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Molecular Simulation Volume 31, 2005 - Issue 9: American Institute of Chemical Engineers
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Original Articles

ALLD: An object-oriented mesoscopic simulation program for polar biomolecules in hydrophobic chromatography or biomembranes

Kosta Makrodimitris Department of Chemical Engineering, University of Virginia, Charlottesville, VA, 22904, USA; Departments of Physiology, Biophysics and Biophysical Chemistry, and Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USACorrespondence[email protected]
,
Erik J. Fernandez Department of Chemical Engineering, University of Virginia, Charlottesville, VA, 22904, USA
,
Thomas B. Woolf Departments of Physiology, Biophysics and Biophysical Chemistry, and Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
&
John P. O'connell Department of Chemical Engineering, University of Virginia, Charlottesville, VA, 22904, USA
Pages 623-636 | Received 01 Nov 2004, Accepted 01 Jan 2005, Published online: 31 Jan 2007
 
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Abstract

The ALLD simulation software implements a mesoscopic lattice method to model hydrophobic chromatographic systems and biomembranes. The basis and some initial results of these applications emphasizing reversed phase chromatography of peptides are reviewed. The program structure and coding are described along with concepts for parallelization to simulate massive systems and large biomolecules. Extensions of the method for simulations with variable temperature, solute and solvent polarization, effects of ionized solutes and added salts and heterogeneous media are presented.

Acknowledgements

The authors are grateful to Professor Curt Breneman and Dr. Alan Grossfield for useful discussions concerning the simulations and to the reviewer who raised the issues associated with angle averaging.

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