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Computational Chemistry: Theories, Methods and Applications by Daria Bove

By Daria Bove

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J. ; Duarte, D. J. ; Miranda, M. ; Esteves da Silva, J. C. G. J. Phys. Chem. A 2014, 118, 1511-1518. ; Na, G. Environ. Sci. Technol. 2010, 44, 7484-7490. -M. Appl. Catal. B: Environ. 2013, 140, 457-467. In: Computational Chemistry Editor: Daria Bove ISBN: 978-1-63321-354-8 © 2014 Nova Science Publishers, Inc. Chapter 3 USING THE NETWORK SIMULATION METHOD TO STUDY IONIC TRANSPORT PROCESSES IN ELECTROCHEMICAL CELLS A. A. Moya Universidad de Jaén, Departamento de Física, Jaén, Spain ABSTRACT The network simulation method is used to numerically study the steady-state, transient and small-signal ac responses of a binary electrolyte solution placed between two electrodes.

J Comput Chem 1983;4:187–217. [63] Kalé L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, et al. NAMD2: Greater Scalability for Parallel Molecular Dynamics. J. Comput Phys 1999;151:283–312. Protein Kinase-Targeting Drug Discovery and Design 21 [64] Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, et al. Scalable molecular dynamics with NAMD. J Comput Chem 2005;26:1781–802. [65] Schames JR, Henchman RH, Siegel JS, Sotriffer C a, Ni H, McCammon JA. Discovery of a novel binding trench in HIV integrase.

G. Esteves da Silva [24] Tan KP, Varadarajan R, Madhusudhan MS. DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins. Nucleic Acids Res 2011;39:W242–W248. [25] Laurie ATR, Jackson RM. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 2005;21:1908– 16. [26] Hernandez M, Ghersi D, Sanchez R. SITEHOUND-web: a server for ligand binding site identification in protein structures. Nucleic Acids Res 2009;37:W413–6.

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