Molecular dynamics simulation of humic substances

Chemical and Biological Technologies in Agriculture

Volumn 1, Issue 1, 2014, Pages

  Orsi, Mario ^a  

^a QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

Humic substances; Molecular dynamics; Molecular modeling; Molecular simulation; Natural organic matter; Soil organic matter

Indexed keywords

EID: 84945916448     PISSN: None     EISSN: 21965641     Source Type: Journal    
DOI: 10.1186/s40538-014-0010-4     Document Type: Review

References (159)

1. Stevenson FJ: Humus chemistry: genesis, composition, reactions. 1994, Wiley, Hoboken
2. Kördel W, Dassenakis M, Lintelmann J, Padberg S: The importance of natural organic material for environmental processes in waters and soils (technical report). Pure Appl Chem. 1997, 69 (7): 1571-1600.
3. Kukkonen J: Binding of organic pollutants to humic and fulvic acids: influence of ph and the structure of humic material. Chemosphere. 1997, 34 (8): 1693-1704.
4. Pignatello JJ: Soil organic matter as a nanoporous sorbent of organic pollutants. Adv Colloid Interface Sci. 1998, 76: 445-467.
5. Lal R: Soil carbon sequestration impacts on global climate change and food security. Science. 2004, 304 (5677): 1623-1627.
6. Hayes MHB, MacCarthy P, Malcolm RL, Swift R: Humic substances II. In search of structure. 1989, Wiley, Hoboken
7. Hayes MH, Clapp CE: Humic substances: considerations of compositions, aspects of structure, and environmental influences. Soil Sci. 2001, 166 (11): 723-737.
8. Piccolo A: The supramolecular structure of humic substances. Soil Sci. 2001, 166 (11): 810-832.
9. Piccolo A: The supramolecular structure of humic substances: a novel understanding of humus chemistry and implications in soil science. Adv Agronomy. 2002, 75: 57-134.
10. Piccolo A, Conte P, Cozzolino A: Chromatographic and spectrophotometric properties of dissolved humic substances compared with macromolecular polymers. Soil Sci. 2001, 166 (3): 174-185.
11. Piccolo A, Conte P, Trivellone E, van Lagen B, Buurman P: Reduced heterogeneity of a lignite humic acid by preparative HPSEC following interaction with an organic acid. Characterization of size-separates by Pyr-GC-MS and 1H-NMR spectroscopy. Environ Sci Technol. 2002, 36 (1): 76-84.
12. Piccolo A: Aggregation and disaggregation of humic supramolecular assemblies by NMR diffusion ordered spectroscopy (DOSY-NMR). Environ Sci Technol. 2007, 42 (3): 699-706.
13. Nebbioso A, Piccolo A: Advances in humeomics: enhanced structural identification of humic molecules after size fractionation of a soil humic acid. Analytica Chimica Acta. 2012, 720: 77-90.
14. Nebbioso A, Piccolo A: Basis of a humeomics science: chemical fractionation and molecular characterization of humic biosuprastructures. Biomacromolecules. 2011, 12 (4): 1187-1199.
15. Piccolo A, Nardi S, Concheri G: Micelle-like conformation of humic substances as revealed by size exclusion chromatography. Chemosphere. 1996, 33 (4): 595-602.
16. Nardi S, Concheri G: Macromolecular changes of humic substances induced by interaction with organic acids. Eur J Soil Sci. 1996, 47 (3): 319-328.
17. Wershaw RL: Molecular aggregation of humic substances. Soil Sci. 1999, 164 (11): 803-813.
18. Stoddard SD, Ford J: Numerical experiments on stochastic behavior of a Lennard-Jones gas system. Phys Rev A. 1973, 8: 1504-1512.
19. Adams DJ, Adams EM, Hills GJ: The computer simulation of polar liquids. Mol Phys. 1979, 38: 387-400.
20. Sokhan VP, Tildesley DJ: The free surface of water: molecular orientation, surface potential and nonlinear susceptibility. Mol Phys. 1997, 92: 625-640.
21. Orsi M: Comparative assessment of the ELBA coarse-grained model for water. Mol Phys. 2014, 112: 1566-1576.
22. Vega C, Abascal JL: Simulating water with rigid non-polarizable models: a general perspective. Phys Chem. 2011, 13: 19663-19688.
23. Mackerell AD: Empirical force fields for biological macromolecules: overview and issues. J Comput Chem. 2004, 25: 1584-1604.
24. Soncini M, Vesentini S, Ruffoni D, Orsi M, Deriu MA, Redaelli A: Mechanical response and conformational changes of alpha-actinin domains during unfolding: a molecular dynamics study. Biomechan Model Mechanobiol. 2007, 6: 399-407.
25. Deriu MA, Soncini M, Orsi M, Patel M, Essex JW, Montevecchi FM, Redaelli A: Anisotropic elastic network modeling of entire microtubules. Biophys J. 2010, 99: 2190-2199.
26. Parton DL, Klingelhoefer JW, Sansom MSP: Aggregation of model membrane proteins, modulated by hydrophobic mismatch, membrane curvature, and protein class. Biophys J. 2011, 101: 691-699.
27. Nielsen SO, Ensing B, Ortiz V, Moore PB, Klein ML: Lipid bilayer perturbations around a transmembrane nanotube: a coarse grain molecular dynamics study. Biophys J. 2005, 88: 3822-3828.
28. Xiang T-X, Anderson BD: Liposomal drug transport: a molecular perspective from molecular dynamics simulations in lipid bilayers. Adv Drug Deliv Rev. 2006, 58: 1357-1378.
29. Orsi M, Sanderson W, Essex JW, Kettner C (2007) Molecular interactions–bringing chemistry to life. In: Hicks MG (ed), 85–205. Beilstein-Institut, Frankfurt.
30. Orsi M, Haubertin DY, Sanderson WE, Essex JW: A quantitative coarse-grain model for lipid bilayers. J Phys Chem B. 2008, 112: 802-815.
31. Orsi M, Essex JW (2010) Molecular simulations and biomembranes: from biophysics to function. In: Biggin PC Sansom MSP (eds), 76–90. RSC, Cambridge.
32. Orsi M, Michel J, Essex JW (2010) Coarse-grain modelling of DMPC and DOPC lipid bilayers. J Phys: Condens Matter 22: 155106.
33. Lyubartsev AP, Rabinovich AL: Recent development in computer simulations of lipid bilayers. Soft Matter. 2011, 7: 25-39.
34. Orsi M, Essex JW (2011) The ELBA force field for coarse-grain modeling of lipid membranes. PLoS ONE 6: 28637.
35. Essex JW: Physical properties of mixed bilayers containing lamellar and nonlamellar lipids: insights from coarse-grain molecular dynamics simulations. Faraday Discuss. 2013, 161: 249-272.
36. Kremer K, Grest GS: Dynamics of entangled linear polymer melts: a molecular-dynamics simulation. J Chem Phys. 1990, 92 (8): 5057-5086.
37. Varnik F, Baschnagel J, Binder K: Molecular dynamics results on the pressure tensor of polymer films. J Chem Phys. 2000, 113: 4444-4453.
38. Rapaport DC (2002) Molecular dynamics simulation of polymer helix formation using rigid-link methods. Phys Rev E 66: 011906.
39. Barrat J-L, Baschnagel J, Lyulin A: Molecular dynamics simulations of glassy polymers. Soft Matter. 2010, 6 (15): 3430-3446.
40. Belytschko T, Xiao S, Schatz G, Ruoff R (2002) Atomistic simulations of nanotube fracture. Phys Rev B 65(23): 235430.
41. Coluci VR, Pugno NM, Dantas SO, Galvao DS, Jorio A (2007) Atomistic simulations of the mechanical properties of ’super’ carbon nanotubes. Nanotechnology 18(33): 335702.
42. Zang J, Ryu S, Pugno N, Wang Q, Tu Q, Buehler MJ, Zhao X: Multifunctionality and control of the crumpling and unfolding of large-area graphene. Nat Mater. 2013, 12 (4): 321-325.
43. Plimpton S: Fast parallel algorithms for short-range molecular dynamics. J Comput Phys. 1995, 117: 1-19.
44. LAMMPS molecular dynamics simulator. Accessed 10 June 2014., [http://lammps.sandia.gov]
45. Hess B, Kutzner C, Lindahl E: Gromacs 4, algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput. 2008, 4: 435-447.
46. Case DA, Darden TA, Cheatham TE, Simmerling CL, Wang J, Duke RE, Luo R, Walker RC, Zhang W, Merz KM, Roberts B, Hayik S, Roitberg A, Seabra G, Swails J, Goetz AW, Kolossváry I, Wong KF, Paesani F, Vanicek J, Wolf RM, Liu J, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Cai Q, Ye X, Wang J, Hsieh MJ, et al: AMBER 12. 2012, University of California, San Francisco
47. Kunz A-PE, Allison JR, Geerke DP, Horta BAC, Hünenberger PH, Riniker S, Schmid N, van Gunsteren WF: New functionalities in the GROMOS biomolecular simulation software. J Comput Chem. 2012, 33 (3): 340-353.
48. Todorov IT, Smith W, Trachenko K, Dove MT: Journal of Materials Chemistry. 2006, 16: 1911-1918.
49. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M: CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem. 1983, 4: 187-217.
50. Allen MP, Tildesley DJ: Computer simulation of liquids. 1987, Oxford Science, Oxford
51. Leach AR: Molecular modelling - principles and applications. 2001, Prentice Hall, Harlow
52. Frenkel D, Smit B: Understanding molecular simulation. 2002, Academic, London
53. Schlick T: Molecular modeling and simulation - an interdisciplinary guide. 2002, Springer, New York
54. Rapaport DC: The art of molecular dynamics simulation. 2004, Cambridge University Press, Cambridge
55. Sutmann G: Classical molecular dynamics. Quantum Simul Complex Many-body Syst: Theory Algorithms. 2002, 10: 211-254.
56. Allen MP (2004) Introduction to molecular dynamics simulation23(Comput Soft Matter): 1–28.
57. Binder K, Horbach J, Varnik F: Molecular dynamics simulations. J Phys: Condens Matter. 2004, 16: 429-453.
58. van Gunsteren WF, Bakowies D, Baron R, Chandrasekhar I, Christen M, Daura X, Gee P, Geerke DP, Glaettli A, Huenenberger PH, Kastenholz MA, Ostenbrink C, Schenk M, Trzesniak D, van der Vegt NFA: Biomolecular modeling: goals, problems, perspectives. Angew Chem-Int Edit. 2006, 45: 4064-4092.
59. Lopes PE, Huang J, Shim J, Luo Y, Li H, Roux B, MacKerell Jr AD: Polarizable force field for peptides and proteins based on the classical drude oscillator. J Chem Theory Comput. 2013, 9 (12): 5430-5449.
60. Swope WC, Andersen HC, Berens PH, Wilson KR: A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: application to small water clusters. J Chem Phys. 1982, 76: 637-649.
61. Schulten H-R: Interactions of dissolved organic matter with xenobiotic compounds molecular modeling in water. Environ Toxicol Chem. 1999, 18 (8): 1643-1655.
62. Sutton R, Sposito G, Diallo MS, Schulten H-R: Molecular simulation of a model of dissolved organic matter. Environ Toxicol Chem. 2005, 24 (8): 1902-1911.
63. Kögel-Knabner I: The macromolecular organic composition of plant and microbial residues as inputs to soil organic matter. Soil Biol Biochem. 2002, 34 (2): 139-162.
64. Parsi Z, Hartog N, Górecki T: Analytical pyrolysis as a tool for the characterization of natural organic matter–a comparison of different approaches. J Anal Appl Pyrolysis. 2007, 79 (1): 9-15.
65. Schulten H-R: Analytical pyrolysis and computational chemistry of aquatic humic substances and dissolved organic matter. J Anal Appl Pyrolysis. 1999, 49 (1): 385-415.
66. Vepsäläinen M, Ghiasvand M, Selin J, Pienimaa J, Repo E, Pulliainen M: Investigations of the effects of temperature and initial sample pH on natural organic matter (nom) removal with electrocoagulation using response surface method (rsm). Separation Purif Technol. 2009, 69 (3): 255-261.
67. Jansen SA, Malaty M, Nwabara S, Johnson E, Ghabbour E, Davies G, Varnum JM: Structural modeling in humic acids. Materials Sci Eng: C. 1996, 4 (3): 175-179.
68. Davies G, Fataftah A, Cherkasskiy A, Ghabbour EA, Radwan A, Jansen SA, Kolla S, Paciolla MD, Sein Jr LT, Buermann W, Balasubramanian M, Budnick J, Xing B (1997) Tight metal binding by humic acids and its role in biomineralization. J Chem Soc Dalton Trans: 4047–4060.
69. Kubicki J, Apitz S: Models of natural organic matter and interactions with organic contaminants. Org Geochem. 1999, 30 (8): 911-927.
70. Sein LT, Varnum JM, Jansen SA: Conformational modeling of a new building block of humic acid approaches to the lowest energy conformer. Environ Sci Technol. 1999, 33 (4): 546-552.
71. Alvarez-Puebla RA, Garrido JJ: Effect of pH on the aggregation of a gray humic acid in colloidal and solid states. Chemosphere. 2005, 59 (5): 659-667.
72. Alvarez-Puebla R, Valenzuela-Calahorro C, Garrido J: Theoretical study on fulvic acid structure, conformation and aggregation: a molecular modelling approach. Sci Total Environ. 2006, 358 (1): 243-254.
73. Leenheer J, Brown G, MacCarthy P, Cabaniss S: Models of metal binding structures in fulvic acid from the Suwannee River, Georgia. Environ Sci Technol. 1998, 32 (16): 2410-2416.
74. Porquet A, Bianchi L, Stoll S: Molecular dynamic simulations of fulvic acid clusters in water. Colloids Surf A: Physicochem Eng Aspects. 2003, 217 (1): 49-54.
75. Diallo MS, Simpson A, Gassman P, Faulon JL, Johnson JH, Goddard WA, Hatcher PG: 3-D structural modeling of humic acids through experimental characterization, computer assisted structure elucidation and atomistic simulations. 1. Chelsea soil humic acid. Environ Sci Technol. 2003, 37 (9): 1783-1793.
76. Aquino AJ, Tunega D, Pasalic H, Schaumann GE, Haberhauer G, Gerzabek MH, Lischka H: Molecular dynamics simulations of water molecule-bridges in polar domains of humic acids. Environ Sci Technol. 2011, 45 (19): 8411-8419.
77. Aquino AJ, Tunega D, Schaumann GE, Haberhauer G, Gerzabek MH, Lischka H: Study of solvent effect on the stability of water bridge-linked carboxyl groups in humic acid models. Geoderma. 2011, 169: 20-26.
78. Schulten H-R, Schnitzer M: Chemical model structures for soil organic matter and soils. Soil Sci. 1997, 162 (2): 115-130.
79. Sutton R, Sposito G: Molecular simulation of humic substance–Ca-montmorillonite complexes. Geochimica et Cosmochimica Acta. 2006, 70 (14): 3566-3581.
80. von Lützow M, Kögel-Knabner I, Ekschmitt K, Flessa H, Guggenberger G, Matzner E, Marschner B: Som fractionation methods: relevance to functional pools and to stabilization mechanisms. Soil Biol Bioch. 2007, 39 (9): 2183-2207.
81. Teppen BJ, Yu C-H, Miller DM, Schäfer L: Molecular dynamics simulations of sorption of organic compounds at the clay mineral/aqueous solution interface. J Comput Chem. 1998, 19 (2): 144-153.
82. Shevchenko SM, Bailey GW, Akim LG: The conformational dynamics of humic polyanions in model organic and organo-mineral aggregates. J Mol Struct: THEOCHEM. 1999, 460 (1): 179-190.
83. Petridis L, Ambaye H, Jagadamma S, Kilbey SM, Lokitz BS, Lauter V, Mayes M: Spatial arrangement of organic compounds on a model mineral surface: implications for soil organic matter stabilization. Environ Sci Technol. 2013, 48: 79-84.
84. Tipping E: Cation Binding by Humic Substances. 2002, Cambridge University Press, Cambridge
85. Cation binding by humic substances. Environ Geol. 2003, 43: 615-616.
86. Alvarez-Puebla RA, Valenzuela-Calahorro C, Garrido JJ: Retention of co(ii), Ni(ii), and Cu(ii) on a purified brown humic acid. Modeling and characterization of the sorption process. Langmuir. 2004, 20 (9): 3657-3664. PMID:15875396
87. Schneider T, Stoll E (1978) Molecular-dynamics study of a three-dimensional one-component model for distortive phase transitions17(Phys Rev B): 1302–1322.
88. − complexation with natural organic matter. Geochimica et Cosmochimica Acta. 2006, 70 (17): 4319-4331.
89. Kalinichev A, Kirkpatrick R: Molecular dynamics simulation of cationic complexation with natural organic matter. Eur J Soil Sci. 2007, 58 (4): 909-917.
90. Iskrenova-Tchoukova E, Kalinichev AG, Kirkpatrick RJ: Metal cation complexation with natural organic matter in aqueous solutions: molecular dynamics simulations and potentials of mean force. Langmuir. 2010, 26 (20): 15909-15919.
91. 2+ on supramolecular aggregation of natural organic matter in aqueous solutions: a comparison of molecular modeling approaches. Geoderma. 2011, 169: 27-32.
92. Dauber-Osguthorpe P, Roberts VA, Osguthorpe DJ, Wolff J, Genest M, Hagler AT: Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase-trimethoprim, a drug-receptor system. Proteins: Struct Funct Bioinformatics. 1988, 4 (1): 31-47.
93. Bashford D, Bellott M, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WEIII, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M: All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B. 1998, 102: 3586-3616.
94. Case DA, Darden TA, Cheatham TE, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews DH, Schafmeister C, et al: Amber 9. 2006, University of California, San Francisco
95. Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J (1981) Intermolecular Forces(Pullman B, ed.), Reidel, Dordrecht.
96. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML: Comparison of simple potential functions for simulating liquid water. J Chem Phys. 1983, 79: 926-935.
97. Kolpin DW, Furlong ET, Meyer MT, Thurman EM, Zaugg SD, Barber LB, Buxton HT: Pharmaceuticals, hormones, and other organic wastewater contaminants in US streams, 1999-2000: a national reconnaissance. Environ Sci Technol. 2002, 36: 1202-1211.
98. Halden RU, Paull DH: Co-occurrence of triclocarban and triclosan in US water resources. Environ Sci Technol. 2005, 39: 1420-1426.
99. Higgins CP, Paesani ZJ, Chalew TEA, Halden RU: Bioaccumulation of triclocarban in Lumbriculus variegatus. Environ Toxicol Chem. 2009, 28: 2580-2586.
100. Boxall AB, Kolpin DW, Halling-Sørensen B, Tolls J: Peer reviewed: are veterinary medicines causing environmental risks?. Environ Sci Technol. 2003, 37 (15): 286-294.
101. Boxall AB, Johnson P, Smith EJ, Sinclair CJ, Stutt E, Levy LS: Uptake of veterinary medicines from soils into plants. J Agric Food Chem. 2006, 54 (6): 2288-2297.
102. Lee LS, Carmosini N, Sassman SA, Dion HM, Sepulveda MS: Agricultural contributions of antimicrobials and hormones on soil and water quality. Adv Agronomy. 2007, 93: 1-68.
103. Kümmerer K: Significance of antibiotics in the environment. J Antimicrob Chemother. 2003, 52 (1): 5-7.
104. Schweizer HP: Triclosan: a widely used biocide and its link to antibiotics. FEMS Microbiol Lett. 2001, 202: 1-7.
105. Chalew TEA, Halden RU: Environmental exposure of aquatic and terrestrial biota to triclosan and triclocarban. J Am Water Resour Assoc. 2009, 45: 4-13.
106. Orsi M, Noro MG, Essex JW: Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes. J R Soc Interface. 2011, 8: 826-841.
107. Aiello AE, Larson EL, Levy SB: Consumer antibacterial soaps: effective or just risky?. Clin Infect Dis. 2007, 45: 137-147.
108. Aryal N, Reinhold DM: Phytoaccumulation of antimicrobials from biosolids: impacts on environmental fate and relevance to human exposure. Water Res. 2011, 45 (17): 5545-5552.
109. Oliver SP, Murinda SE, Jayarao BM: Impact of antibiotic use in adult dairy cows on antimicrobial resistance of veterinary and human pathogens: a comprehensive review. Foodborne Pathogens Disease. 2011, 8 (3): 337-355.
110. Marshall BM, Levy SB: Food animals and antimicrobials: impacts on human health. Clin Microbiol Rev. 2011, 24 (4): 718-733.
111. Aristilde L, Sposito G: Binding of ciprofloxacin by humic substances: a molecular dynamics study. Environ Toxicol Chem. 2010, 29 (1): 90-98.
112. Hartmann A, Alder AC, Koller T, Widmer RM: Identification of fluoroquinolone antibiotics as the main source of umuC, genotoxicity in native hospital wastewater. Environ Toxicol Chem. 1998, 17 (3): 377-382.
113. Haigh SD: A review of the interaction of surfactants with organic contaminants in soil. Sci Total Environ. 1996, 185 (1): 161-170.
114. Käcker T, Haupt ET, Garms C, Francke W, Steinhart H: Structural characterisation of humic acid-bound pah residues in soil by 13c-cpmas-nmr-spectroscopy: evidence of covalent bonds. Chemosphere. 2002, 48 (1): 117-131.
115. Laor Y, Rebhun M: Evidence for nonlinear binding of PAHs to dissolved humic acids. Environ Sci Technol. 2002, 36 (5): 955-961.
116. Golobočanin DD, Škrbić BD, Miljević NR (2004) Principal component analysis for soil contamination with pahs Chemometrics Intell Lab Syst72(2): 219–223.
117. Zhou W, Zhu L: Distribution of polycyclic aromatic hydrocarbons in soil–water system containing a nonionic surfactant. Chemosphere. 2005, 60 (9): 1237-1245.
118. Zhang H, Luo Y, Wong M, Zhao Q, Zhang G: Distributions and concentrations of pahs in Hong Kong soils. Environ Pollut. 2006, 141 (1): 107-114.
119. Saparpakorn P, Kim JH, Hannongbua S: Investigation on the binding of polycyclic aromatic hydrocarbons with soil organic matter: a theoretical approach. Molecules. 2007, 12 (4): 703-715.
120. Buffle J, Greter FL, Haerdi W: Measurement of complexation properties of humic and fulvic acids in natural waters with lead and copper ion-selective electrodes. Anal Chem. 1977, 49 (2): 216-222.
121. Schulten H-R, Thomsen M, Carlsen L: Humic complexes of diethyl phthalate: molecular modelling of the sorption process. Chemosphere. 2001, 45 (3): 357-369.
122. 60 apparent solubility A molecular mechanics and density functional theory study. Environ Int. 2011, 37 (6): 1078-1082.
123. Bosi S, Spalluto G, Prato M: Fullerene derivatives: an attractive tool for biological applications. Eur J Med Chem. 2003, 38: 913-923.
124. Nakamura E, Isobe H: Functionalized fullerenes in water. The first 10 years of their chemistry, biology, and nanoscience. Acc Chem Res. 2003, 36: 807-815.
125. Oberdörster G, Sharp Z, Atudorei A, Elder V, Gelein R, Kreyling W, Cox C: Translocation of inhaled ultrafine particles to the brain. Inhal Toxicol. 2004, 16: 437-445.
126. Sayes CM, Fortner JD, Guo W, Lyon D, Boyd AM, Ausman KD, Tao YJ, Sitharaman B, Wilson LJ, Hughes JB, West JL, Colvin VL: The differential cytotoxicity of water-soluble fullerenes. Nano Lett. 2004, 4: 1881-1887.
127. 60. Chemosphere. 2013, 92 (4): 429-434.
128. Wu F, Bai Y, Mu Y, Pan B, Xing B: Fluorescence quenching of fulvic acids by fullerene in water. Environ Pollut. 2013, 172: 100-107.
129. Molecular dynamic simulations of the sorption of toluene in a dry humic acid model: a preliminary study. Colloids Surf A: Physicochem Eng Aspects. 2006, 275 (1): 183-186.
130. Lee S, Cho J, Elimelech M: Combined influence of natural organic matter (nom) and colloidal particles on nanofiltration membrane fouling. J Membrane Sci. 2005, 262 (1): 27-41.
131. Wang Z, Zhao Y, Wang J, Wang S: Studies on nanofiltration membrane fouling in the treatment of water solutions containing humic acids. Desalination. 2005, 178 (1): 171-178.
132. Li Q, Elimelech M: Synergistic effects in combined fouling of a loose nanofiltration membrane by colloidal materials and natural organic matter. J Membrane Sci. 2006, 278 (1): 72-82.
133. Jarusutthirak C, Mattaraj S, Jiraratananon R: Influence of inorganic scalants and natural organic matter on nanofiltration membrane fouling. J Membrane Sci. 2007, 287 (1): 138-145.
134. Her N, Amy G, Chung J, Yoon J, Yoon Y: Characterizing dissolved organic matter and evaluating associated nanofiltration membrane fouling. Chemosphere. 2008, 70 (3): 495-502.
135. Xiang Y, Liu Y, Mi B, Leng Y: Hydrated polyamide membrane and its interaction with alginate: a molecular dynamics study. Langmuir. 2013, 29 (37): 11600-11608.
136. Ahn W-Y, Kalinichev AG, Clark MM: Effects of background cations on the fouling of polyethersulfone membranes by natural organic matter: experimental and molecular modeling study. J Membrane Sci. 2008, 309 (1): 128-140.
137. Hughes ZE, Gale JD: A computational investigation of the properties of a reverse osmosis membrane. J Mater Chem. 2010, 20 (36): 7788-7799.
138. Hughes ZE, Gale JD: Molecular dynamics simulations of the interactions of potential foulant molecules and a reverse osmosis membrane. J Mater Chem. 2012, 22 (1): 175-184.
139. Myat DT, Stewart MB, Mergen M, Zhao O, Orbell JD, Gray S: Experimental and computational investigations of the interactions between model organic compounds and subsequent membrane fouling. Water Res. 2014, 48: 108-118.
140. Majorek KA, Porebski PJ, Dayal A, Zimmerman MD, Jablonska K, Stewart AJ, Chruszcz M, Minor W: Structural and immunologic characterization of bovine, horse, and rabbit serum albumins. Mol Immunol. 2012, 52 (3): 174-182.
141. Momany FA, Dombrink-Kurtzman MA: Molecular dynamics simulations on the mycotoxin fumonisin B1. J Agric Food Chem. 2001, 49 (2): 1056-1061.
142. Mahfoud R, Maresca M, Santelli M, Pfohl-Leszkowicz A, Puigserver A, Fantini J: pH-dependent interaction of fumonisin B1 with cholesterol physicochemical and molecular modeling studies at the air-water interface. J Agric Food Chem. 2002, 50 (2): 327-331.
143. Thiele-Bruhn S: Molecular modeling of soil organic matter: squaring the circle?. Geoderma. 2011, 166 (1): 1-14.
144. Schulten H-R: The three-dimensional structure of humic substances and soil organic matter studied by computational analytical chemistry. Fresenius’ J Anal Chem. 1995, 351 (1): 62-73.
145. Schulten H-R: The three-dimensional structure of soil organo-mineral complexes studied by analytical pyrolysis. J Anal Appl Pyrolysis. 1995, 32: 111-126.
146. Schulten H-R, Leinweber P: Characterization of humic and soil particles by analytical pyrolysis and computer modeling. J Anal Appl Pyrolysis. 1996, 38 (1): 1-53.
147. Shevchenko SM, Bailey GW: Non-bonded organo-mineral interactions and sorption of organic compounds on soil surfaces: a model approach. J Mol Struct: Theochem. 1998, 422 (1): 259-270.
148. Schulten H, Leinweber P, Schnitzer M, Huang P, Senesi N, Buffle J: Analytical pyrolysis and computer modelling of humic and soil particles. Environmental particles: structure and surface reactions of soil particles. 1998, Wiley, Chichester, 281-324.
149. Schulten H-R, Leinweber P: New insights into organic-mineral particles: composition, properties and models of molecular structure. Biol Fertil Soils. 2000, 30 (5–6): 399-432.
150. Johnson J (2001) Binding of hydrophobic organic compounds to dissolved humic substances: a predictive approach based on computer assisted structure elucidation, atomistic simulations and Flory-Huggins solution theory. Humic Subst Struct Models Funct 273: 221.
151. Kubicki J (2000) Molecular modeling of humic and fulvic acid. In: Abstracts of Papers of the American Chemical Society, 361–361. vol. 220.
152. Ayton GS, Noid WG, Voth GA: Multiscale modeling of biomolecular systems: in serial and in parallel. Curr Opin Struct Biol. 2007, 17: 192-198.
153. Sherwood P, Brooks BR, Sansom MSP: Multiscale methods for macromolecular simulations. Curr Opin Struct Biol. 2008, 18: 630-640.
154. Michel J, Orsi M, Essex JW: Prediction of partition coefficients by multiscale hybrid atomic level/coarse-grain simulations. J Phys Chem B. 2008, 112: 657-660.
155. Orsi M, Sanderson WE, Essex JW: Permeability of small molecules through a lipid bilayer: a multiscale simulation study. J Phys Chem B. 2009, 113: 12019-12029.
156. Orsi M, Essex JW: Permeability of drugs and hormones through a lipid bilayer: insights from dual-resolution molecular dynamics. Soft Matter. 2010, 6: 3797-3808.
157. Kamerlin SCL, Vicatos S, Dryga A, Warshel A: Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems. Annu Rev Phys Chem. 2011, 62: 41-64.
158. Chen Y, Aviad T (1990) Effects of humic substances on plant growth. In: Humic substances in soil and crop sciences: selected readings (humic substances), Soil Science Society of America, 161–186, USA.
159. Matilainen A, Gjessing ET, Lahtinen T, Hed L, Bhatnagar A: An overview of the methods used in the characterisation of natural organic matter (nom) in relation to drinking water treatment. Chemosphere. 2011, 83 (11): 1431-1442.