PREFACE
A Special Issue on Computational Intelligence for Bioinformatics
Nikola Kasabov and Ilkka Havukkala
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REVIEW
pp. 473–491 Computational Intelligence, Bioinformatics and Computational Biology: A Brief Overview of Methods, Problems and Perspectives
Nikola Kasabov, Igor A. Sidorov, and Dimiter S. Dimitrov
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RESEARCH ARTICLES
pp. 492–498 Visual Mining and Spatio-Temporal Querying in Molecular Dynamics
Olga Sourina and Nikolay Korolev
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pp. 499–505 A Genetic Algorithm Approach to Solving DNA Fragment Assembly Problem
Shu-Cherng Fang, Yong Wang, and Jie Zhong
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pp. 506–513 Classifying MicroRNAs by Gabor Filter Features from 2D Structure Bitmap Images on a Case Study of Human MicroRNAs
Ilkka Havukkala, Shaoning Pang, Vishal Jain, and Nikola Kasabov
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pp. 514–523 Novel Techniques for Microarray Data Analysis: Probabilistic Principal Surfaces and Competitive Evolution on Data
Roberto Amato, Angelo Ciaramella, Carmine Del Mondo, Lara De Vinco, Ciro Donalek, Giuseppe Longo, Gennaro Miele, Giancarlo Raiconi, Antonino Staiano, and Roberto Tagliaferri
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pp. 524–533 Evolutionary Fuzzy Clustering Algorithm with Knowledge-Based Evaluation and Applications for Gene Expression Profiling
Han-Saem Park, Si-Ho Yoo, and Sung-Bae Cho
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pp. 534–542 Multi-SVM Fuzzy Classification and Fusion Method and Applications in Bioinformatics
Xiujuan Chen, Robert Harrison, and Yan-Qing Zhang
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pp. 543–550 Artificial Immune Networks as a Paradigm for Classification and Profiling of Gene Expression Data
Diana Tsankova, Velichka Georgieva, and Nikola Kasabov
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pp. 551–560 Cluster-Based Local Modeling Approach to Protein Secondary Structure Prediction
Shing H. Doong and Chi Y. Yeh
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pp. 561–568 Quantum-Inspired Evolutionary Algorithms and Binary Particle Swarm Optimization for Training MLP and SRN Neural Networks
Ganesh K. Venayagamoorthy and Gaurav Singhal
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pp. 569–573 Biologically Plausible Computational Neurogenetic Models: Modeling the Interaction Between Genes, Neurons and Neural Networks
Nikola Kasabov, Lubica Benuskova, and Simei Gomes Wysoski
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pp. 574–582 Towards Automated Configuration of Multi-Sensor Systems Using Evolutionary Computation— A Method and a Case Study
Kuncup Iswandy, Andreas Koenig, Thomas Fricke, Marc Baumbach, and Andreas Schuetze
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pp. 583–586 Table of Contents to Volume 2, Number 1–4, 2005
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pp. 587–590 Author Index to Volume 2, Number 1–4, 2005
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pp. 591–593 Subject Index to Volume 2, Number 1–4, 2005
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REVIEWS
pp. 329–347 Properties of Mesoscopic Hybrid Superconducting Systems
Fabio Taddei, Francesco Giazotto and Rosario Fazio
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RESEARCH ARTICLES
pp. 348–353 An Atomistic Simulation Study of Carbon Nanotube Electromechanical Memory
Jeong Won Kang and Ho Jung Hwang
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pp. 354–361 Conformational Sampling of Protein Flexibility in Generalized Coordinates: Application to Ligand Docking
Julio A. Kovacs, Claudio Cavasotto and Ruben Abagyan
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pp. 362–369 Electron in an Interaction Potential of General Shape
Michael Rieth and Wolfram Schommers
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pp. 370–377 Interaction of Porphine and its Metal Complexes with C₆₀ Fullerene: A DFT B3LYP/LANL2MB Study Vladimir A. Basiuk
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pp. 378–384 DNA-Dendrimer Nano-Cluster Electrostatics Prediction with the Nonlinear Poisson-Boltzmann Equation
Ali Nikakhtar, Asadollah Nasehzadeh, Hossein Naghibi-Beidokhti and G. Ali Mansoori
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pp. 385–388 A Molecular Dynamics and Quantum Mechanics Modeling of Single Crystal Silicon Nanowire Structures
Kausala Mylvaganam and L. C. Zhang
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pp. 389–395 Sensing DNA-DNA as Nanosensor: A Perspective towards Nanotechnology
Ralf Metzler and Tobias Ambjörnsson.
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pp. 396–400 Analytical Theory of Persistent Currents in Mesoscopic Rings
Yu. V. Pershin and I.D. Vagner
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pp. 401–413 Free Volume Properties of Sphingomyelin, DMPC, DPPC, and PLPC Bilayers
M. Kupiainen, E. Falck, S. Ollila, P. Niemelä, A.A Gurtovenko, M.T. Hyvönen, M. Patra, M. Karttunen and I. Vattulainen
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pp. 414–422 Two Dimensional Numerical Modeling of Lightly Doped Nano-scale Double-Gate MOSFET
Deepanjan Datta, A. Annada Prasad Sarab and S.Dasgupta
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pp. 423–437 The Einstein Relation in Quantum Wells and Wires of Heavily Doped Nonlinear Optical and Optoelectronic Materials: Simplified Theory and Suggestion for Experimental Determination
K.P. Ghatak, P.K.Bose, A.R.Ghatak, D. De, S. Pahari, S. K. Chakraborty and S.K. Biswas
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pp. 438–442 Molecular Dynamics Simulation of the Thermal Conductivity of fcc Metallic Nanocrystals
M. Neek-Amal and H. Rafii-Tabar
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pp. 443–447 AMPHI-PIC J-aggregates: Degree of Disordering And of Thermal Relaxation of Photoproduced Excitons
M. A. Ratner and Yu. V. Malyukin
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pp. 448–455 Magnetic Nanorod in the Transition Temperature Vicinity
Danilo Backovic, Vjekoslav Sajfert, Jovan Šetrajcic and Bratislav Tošic
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pp. 456–468 Multilevel Quantum Chemistry Approach to the Development of a Database of the SAM-Ligand-Metal Ion-protein Interactions
Bartosz Trzaskowski, Andrzej Les, Ludwik Adamowicz, Pierre A. Deymier, Roberto Guzman, and Stepan G. Stepanian
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REVIEWS
pp. 161–179 Foundations of Quantum Technology
G. J. Milburn
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pp. 180–201 Modeling of Stability and Phase Transformations in Quasi-Zero Dimensional Nanocarbon Systems
A. S. Barnard, S. P. Russo, and I. K. Snook
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RESEARCH ARTICLES
pp. 202–206 Broadband Sub-wavelength Imaging by Mechanically Tunable Photonic Crystal
Q. Wu and W. Park
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pp. 207–213 Theoretical Studies of CN and C₂ Addition to a (100)–(2 ´ 1) Diamond Surface: Nanocrystalline Diamond Growth Mechanisms
Michael Sternberg, David A. Horner, Paul C. Redfern, Peter Zapol, and Larry A. Curtiss
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pp. 214–226 Analysis and Geometric Optimization of Single Electron Transistors for Read-Out in Solid-State Quantum Computing
Vincent I. Conrad, Andrew D. Greentree, David N. Jamieson, and Lloyd C. L. Hollenberg
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pp. 227–239 Simulation of Quantum Computation: A Deterministic Event-Based Approach
K. Michielsen, K. De Raedt, and H. De Raedt
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pp. 240–250 Metallic Photonic Crystals at Optical Frequencies
Christian Hafner, Cui Xudong, and Rüdiger Vahldieck
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pp. 251–255 Nanotube Bending Due to Central Loading
Kausala Mylvaganam and L. C. Zhang
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pp. 256–262 Ordering of Nanovoids in an Anisotropic Solid Driven by Surface Misfit
Hui-Chia Yu and Wei Lu
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pp. 263–271 Peyrard-Bishop-Dauxois Model of DNA Dynamics and Impact of Viscosity
S. Zdravkovic', J. A. Tuszyn'ski, and M. V. Sataric'
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pp. 272–276 Ab initio Modelling of K_a X-ray Spectra in Single Walled Carbon Nanotubes
J. Srbinovsky, N. C. Wilson, C. M. MacRae, and S. P. Russo
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pp. 277–286 Mesoscopic Relaxation and Elastic Properties of Two Dimensional Magnetic Nano Structured Materials
Yoshitake Yamazaki, Zhong-can Ou-Yang, Kunquan Lu, Herbert Gleiter, Xing Zhu, Gerhard Wilde, Dianhong Shen, Yutaka Abe, and Masahiro Watanabe
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pp. 287–292 Electronic Contribution to the Elastic Constants in Strained Layer Quantum Dot Superlattices of Non-Parabolic Semiconductors with Graded Interfaces
L. J. Singh, S. Choudhary, A. Mallik, and K. P. Ghatak
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pp. 293–297 First-Principles Calculation of Hydrogen Diffusion Barriers on Si(001)-2 ´ 1 Surface
Jingping Peng, David J. Mann, and John Randall
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pp. 298–318 Mechanical Properties Modeling of Carbon Single-Walled Nanotubes: A Finite Element Method
Mehrdad N. Ghasemi-Nejhad and Davood Askari
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pp. 319–327 Thermodynamics and Adsorption Behaviour of the Nano Phases in the Bi-Sn System
J. P. Hajra, T. Ray, and S. Acharya
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REVIEWS
pp. 1-25 Current Status of Nanomedicine and Medical Nanorobotics
Robert A. Freitas, Jr.
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pp. 26-44 Gate Current Modeling for MOSFETs
Andreas Gehring and Siegfried Selberherr
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RESEARCH ARTICLES
pp. 45-55 Design and Analysis of a Molecular Tool for Carbon Transfer in Mechanosynthesis
Damian G. Allis and K. Eric Drexler
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pp. 56-67 Self-Consistent Particle Simulation of Ion Channels
Campbell Millar, Asen Asenov and S. Roy
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pp. 68-74 Visualization of Hybridization in Nanocarbon Systems
A. S. Barnard, S. P. Russo, and I. K. Snook
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pp. 75-87 Surface-Plasmon Coupled Nonequilibrium Thermoelectric Refrigerators and Power Generators
Ronggui Yang, Arvind Narayanaswamy and Gang Chen
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pp. 88-98 Drude Model Replacement by Symbolic Regression
Christian Hafner
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pp. 99-107 Modeling the Dynamic Behavior of Mixtures of Diblock Copoymers and Dipolar Nanoparticles
Gang He and Anna C. Balazs
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pp. 108-116 Ab-Initio Study of Structural, Electronic, and Mechanical Properties of BiN (N = 1–5) Nanowires
Pankaj Srivastava, Sarika Shrivastava, and A. K. Shrivastava
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pp. 117-123 Molecular Roller and Rocker on Surfaces
Bidisa Das and K. L. Sebastian
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pp. 124-131 Mechanical Properties Modeling of Carbon Single-Walled Nanotubes: An Asymptotic Homogenization Method
Alexander L. Kalamkarov, Vinod P. Veedu, and Mehrdad N. Ghasemi-Nejhad
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pp. 132-137 Point-Contact Andreev Reflection in Ferromagnet/Superconductor Ballistic Nanojunctions
F. Taddei, S. Sanvito and C.J. Lambert
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pp. 138-147 Nonextensivity and Nonintensivity in Nanosystems: A Molecular Dynamics Simulation
Pirooz Mohazzabi and G. Ali Moansoori
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pp. 148-153 Conductance Properties of Cylindrical Quantum Nanodots
Vjekoslav Sajfert, Bratislav Tošic
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pp. 154-160 Localization of an Excitation in a Quantum Dot Molecule by an Electric Field
Andreas F. Terzis and Emmanuel Paspalakis
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EDITORIAL
pp. 341-342 Special Issues, Special Sections, and Papers on Basic Physics
Michael Rieth and Wolfram Schommers
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REVIEWS
pp. 343-366 First-Principle Quantum Modeling of Optical Power Limiting Materials
Patrick Norman and Hans Ågren
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RESEARCH ARTICLES
pp. 367-377 Molecular Dynamics of Colliding Nanoclusters
Marco Kalweit and Dimitris Drikakis
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pp. 378-384 ONIOM Studies of Amidation at Carbon Nanotube Tips: B3LYP for the Expanded Higher Level
Vladimir A. Basiuk
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pp. 385-391 Finite-Amplitude Motions of Beam Resonators and Their Stability
Eihab M. Abdel-Rahman, Mohammad I. Younis, and Ali H. Nayfeh
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pp. 392-397 Results of Molecular Dynamics Computations of the Structural and Electrostatic Properties of Tubulin and Their Consequences for Microtubules
J. A. Tuszynski, T. Luchko, E. J. Carpenter, and E. Crawford
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pp. 398-411 Molecular Description of Electrosorption in a Nanoporous Carbon Electrode
Andriy Kovalenko
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pp. 412-416 Critical External Pressure for Empty or Filled Multiwall Carbon Nanotubes
C. Y. Wang, A. Mioduchowski, and C. Q. Ru
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pp. 417-423 Simulation of Electroosmotic Flows in Micro- and Nanochannels Using a Lattice Boltzmann Model
Fuzhi Tian, Baoming Li, and Daniel Y. Kwok
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pp. 424-428 Modeling Constrained Capacitive Systems
J. A. Pelesko, and G. Goldsztein
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pp. 429-437 Deformation of a Droplet in an Electrical Field: Transient Response in Dielectric Media
Graeme Supeene, Charles R. Koch, and Subir Bhattacharjee
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pp. 438-444 An Electrostatic--Peristaltic Colloidal Micropump: A Finite Element Analysis
N. Quddus, S. Bhattacharjee, and W. Moussa
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REVIEW
pp. 231-255 Optical Properties of Nanostructures from Time-Dependent Density Functional Theory
Alberto Castro, Miguel A. L. Marques, Julio A. Alonso, and Angel Rubio Jijun Zhao and Rui-Hua Xie
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RESEARCH ARTICLES
pp. 256-260 Excursions of the Fermi Level from the HOMO-LUMO Gap in Finite Systems
Karl Sohlberg and Natalie Vedova-Brook
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pp. 261-264 Defect Nucleation During Nanoindentation: An Atomistic Analysis
R. W. Leger, Y.-L. Shen, and T. A. Khraishi
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pp. 265-279 Multiscale Simulation of the Synthesis, Assembly and Properties of Nanostructured Organic/Inorganic Hybrid Materials
Clare McCabe, Sharon C. Glotzer, John Kieffer, Matthew Neurock, and Peter T. Cummings
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pp. 280-287 Branched Electron Current from Quantum Point Contacts and Novel Device Concepts
J. Kingsley and A. M. Song
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pp. 288-297 Investigation of Nanostructured Germanium/Silicon Dioxide Interfaces
Wolfgang Windl, Tao Liang, Sergei Lopatin, and Gerd Duscher
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pp. 298-302 Effects of Stacking Faults on the Electronic Structures of Quantum Rods
Lin-Wang Wang
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pp. 303-308 Target-Rate Kinetic Monte Carlo Method for Simulation of Nanoscale Structural Evolution
M. A. Gosálvez and R. M. Nieminen
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pp. 309-316 Quantum Dynamics of Gate Operations on Charge Qubits
R. Green and J. B. Wang
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pp. 317-321 Binding Energy of Donor States in a Quantum Dot with Parabolic Confinement
S. Baskoutas, A. F. Terzis, and E. Voutsinas
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pp. 322-333 Polar Optical Oscillation Modes in Semiconductor Nanostructures
E. Roca, J. L. Marín, R. Riera, and R. Rosas
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pp. 334-339 Shape and Energetics of TiN Nanoparticles
A. S. Barnard
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REVIEW
pp.117-131 Genetic Algorithms for the Geometry Optimization of Atomic and Molecular Clusters
Jijun Zhao and Rui-Hua Xie
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pp.132-143 Evaluation of Decoherence for Quantum Control and Computing
Arkady Fedorov, Leonid Fedichkin, and Vladimir Privman
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RESEARCH ARTICLES
pp.144-168 Generalized Semiconductor Bloch Equations
F. A. Buot
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pp.169-179 Biophysical Implications of the Peyrard-Bishop-Dauxois Model of DNA Dynamics
S. Zdravkovi, M. Satari and J. Tuszynski
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pp.180-186 Simulating Microwave-Heated Diffusion in Zeolite Nanopores
Cristian Blanco and Scott M. Auerbach
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pp.187-192 Modeling of a Molecular Device: The Quaterthiophene-Substituted Azobenzene Molecule
Xiange Zheng and Karl Sohlberg
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pp.193-198 Mathematical Description of Dendrimer Structure
István J. Majoros, Chandan B. Mehta, and James R. Baker Jr.
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pp.199-203 Fullerene Shuttle Memory Device Based on Nanopeapod: Classical Molecular Dynamics Study
Jeong Won Kang, Won Young Choi, and Ho Jung Hwang
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pp.204-215 Mechanical Properties of Carbon Nanotubes Composites
David Hui, Mircea Chipara, Jagannathan Sankar, and K. T. Lau
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pp.216-220 Vibrational Dynamics and Excess Entropy of Multi-grain Nanoparticles
Abdelkader Kara, Ahlam N. Al-Rawi, and Talat S. Rahman
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pp.221-226 Dimer Reference Embedded Atom Method
Kunio Takahashi
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pp.227-229 An Application of Non-Extensive Statistical Mechanics to Nanosystems
G. R. Vakili-Nezhaad and G. A. Mansoori
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REVIEW
Tight-Binding Molecular Dynamics for Carbon and Applications to Nanostructure Formationroman-12, C. Z. Wang and K. M. Ho
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RESEARCH ARTICLES
Computational Studies of Viral Protein Nano-Actuators
A. Dubey,G. Sharma, C. Mavroidis, S. M. Tomassone, K. Nikitczuk, and M. L. Yarmush
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Multi-scale Modeling of Si and C Nanocluster Nucleation During Non-equilibrium Gas Phase Processing
Gregory A. Johnson and Nasr M. Ghoniem
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Metallic Nanoclusters – Computational Investigations of Their Applications as Building Blocks in Nanotechnology
Michael Rieth and Wolfram Schommers
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Computational Neurogenetics
Nikola Kasabov and Lubica Benuskova
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Theoretical Analysis Of Diamond Mechanosynthesis. Part I. Stability Of C₂ Mediated Growth of Nanocrystalline Diamond C(110) Surface
Jingping Peng, Robert A. Freitas Jr., and Ralph C. Merkle
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Theoretical Analysis of Diamond Mechanosynthesis. Part II. C₂ Mediated Growth of Diamond C(110) Surface via Si/Ge-Triadamantane Dimer Placement Tools
David J. Mann, Jingping Peng, Robert A. Freitas Jr., and Ralph C. Merkle
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A Nanoscale Spring-Loaded Valve Actuated to Colloidal Forces
Jonathan Fuchser, Prodip K. Das, Walied Moussa, and Subir Bhattacharjee
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Adsorption and Vibrational Properties of H₂O Monomer on NaCl(100) Surface
Yong Yang and E. G. Wang
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Structural Transition of Copper Nanowires Confined in Single-walled Carbon Nanotubes
Yufeng Guo; Yong Kong, Wanlin Guo, and Huajian Gao
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Computational Analysis of Transition Metal Doped Nanotubes and Their Application to Molecular Electronics
Dan A. Buzatu, Freddy T. Nguyen, Shreedhar N. Reddy, and Jerry A. Darsey
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Infrared, Raman, NMR Spectra, and Low-Energy Optical Excitations of Heterofullerene C₄₈B₁₂
Rui-Hua Xie, Qin Rao and Vedene H. Smith Jr.
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