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ALLD: an object-oriented mesoscopic simulation program for polar biomolecules in hydrophobic chromatography or biomembranes. (English) Zbl 1096.92018
Summary: 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.
MSC:
92C40 Biochemistry, molecular biology
65C20 Probabilistic models, generic numerical methods in probability and statistics
Software:
ALLD; MMTK; MPI
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[1] DOI: 10.1002/1097-0134(20001101)41:2<211::AID-PROT60>3.0.CO;2-9 · doi:10.1002/1097-0134(20001101)41:2<211::AID-PROT60>3.0.CO;2-9
[2] Makrodimitris K, Anal. Chem. (2004)
[3] Langevin P, Anal. Chem. 5 pp 245– (1905)
[4] Debye P, Polar Molecules (1929)
[5] DOI: 10.1017/S0033583500005333 · doi:10.1017/S0033583500005333
[6] DOI: 10.1146/annurev.biophys.28.1.319 · doi:10.1146/annurev.biophys.28.1.319
[7] DOI: 10.1073/pnas.91.24.11631 · doi:10.1073/pnas.91.24.11631
[8] DOI: 10.1002/(SICI)1097-0134(199601)24:1<92::AID-PROT7>3.0.CO;2-Q · doi:10.1002/(SICI)1097-0134(199601)24:1<92::AID-PROT7>3.0.CO;2-Q
[9] Hearn MTW, HPLC of Biological Macromolecules: Methods and Applications pp 99– (2001)
[10] DOI: 10.1016/S0021-9673(03)00182-1 · doi:10.1016/S0021-9673(03)00182-1
[11] DOI: 10.1021/jp953301h · doi:10.1021/jp953301h
[12] DOI: 10.1021/la00009a036 · doi:10.1021/la00009a036
[13] DOI: 10.1021/jp984003y · doi:10.1021/jp984003y
[14] DOI: 10.1021/ac00109a038 · doi:10.1021/ac00109a038
[15] DOI: 10.1021/jp972232z · doi:10.1021/jp972232z
[16] DOI: 10.1073/pnas.77.3.1632 · doi:10.1073/pnas.77.3.1632
[17] DOI: 10.1016/S0021-9673(00)93816-0 · doi:10.1016/S0021-9673(00)93816-0
[18] DOI: 10.1002/btpr.5420050304 · doi:10.1002/btpr.5420050304
[19] DOI: 10.1021/j100291a060 · doi:10.1021/j100291a060
[20] DOI: 10.1021/ac010797s · doi:10.1021/ac010797s
[21] Böttcher CJF, Theory of Electric Polarization (1973)
[22] DOI: 10.1021/ja00124a002 · doi:10.1021/ja00124a002
[23] DOI: 10.1002/jcc.540040211 · doi:10.1002/jcc.540040211
[24] DOI: 10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P · Zbl 05428535 · doi:10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P
[25] Israelachvili J, Intermolecular and Surface Forces (1991)
[26] DOI: 10.1021/j100785a001 · doi:10.1021/j100785a001
[27] DOI: 10.1016/S0079-6565(97)00006-X · doi:10.1016/S0079-6565(97)00006-X
[28] Davidson N, Statistical Mechanics, McGraw-Hill Book Company, Inc. (1962)
[29] Makrodimitris K, Biotechnol. Prog.
[30] Cogswell J, C++ All-In-One Desk Reference For Dummies 2 (2003)
[31] DOI: 10.1063/1.1748233 · doi:10.1063/1.1748233
[32] Molecular Operating Environment, Chemical Computing Group Inc (2003)
[33] Hinsen K, The Molecular Modeling Toolkit: A Case Study of a Large Scientific Application in Python in Proceedings of the 6th International Python Conference, CNRI (1997)
[34] Gropp W, MPI -THE COMPLETE REFERENCE Volume 2. The MPI Extensions 1 (1998)
[35] Snir M, MPI -THE COMPLETE REFERENCE Volume 1. The MPI Core (1998)
[36] Smith W, Comput. Phys. Commun. 62 pp 229– · doi:10.1016/0010-4655(91)90097-5
[37] DOI: 10.1006/jcph.1999.6201 · Zbl 0948.92004 · doi:10.1006/jcph.1999.6201
[38] DOI: 10.1016/S0021-9673(03)00979-8 · doi:10.1016/S0021-9673(03)00979-8
[39] DOI: 10.1063/1.1501579 · doi:10.1063/1.1501579
[40] DOI: 10.1021/jp9705075 · doi:10.1021/jp9705075
[41] Makrodimitris K, (In preparation) (2005)
[42] DOI: 10.1002/bip.360360210 · doi:10.1002/bip.360360210
[43] DOI: 10.1002/jcc.10240 · Zbl 05429529 · doi:10.1002/jcc.10240
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