statistics of single enzymes
  Martin Lindén
  Phys. Rev. E 78, 010901 (2008)
• Interaction between motor domains can explain the complex dynamics of heterodimeric kinesins
  Rahul Kumar Das and Anatoly B. Kolomeisky
  Phys. Rev. E 77, 061912 (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)
• Accessibility and occlusion of biopolymers, ray tracing of radiating tubes, and the temperature of a tangle
  Gregory Buck, Robert G. Scharein, Jeffrey Schnick, and Jonathan Simon
  Phys. Rev. E 77, 011803 (2008)
• Electrical conductivity of double stranded DNA measured with ac impedance spectroscopy
  Jiaxiong Wang
  Phys. Rev. B 78, 245304 (2008)
• Discrete Breathers in Nonlinear Network Models of Proteins
  B. Juanico, Y.-H. Sanejouand, F. Piazza, and P. De Los Rios
  Phys. Rev. Lett. 99, 238104 (2007)
• Quantifying Intrinsic Specificity: A Potential Complement to Affinity in Drug Screening
  Jin Wang, Xiliang Zheng, Yongliang Yang, Dale Drueckhammer, Wei Yang, Gennardy Verkhivker, and Erkang Wang
  Phys. Rev. Lett. 99, 198101 (2007)
• Nonequilibrium Dynamic Mechanism for Allosteric Effect
  Jianhua Xing
  Phys. Rev. Lett. 99, 168103 (2007)
• Molecular Synchronization Waves in Arrays of Allosterically Regulated Enzymes
  Vanessa Casagrande, Yuichi Togashi, and Alexander S. Mikhailov
  Phys. Rev. Lett. 99, 048301 (2007)
• Scaling and Continuum Percolation Model for Enzyme -Catalyzed Gel Degradation
  D. Lairez, J.-P. Carton, G. Zalczer, and J. Pelta
  Phys. Rev. Lett. 98, 228302 (2007)
• Stochastic Resonant Signaling in Enzyme Cascades
  Yueheng Lan and Garegin A. Papoian
  Phys. Rev. Lett. 98, 228301 (2007)
• Manipulating Single Enzymes by an External Harmonic Force
  Michael A. Lomholt, Michael Urbakh, Ralf Metzler, and Joseph Klafter
  Phys. Rev. Lett. 98, 168302 (2007)
• Subdiffusive target problem: Survival probability
  S. B. Yuste and Katja Lindenberg
  Phys. Rev. E 76, 051114 (2007)
• Torque and dynamics of linking number relaxation in stretched supercoiled DNA
  John F. Marko
  Phys. Rev. E 76, 021926 (2007)
• Single molecule Michaelis-Menten equation beyond quasistatic disorder
  Xiaochuan Xue, Fei Liu, and Zhong-can Ou-Yang
  Phys. Rev. E 74, 030902 (2006)
• Erratum: Origin of bursting pH oscillations in an enzyme model reaction system [Phys. Rev. E 72, 066205 (2005)]
  Ronny Straube, Dietrich Flockerzi, Stefan C. Müller, and Marcus J. B. Hauser
  Phys. Rev. E 74, 019901 (2006)
• Generalized Haldane equation and fluctuation theorem in the steady-state cycle kinetics of single enzymes
  Hong Qian and X. Sunney Xie
  Phys. Rev. E 74, 010902 (2006)
• Application of a random network with a variable geometry of links to the kinetics of drug elimination in healthy and diseased livers
  P. Chelminiak, J. M. Dixon, J. A. Tuszyński, and R. E. Marsh
  Phys. Rev. E 73, 051912 (2006)
• Powering a burnt bridges Brownian ratchet: A model for an extracellular motor driven by proteolysis of collagen
  Saveez Saffarian, Hong Qian, Ivan Collier, Elliot Elson, and Gregory Goldberg
  Phys. Rev. E 73, 041909 (2006)
• Improving the speed of the genetic toggle switch without sacrificing its dynamic stability
  Jiunn R. Chen
  Phys. Rev. E 73, 041901 (2006)
• Allosteric Control through Mechanical Tension
  Brian Choi, Giovanni Zocchi, Yim Wu, Sum Chan, and L. Jeanne Perry
  Phys. Rev. Lett. 95, 078102 (2005)
• Quantum Mechanical Free Energy Barrier for an Enzymatic Reaction
  Thomas H. Rod and Ulf Ryde
  Phys. Rev. Lett. 94, 138302 (2005)
• Unravelling the Mechanism of RNA-Polymerase Forward Motion by Using Mechanical Force
  Philippe Thomen, Pascal J. Lopez, and FranÃ
  Phys. Rev. Lett. 94, 128102 (2005)
• Origin of bursting pH oscillations in an enzyme model reaction system
  Ronny Straube, Dietrich Flockerzi, Stefan C. Müller, and Marcus J. Hauser
  Phys. Rev. E 72, 066205 (2005)
• Automatic network coupling analysis for dynamical systems based on detailed kinetic models
  Dirk Lebiedz, Julia Kammerer, and Ulrich Brandt-Pollmann
  Phys. Rev. E 72, 041911 (2005)
• Glassy behavior of a percolative water-protein system
  S. E. Pagnotta, R. Gargana, F. Bruni, and A. Bocedi
  Phys. Rev. E 71, 031506 (2005)
• Percolation Model for Enzyme Gel Degradation
  T. Abete, A. de Candia, D. Lairez, and A. Coniglio
  Phys. Rev. Lett. 93, 228301 (2004)
• Reliable biological communication with realistic constraints
  Gonzalo G. de Polavieja
  Phys. Rev. E 70, 061910 (2004)
• Stabilization of surface-immobilized enzymes using grafted polymers
  Yevgeny Moskovitz and Simcha Srebnik
  Phys. Rev. E 70, 032902 (2004)
• Near-field-magnetic-tweezer manipulation of single DNA molecules
  Jie Yan, Dunja Skoko, and John F. Marko
  Phys. Rev. E 70, 011905 (2004)
• Dynamic Force Spectroscopy of Protein-DNA Interactions by Unzipping DNA
  Steven J. Koch and Michelle D. Wang
  Phys. Rev. Lett. 91, 028103 (2003)
• Two-electron transfer reactions in proteins: Bridge-mediated and proton-assisted processes
  E. G. Petrov, V. I. Teslenko, and V. May
  Phys. Rev. E 68, 061916 (2003)
• Intrinsic fluorescence spectroscopy of glutamate dehydrogenase: Integrated behavior and deconvolution analysis
  P. P. Pompa, R. Cingolani, and R. Rinaldi
  Phys. Rev. E 68, 011907 (2003)
• Optical characterization of glutamate dehydrogenase monolayers chemisorbed on SiO2
  P. P. Pompa, L. Blasi, L. Longo, R. Cingolani, G. Ciccarella, G. Vasapollo, R. Rinaldi, A. Rizzello, C. Storelli, and M. Maffia
  Phys. Rev. E 67, 041902 (2003)
• Nonequilibrium phase transition in a self-activated biological network
  Hugues Berry
  Phys. Rev. E 67, 031907 (2003)
• Heavy-Atom Skeleton Quantization and Proton Tunneling in “Intermediate-Barrier” Hydrogen Bonds
  Mark E. Tuckerman and Dominik Marx
  Phys. Rev. Lett. 86, 4946 (2001)
• Glassy dynamics and enzymatic activity of lysozyme
  F. Pizzitutti and F. Bruni
  Phys. Rev. E 64, 052905 (2001)
• Quantitative analysis of the frequency spectrum of the radiation emitted by cytochrome oxidase enzymes
  J. A. Tuszyński and J. M. Dixon
  Phys. Rev. E 64, 051915 (2001)
• Single-particle study of protein assembly
  Ching-Hwa Kiang
  Phys. Rev. E 64, 041911 (2001)
• Statistical analysis of the fractal gating motions of the enzyme acetylcholinesterase
  T. Y. Shen, Kaihsu Tai, and J. Andrew McCammon
  Phys. Rev. E 63, 041902 (2001)
• Kinetic proofreading can explain the supression of supercoiling of circular DNA molecules by type-II topoisomerases
  Jie Yan, Marcelo O. Magnasco, and John F. Marko
  Phys. Rev. E 63, 031909 (2001)
• Group selection models in prebiotic evolution
  D. Alves, P. R. Campos, A. T. Silva, and J. F. Fontanari
  Phys. Rev. E 63, 011911 (2001)
• Spontaneous base flipping in DNA and its possible role in methyltransferase binding
  Y. Z. Chen, V. Mohan, and R. H. Griffey
  Phys. Rev. E 62, 1133 (2000)