Bibliografic database on Semiconductors, Heterostructures and Biophysics

Molecular Dynamics (MD) Simulations

• Molecular Dynamics Characterization of Protein Crystal Contacts in Aqueous Solutions
  Giuseppe Pellicane, Graham Smith, and Lev Sarkisov
  Phys. Rev. Lett. 101, 248102 (2008)
• Advillin Folding Takes Place on a Hypersurface of Small Dimensionality
  Stefano Piana and Alessandro Laio
  Phys. Rev. Lett. 101, 208101 (2008)
• Role of Reversibility in Viral Capsid Growth: A Paradigm for Self-Assembly
  D. C. Rapaport
  Phys. Rev. Lett. 101, 186101 (2008)
• Sequence Dependent Electron Transport in Wet DNA : Ab initio and Molecular Dynamics Studies
  Sairam S. Mallajosyula, J. C. Lin, D. L. Cox, S. K. Pati, and R. R. P. Singh
  Phys. Rev. Lett. 101, 176805 (2008)
• Studies of Phononlike Low-Energy Excitations of Protein Molecules by Inelastic X-Ray Scattering
  Dazhi Liu, Xiang-qiang Chu, Marco Lagi, Yang Zhang, Emiliano Fratini, Piero Baglioni, Ahmet Alatas, Ayman Said, Ercan Alp, and Sow-Hsin Chen
  Phys. Rev. Lett. 101, 135501 (2008)
• Strain Softening in Stretched DNA
  Binquan Luan and Aleksei Aksimentiev
  Phys. Rev. Lett. 101, 118101 (2008)
• Supercoiling and Denaturation of DNA Loops
  T. B. Liverpool, S. A. Harris, and C. A. Laughton
  Phys. Rev. Lett. 100, 238103 (2008)
• Hydration-Dependent Dynamical Transition in Protein : Protein Interactions at ≈240 K
  Vandana Kurkal-Siebert, Ritesh Agarwal, and Jeremy C. Smith
  Phys. Rev. Lett. 100, 138102 (2008)
• Molecular Dynamics Simulation of Multivalent-Ion Mediated Attraction between DNA Molecules
  Liang Dai, Yuguang Mu, Lars Nordenskiöld, and Johan R. C. van der Maarel
  Phys. Rev. Lett. 100, 118301 (2008)
• Solvent-Induced DNA Conformational Transition
  B. Gu, F. S. Zhang, Z. P. Wang, and H. Y. Zhou
  Phys. Rev. Lett. 100, 088104 (2008)
• Computational Study of the Force Dependence of Phosphoryl Transfer during DNA Synthesis by a High Fidelity Polymerase
  Ravindra Venkatramani and Ravi Radhakrishnan
  Phys. Rev. Lett. 100, 088102 (2008)
• Atomic hydrodynamics of DNA : Coil-uncoil-coil transitions in a wall-bounded shear flow
  William C. Sandberg and Guan M. Wang
  Phys. Rev. E 78, 061910 (2008)
• Dynamical transition, hydrophobic interface, and the temperature dependence of electrostatic fluctuations in proteins
  David N. LeBard and Dmitry V. Matyushov
  Phys. Rev. E 78, 061901 (2008)
• Perturbational formulation of principal component analysis in molecular dynamics simulation
  Yohei M. Koyama, Tetsuya J. Kobayashi, Shuji Tomoda, and Hiroki R. Ueda
  Phys. Rev. E 78, 046702 (2008)
• Free-energy landscape of mechanically unfolded model proteins : Extended Jarzinsky versus inherent structure reconstruction
  Stefano Luccioli, Alberto Imparato, and Alessandro Torcini
  Phys. Rev. E 78, 031907 (2008)
• Electro-osmotic screening of the DNA charge in a nanopore
  Binquan Luan and Aleksei Aksimentiev
  Phys. Rev. E 78, 021912 (2008)
• Peptide folding kinetics from replica exchange molecular dynamics
  Nicolae-Viorel Buchete and Gerhard Hummer
  Phys. Rev. E 77, 030902 (2008)
• New Insight into Cataract Formation: Enhanced Stability through Mutual Attraction
  A. Stradner, G. Foffi, N. Dorsaz, G. Thurston, and P. Schurtenberger
  Phys. Rev. Lett. 99, 198103 (2007)
• Wormlike Chain Theory and Bending of Short DNA
  Alexey K. Mazur
  Phys. Rev. Lett. 98, 218102 (2007)
• Counterion-Hopping along the Backbone of Single-Stranded DNA in Nanometer Pores: A Mechanism for Current Conduction
  S. T. Cui
  Phys. Rev. Lett. 98, 138101 (2007)
• Exploring the Mechanism of Flexible Biomolecular Recognition with Single Molecule Dynamics
  Qiang Lu, H. Peter Lu, and Jin Wang
  Phys. Rev. Lett. 98, 128105 (2007)
• Conformational Temperature Characterizing the Folding of a Protein
  Naoko Nakagawa
  Phys. Rev. Lett. 98, 128104 (2007)
• Anharmonicity and Self-Similarity of the Free Energy Landscape of Protein G
  F. Pontiggia, G. Colombo, C. Micheletti, and H. Orland
  Phys. Rev. Lett. 98, 048102 (2007)
• Dynamics of essential collective motions in proteins : Theory
  Maria Stepanova
  Phys. Rev. E 76, 051918 (2007)
• Simulation via direct computation of partition functions
  Cheng Zhang and Jianpeng Ma
  Phys. Rev. E 76, 036708 (2007)
• Atomistic model of DNA : Phonons and base-pair opening
  F. Merzel, F. Fontaine-Vive, M. R. Johnson, and G. J. Kearley
  Phys. Rev. E 76, 031917 (2007)
• Structure optimization and folding mechanisms of off-lattice protein models using statistical temperature molecular dynamics simulation : Statistical temperature annealing
  Jaegil Kim, John E. Straub, and Thomas Keyes
  Phys. Rev. E 76, 011913 (2007)
• Wang-Landau molecular dynamics technique to search for low-energy conformational space of proteins
  Takehiro Nagasima, Akira R. Kinjo, Takashi Mitsui, and Ken Nishikawa
  Phys. Rev. E 75, 066706 (2007)
• Non-Gaussian behavior of elastic incoherent neutron scattering profiles of proteins studied by molecular dynamics simulation
  Atsushi Tokuhisa, Yasumasa Joti, Hiroshi Nakagawa, Akio Kitao, and Mikio Kataoka
  Phys. Rev. E 75, 041912 (2007)
• Sympathetic Cooling of Complex Molecular Ions to Millikelvin Temperatures
  A. Ostendorf, C. B. Zhang, M. A. Wilson, D. Offenberg, B. Roth, and S. Schiller
  Phys. Rev. Lett. 97, 243005 (2006)
• Glass Transition in Biomolecules and the Liquid-Liquid Critical Point of Water
  Pradeep Kumar, Z. Yan, L. Xu, M. G. Mazza, S. V. Buldyrev, S.-H. Chen, S. Sastry, and H. E. Stanley
  Phys. Rev. Lett. 97, 177802 (2006)
• Protein Folding Kinetics and Thermodynamics from Atomistic Simulations
  David van der Spoel and M. Marvin Seibert
  Phys. Rev. Lett. 96, 238102 (2006)
• Lateral Diffusion and Percolation in Membranes
  Bong June Sung and Arun Yethiraj
  Phys. Rev. Lett. 96, 228103 (2006)
• Cyclic Motion of a Grafted Polymer under Shear Flow
  Rafael Delgado-Buscalioni
  Phys. Rev. Lett. 96, 088303 (2006)
• Equilibration of experimentally determined protein structures for molecular dynamics simulation
  Emily B. Walton and Krystyn J. VanVliet
  Phys. Rev. E 74, 061901 (2006)
• Modeling protein thermodynamics and fluctuations at the mesoscale
  Naoko Nakagawa and Michel Peyrard
  Phys. Rev. E 74, 041916 (2006)
• Hydration dependence of the mass fractal dimension and anomalous diffusion of vibrational energy in proteins
  Matthew B. Enright, Xin Yu, and David M. Leitner
  Phys. Rev. E 73, 051905 (2006)
• Self-healing properties of flaws in nanoscale materials: Effects of soft and hard molecular dynamics simulations and boundaries studied using a continuum mechanical model
  Yufeng Guo and Wanlin Guo
  Phys. Rev. B 73, 085411 (2006)
• Can One Predict DNA Transcription Start Sites by Studying Bubbles?
  Titus S. van Erp, Santiago Cuesta-Lopez, Johannes-Geert Hagmann, and Michel Peyrard
  Phys. Rev. Lett. 95, 218104 (2005)
• Correlated Dynamics Determining X-Ray Diffuse Scattering from a Crystalline Protein Revealed by Molecular Dynamics Simulation
  Lars Meinhold and Jeremy C. Smith
  Phys. Rev. Lett. 95, 218103 (2005)
• Coarse-Grained Model of Proteins Incorporating Atomistic Detail of the Active Site
  Marilisa Neri, Claudio Anselmi, Michele Cascella, Amos Maritan, and Paolo Carloni
  Phys. Rev. Lett. 95, 218102 (2005)
• Structure and Stability of Self-Assembled Actin-Lysozyme Complexes in Salty Water
  Lori K. Sanders, Camilo Guáqueta, Thomas E. Angelini, Jae-Wook Lee, Scott C. Slimmer, Erik Luijten, and Gerard C. Wong
  Phys. Rev. Lett. 95, 108302 (2005)
• DNA in Nanopores: Counterion Condensation and Coion Depletion
  Yitzhak Rabin and Motohiko Tanaka
  Phys. Rev. Lett. 94, 148103 (2005)
• Pressure-dependent transition in protein dynamics at about 4 kbar revealed by molecular dynamics simulation
  Lars Meinhold and Jeremy C. Smith
  Phys. Rev. E 72, 061908 (2005)
• Unfolding dynamics of the protein ubiquitin: Insight from simulation
  Shubhra Ghosh Dastidar and Chaitali Mukhopadhyay
  Phys. Rev. E 72, 051928 (2005)
• Analytical theory of the stochastic dynamics of the power stroke in nonprocessive motor proteins
  H. J. Woo and Christopher L. Moss
  Phys. Rev. E 72, 051924 (2005)
• Apparent persistence length renormalization of bent DNA
  Igor M. Kulić, Hervé Mohrbach, Vladimir Lobaskin, Rochish Thaokar, and Helmut Schiessel
  Phys. Rev. E 72, 041905 (2005)
• Temperature dependence and counter effect of the correlations of folding rate with chain length and with native topology
  Hironori K. Nakamura and Mitsunori Takano
  Phys. Rev. E 71, 061913 (2005)
• Molecular dynamics simulations of the indentation of a crystalline surface by an atomic force microscope tip
  R. Ferrando, M. Andrei, A. Relini, R. Rolandi, and A. Gliozzi
  Phys. Rev. B 72, 045412 (2005)
• Reversible Temperature and Pressure Denaturation of a Protein Fragment: A Replica Exchange Molecular Dynamics Simulation Study
  Dietmar Paschek and Angel E. García
  Phys. Rev. Lett. 93, 238105 (2004)
• Long Time Molecular Dynamics for Enhanced Conformational Sampling in Biomolecular Systems
  P. Minary, M. E. Tuckerman, and G. J. Martyna
  Phys. Rev. Lett. 93, 150201 (2004)
• Folding and Unfolding of an Elastinlike Oligopeptide:
  Eduard Schreiner, Chiara Nicolini, Björn Ludolph, Revanur Ravindra, Nikolaj Otte, Axel Kohlmeyer, Roger Rousseau, Roland Winter, and Dominik Marx
  Phys. Rev. Lett. 92, 148101 (2004)
• Model for the dynamics of a water cluster in an x-ray free electron laser beam
  Magnus Bergh, Nicuşor Tîmneanu, and David van der Spoel
  Phys. Rev. E 70, 051904 (2004)
• Stretching of homopolymers and contact order
  Marek Cieplak, Trinh Xuan Hoang, and Mark O. Robbins
  Phys. Rev. E 70, 011917 (2004)
• Effect of chain connectivity on the structure of Lennard-Jones liquid and its implicationon statistical potentials for protein folding
  W. C. Lu, C. Z. Wang, and K. M. Ho
  Phys. Rev. E 69, 061920 (2004)
• Liquid-liquid phase transitions for soft-core attractive potentials
  A. Skibinsky, S. V. Buldyrev, G. Franzese, G. Malescio, and H. E. Stanley
  Phys. Rev. E 69, 061206 (2004)
• Stretching of proteins in the entropic limit
  Marek Cieplak, Trinh Xuan Hoang, and Mark O. Robbins
  Phys. Rev. E 69, 011912 (2004)
• Principal Components of the Protein Dynamical Transition
  Alexander L. Tournier and Jeremy C. Smith
  Phys. Rev. Lett. 91, 208106 (2003)
• Nuclear quantum effects on electron transfer reactions in DNA hairpins
  Shigenori Tanaka and Yasuo Sengoku
  Phys. Rev. E 68, 031905 (2003)
• Structure, dynamics , and energetics of water at the surface of a small globular protein : A molecular dynamics simulation
  Shubhra Ghosh Dastidar and Chaitali Mukhopadhyay
  Phys. Rev. E 68, 021921 (2003)
• Quasiequilibrium unfolding thermodynamics of a small protein studied by molecular dynamics simulation with an explicit water model
  Jihua Wang, Zhiyong Zhang, Haiyan Liu, and Yunyu Shi
  Phys. Rev. E 67, 061903 (2003)
• Molecular dynamics simulation of compression-induced solid-to-solid phase transitions in colloidal monolayers
  Jizhong Sun and T. Stirner
  Phys. Rev. E 67, 051107 (2003)
• Unfolding proteins in an external field: Can we always observe the intermediate states?
  Alexander S. Lemak, James R. Lepock, and Jeff Z. Chen
  Phys. Rev. E 67, 031910 (2003)
• Glass transition in an off-lattice protein model studied by molecular dynamics simulations
  A. Baumketner, J.-E. Shea, and Y. Hiwatari
  Phys. Rev. E 67, 011912 (2003)
• Single-Particle and Collective Dynamics of Protein Hydration Water: A Molecular Dynamics Study
  M. Tarek and D. J. Tobias
  Phys. Rev. Lett. 89, 275501 (2002)
• Role of Protein -Water Hydrogen Bond Dynamics in the Protein Dynamical Transition
  M. Tarek and D. J. Tobias
  Phys. Rev. Lett. 88, 138101 (2002)
• Metastable liquid-liquid phase transition in a single-component system with only one crystal phase and no density anomaly
  G. Franzese, G. Malescio, A. Skibinsky, S. V. Buldyrev, and H. E. Stanley
  Phys. Rev. E 66, 051206 (2002)
• Molecular dynamics simulation of polymer helix formation using rigid-link methods
  D. C. Rapaport
  Phys. Rev. E 66, 011906 (2002)
• Diffusive dynamics of protein folding studied by molecular dynamics simulations of an off-lattice model
  A. Baumketner and Y. Hiwatari
  Phys. Rev. E 66, 011905 (2002)
• Excitons in a photosynthetic light-harvesting system: A combined molecular dynamics , quantum chemistry, and polaron model study
  Ana Damjanović, Ioan Kosztin, Ulrich Kleinekathöfer, and Klaus Schulten
  Phys. Rev. E 65, 031919 (2002)
• Convergence of sampling in protein simulations
  Berk Hess
  Phys. Rev. E 65, 031910 (2002)
• Thermodynamics of local DNA openings
  Tomasz Lipniacki
  Phys. Rev. E 64, 051919 (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)
• Comment on
  M. Marchi and P. Procacci
  Phys. Rev. E 63, 028701 (2001)
• Bubble propagation in a helicoidal molecular chain
  Alessandro Campa
  Phys. Rev. E 63, 021901 (2001)
• DNA Electrophoresis on a Flat Surface
  N. Pernodet, V. Samuilov, K. Shin, J. Sokolov, M. H. Rafailovich, D. Gersappe, and B. Chu
  Phys. Rev. Lett. 85, 5651 (2000)
• Vibrational Energy Transfer in a Protein Molecule
  Kei Moritsugu, Osamu Miyashita, and Akinori Kidera
  Phys. Rev. Lett. 85, 3970 (2000)
• Similarities between principal components of protein dynamics and random diffusion
  Berk Hess
  Phys. Rev. E 62, 8438 (2000)
• Effects of electric charges on hydrophobic forces. II.
  D. Bulone, V. Martorana, P. L. San Biagio, and M. B. Palma-Vittorelli
  Phys. Rev. E 62, 6799 (2000)
• Dynamical chaos and power spectra in toy models of heteropolymers and proteins
  Mai Suan Li, Marek Cieplak, and Nazar Sushko
  Phys. Rev. E 62, 4025 (2000)
• Glasslike dynamical behavior of the plastocyanin hydration water
  Anna Rita Bizzarri, Alessandro Paciaroni, and Salvatore Cannistraro
  Phys. Rev. E 62, 3991 (2000)
• Proteins in vacuo: A molecular dynamics study of the unfolding behavior of highly charged disulfide-bond-intact lysozyme subjected to a temperature pulse
  C. T. Reimann, I. Velázquez, M. Bittner, and O. Tapia
  Phys. Rev. E 60, 7277 (1999)
• Origin of the low-frequency modes of globular proteins
  Simone Melchionna and Alessandro Desideri
  Phys. Rev. E 60, 4664 (1999)
• Recurrence quantification analysis as a tool for characterization of molecular dynamics simulations
  Cesare Manetti, Marc-Antoine Ceruso, Alessandro Giuliani, Charles L. Webber, and Joseph P. Zbilut
  Phys. Rev. E 59, 992 (1999)
• Molecular -dynamics simulation evidences of a boson peak in protein hydration water
  Alessandro Paciaroni, Anna Rita Bizzarri, and Salvatore Cannistraro
  Phys. Rev. E 57, R6277 (1998)
• Solvent diffusion outside macromolecular surfaces
  Erik Lindahl and Olle Edholm
  Phys. Rev. E 57, 791 (1998)
• Water dynamical anomalies evidenced by molecular -dynamics simulations at the solvent-protein interface
  Claudia Rocchi, Anna Rita Bizzarri, and Salvatore Cannistraro
  Phys. Rev. E 57, 3315 (1998)
• Theory of DNA melting based on the Peyrard-Bishop model
  Yong-li Zhang, Wei-Mou Zheng, Ji-Xing Liu, and Y. Z. Chen
  Phys. Rev. E 56, 7100 (1997)
• Electronic-structure-based molecular -dynamics method for large biological systems: Application to the 10 basepair poly(dG)⋅poly(dC) DNA double helix
  James P. Lewis, Pablo Ordejón, and Otto F. Sankey
  Phys. Rev. B 55, 6880 (1997)
• First-Order Disorder-to-Order Transition in an Isolated Homopolymer Model
  Yaoqi Zhou, Carol K. Hall, and Martin Karplus
  Phys. Rev. Lett. 77, 2822 (1996)
• Molecular dynamics simulation evidence of anomalous diffusion of protein hydration water
  Anna Rita Bizzarri and Salvatore Cannistraro
  Phys. Rev. E 53, R3040 (1996)
• Predicting slow structural transitions in macromolecular systems: Conformational flooding
  Helmut Grubmüller
  Phys. Rev. E 52, 2893 (1995)
• Temperature echoes in molecular dynamics simulations of proteins
  O. M. Becker and M. Karplus
  Phys. Rev. Lett. 70, 3514 (1993)
• Dynamics and thermodynamics of a nonlinear model for DNA denaturation
  Thierry Dauxois, Michel Peyrard, and A. R. Bishop
  Phys. Rev. E 47, 684 (1993)