Volume 13, Number 1

Editorial Board.
Commun. Comput. Phys., No. 1, 13 (2013).

Articles in the Issue:

Preface  

Full Article
Regular Articles:  

Xiaodong Pang and Huan-Xiang Zhou
Poisson-Boltzmann calculations: van der Waals or molecular surface?
Commun. Comput. Phys., 13 (2013
), pp. 1-12.
Published Online: June 12, 2012. Abstract

 

Full Article
   

Lin Wang, Zhe Zhang, Walter Rocchia and Emil Alexov
Using DelPhi capabilities to mimic protein's conformational reorganization with amino acid specific dielectric constants.
Commun. Comput. Phys., 13 (2013
), pp. 13-30.
Published Online: June 12, 2012. Abstract

 

Full Article
   

Fang Zheng and Chang-Guo Zhan
Computational modeling of solvent effects on protein-ligand interactions using fully polarizable continuum model and rational drug design.
Commun. Comput. Phys., 13 (2013
), pp. 31-60.
Published Online: June 12, 2012. Abstract

 

Full Article
   

Sergio Decherchi, José Colmenares, Chiara Eva Catalano, Michela Spagnuolo, Emil Alexov and Walter Rocchia
Between algorithm and model: different molecular surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution.
Commun. Comput. Phys., 13 (2013
), pp. 61-89.
Published Online: June 12, 2012. Abstract

 

Full Article
   

Mihir S. Date and Brian N. Dominy
Modeling the influence of salt on the hydrophobic effect and protein fold stability.
Commun. Comput. Phys., 13 (2013
), pp. 90-106.
Published Online: June 12, 2012. Abstract

 

Full Article
   

Bo Zhang, Benzhuo Lu, Xiaolin Cheng, Jingfang Huang, Nikos P. Pitsianis, Xiaobai Sun and J. Andrew McCammon
Mathematical and numerical aspects of the adaptive fast multipole Poisson-Boltzmann solver.
Commun. Comput. Phys., 13 (2013
), pp. 107-128.
Published Online: June 12, 2012. Abstract

 

Full Article
   

Wei Song, Yuchun Lin, Andrij Baumketner, Shaozhong Deng, Wei Cai and Donald J. Jacobs
Effect of the reaction field on molecular forces and torques revealed by an image-charge solvation model.
Commun. Comput. Phys., 13 (2013
), pp. 129-149.
Published Online: June 12, 2012. Abstract

 

Full Article
   

Mohammad Mirzadeh, Maxime Theillard, Asdís Helgadóttir, David Boy and Frédéric Gibou
An adaptive, finite difference solver for the nonlinear Poisson-Boltzmann equation with applications to biomolecular computations.
Commun. Comput. Phys., 13 (2013
), pp. 150-173.
Published Online: June 12, 2012. Abstract

 

Full Article
   

Dexuan Xie and Hans W. Volkmer
A modified nonlocal continuum electrostatic model for protein in water and its analytical solutions for ionic Born models.
Commun. Comput. Phys., 13 (2013
), pp. 174-194.
Published Online: June 12, 2012. Abstract

 

Full Article
   

Travis Mackoy, Robert C. Harris, Jesse Johnson, Michael Mascagni and Marcia O. Fenley
Numerical optimization of a walk-on-spheres solver for the linear Poisson-Boltzmann equation
Commun. Comput. Phys., 13 (2013
), pp. 195-206.
Published Online: June 12, 2012. Abstract

 

Full Article
   

Lin Wang, Shawn Witham, Zhe Zhang, Lin Li, Michael Hodsdon and Emil Alexov
In silico investigation of pH-dependence of prolactin and human growth hormone binding to human prolactin receptor.
Commun. Comput. Phys., 13 (2013
), pp. 207-222.
Published Online: June 12, 2012. Abstract

 

Full Article
   

Allyn R. Brice and Brian N. Dominy
Examining electrostatic influences on base-flipping: a comparison of TIP3P and GB solvent models.
Commun. Comput. Phys., 13 (2013
), pp. 223-237.
Published Online: June 12, 2012. Abstract

 

Full Article
   

Joao M. Martins, Rui M. Ramos and Irina S. Moreira
Structural determinants of a typical leucine-rich repeat protein.
Commun. Comput. Phys., 13 (2013
), pp. 238-255.
Published Online: June 12, 2012. Abstract

 

Full Article
   

Lane W. Votapka, Luke Czapla, Maxim Zhenirovskyy and Rommie E. Amaro
DelEnsembleElec: computing ensemble-averaged electrostatics using DelPhi.
Commun. Comput. Phys., 13 (2013
), pp. 256-268.
Published Online: June 12, 2012. Abstract

 

Full Article
   

Subhra Sarkar, Shawn Witham, Jie Zhang, Maxim Zhenirovskyy, Walter Rocchia and Emil Alexov
DelPhi web server: a comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes.
Commun. Comput. Phys., 13 (2013
), pp. 269-284.
Published Online: June 12, 2012. Abstract

 

Full Article
   

Duan Chen and Guo-Wei Wei
Quantum dynamics in continuum for proton transport I: basic formulation.
Commun. Comput. Phys., 13 (2013
), pp. 285-324.
Published Online: June 12, 2012. Abstract

 

Full Article
   
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