34
Z. Wang and J. Chen
49. Zhang Q, Pi J, Woods CG, Andersen ME (2010) A systems biology perspective on Nrf2mediated antioxidant response. Toxicol Appl Pharmacol 244(1):84–97
50. Birbaumer M, Schweitzer F (2011) Agent-based modeling of intracellular transport. Eur Phys
J B 82(3–4):245–255
51. Dalmasso G, Zapata PAM, Brady NR, Hamacher-Brady A (2017) Agent-based modeling of
mitochondria links sub-cellular dynamics to cellular homeostasis and heterogeneity. PLoS
ONE 12(1):e0168198
52. Bonabeau E (2002) Agent-based modeling: methods and techniques for simulating human
systems. Proc Natl Acad Sci U S A 99:7280–7287
53. Grimm V, Revilla E, Berger U, Jeltsch F, Mooij WM, Railsback SF, Thulke HH, Weiner J,
Wiegand T, DeAngelis DL (2005) Pattern-oriented modeling of agent-based complex systems:
lessons from ecology. Science 310(5750):987–991
54. Kleinstreuer N, Dix D, Rountree M, Baker N, Sipes N, Reif D, Spencer R, Knudsen T (2013)
A computational model predicting disruption of blood vessel development. PLoS Comput Biol
9(4):e1002996
55. Swat MH, Thomas GL, Belmonte JM, Shirinifard A, Hmeljak D, Glazier JA (2012) Multi-scale
modeling of tissues using CompuCell 3D. In: Asthagiri AR, Arkin AP (eds) Computational
methods in cell biology, vol 110. Academic Press, Waltham, pp 325–366
56. Wambaugh J, Shah I (2010) Simulating microdosimetry in a virtual hepatic lobule. PLoS
Comput Biol 6(4):e1000756
57. Shah I, Wambaugh J (2010) Virtual tissues in toxicology. J Toxicol Environ Health-Pt b-Crit
Rev 13(2–4):314–328
58. Allen TEH, Goodman JM, Gutsell S, Russell PJ (2014) Defining molecular initiating
events in the adverse outcome pathway framework for risk assessment. Chem Res Toxicol
27(12):2100–2112
59. Bobrowicz FW, Goddard WA III (1977) The self-consistent field equations for generalized
valence bond and open-shell hartree-fock wave functions. Plenum, New York
60. Pople JA, Headgordon M, Raghavachari K (1987) Quadratic configuration-interaction—a general technique for determining electron correlation energies. J Chem Phys 87(10):5968–5975
61. Bartlett RJ (1981) Many-body perturbation-theory and coupled cluster theory for electron
correlation in molecules. Annu Rev Phys Chem 32:359–401
62. Dewar MJS, Thiel W (1977) Ground-states of molecules. 38. MNDO method—approximations
and parameters. J Am Chem Soc 99(15):4899–4907
63. Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP (1985) The development and use
of quantum-mechanical molecular-models. 76. AM1—a new general-purpose quantummechanical molecular-model. J Am Chem Soc 107(13):3902–3909
64. Zhang HQ, Xie HB, Chen JW, Zhang SS (2015) Prediction of hydrolysis pathways and kinetics
for antibiotics under environmental pH conditions: a quantum chemical study on cephradine.
Environ Sci Technol 49(3):1552–1558
65. Shaik S, Kumar D, de Visser SP, Altun A, Thiel W (2005) Theoretical perspective on the
structure and mechanism of cytochrome P450 enzymes. Chem Rev 105(6):2279–2328
66. Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, de Groot BL, Grubmueller H, MacKerell
AD Jr (2017) CHARMM36m: an improved force field for folded and intrinsically disordered
proteins. Nat Methods 14(1):71–73
67. Salomon-Ferrer R, Case DA, Walker RC (2013) An overview of the AMBER biomolecular
simulation package. WIREs Comput Mol Sci 3(2):198–210
68. Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O,
Lopes P, Vorobyov I, MacKerell AD Jr (2010) CHARMM general force field: a force field for
drug-like molecules compatible with the CHARMM all-atom additive biological force fields.
J Comput Chem 31(4):671–690
69. Wang JM, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of
a general amber force field. J Comput Chem 25(9):1157–1174
70. Senn HM, Thiel W (2009) QM/MM methods for biomolecular systems. Angew Chem Int Ed
48(7):1198–1229
Z. Wang and J. Chen
49. Zhang Q, Pi J, Woods CG, Andersen ME (2010) A systems biology perspective on Nrf2mediated antioxidant response. Toxicol Appl Pharmacol 244(1):84–97
50. Birbaumer M, Schweitzer F (2011) Agent-based modeling of intracellular transport. Eur Phys
J B 82(3–4):245–255
51. Dalmasso G, Zapata PAM, Brady NR, Hamacher-Brady A (2017) Agent-based modeling of
mitochondria links sub-cellular dynamics to cellular homeostasis and heterogeneity. PLoS
ONE 12(1):e0168198
52. Bonabeau E (2002) Agent-based modeling: methods and techniques for simulating human
systems. Proc Natl Acad Sci U S A 99:7280–7287
53. Grimm V, Revilla E, Berger U, Jeltsch F, Mooij WM, Railsback SF, Thulke HH, Weiner J,
Wiegand T, DeAngelis DL (2005) Pattern-oriented modeling of agent-based complex systems:
lessons from ecology. Science 310(5750):987–991
54. Kleinstreuer N, Dix D, Rountree M, Baker N, Sipes N, Reif D, Spencer R, Knudsen T (2013)
A computational model predicting disruption of blood vessel development. PLoS Comput Biol
9(4):e1002996
55. Swat MH, Thomas GL, Belmonte JM, Shirinifard A, Hmeljak D, Glazier JA (2012) Multi-scale
modeling of tissues using CompuCell 3D. In: Asthagiri AR, Arkin AP (eds) Computational
methods in cell biology, vol 110. Academic Press, Waltham, pp 325–366
56. Wambaugh J, Shah I (2010) Simulating microdosimetry in a virtual hepatic lobule. PLoS
Comput Biol 6(4):e1000756
57. Shah I, Wambaugh J (2010) Virtual tissues in toxicology. J Toxicol Environ Health-Pt b-Crit
Rev 13(2–4):314–328
58. Allen TEH, Goodman JM, Gutsell S, Russell PJ (2014) Defining molecular initiating
events in the adverse outcome pathway framework for risk assessment. Chem Res Toxicol
27(12):2100–2112
59. Bobrowicz FW, Goddard WA III (1977) The self-consistent field equations for generalized
valence bond and open-shell hartree-fock wave functions. Plenum, New York
60. Pople JA, Headgordon M, Raghavachari K (1987) Quadratic configuration-interaction—a general technique for determining electron correlation energies. J Chem Phys 87(10):5968–5975
61. Bartlett RJ (1981) Many-body perturbation-theory and coupled cluster theory for electron
correlation in molecules. Annu Rev Phys Chem 32:359–401
62. Dewar MJS, Thiel W (1977) Ground-states of molecules. 38. MNDO method—approximations
and parameters. J Am Chem Soc 99(15):4899–4907
63. Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP (1985) The development and use
of quantum-mechanical molecular-models. 76. AM1—a new general-purpose quantummechanical molecular-model. J Am Chem Soc 107(13):3902–3909
64. Zhang HQ, Xie HB, Chen JW, Zhang SS (2015) Prediction of hydrolysis pathways and kinetics
for antibiotics under environmental pH conditions: a quantum chemical study on cephradine.
Environ Sci Technol 49(3):1552–1558
65. Shaik S, Kumar D, de Visser SP, Altun A, Thiel W (2005) Theoretical perspective on the
structure and mechanism of cytochrome P450 enzymes. Chem Rev 105(6):2279–2328
66. Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, de Groot BL, Grubmueller H, MacKerell
AD Jr (2017) CHARMM36m: an improved force field for folded and intrinsically disordered
proteins. Nat Methods 14(1):71–73
67. Salomon-Ferrer R, Case DA, Walker RC (2013) An overview of the AMBER biomolecular
simulation package. WIREs Comput Mol Sci 3(2):198–210
68. Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O,
Lopes P, Vorobyov I, MacKerell AD Jr (2010) CHARMM general force field: a force field for
drug-like molecules compatible with the CHARMM all-atom additive biological force fields.
J Comput Chem 31(4):671–690
69. Wang JM, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of
a general amber force field. J Comput Chem 25(9):1157–1174
70. Senn HM, Thiel W (2009) QM/MM methods for biomolecular systems. Angew Chem Int Ed
48(7):1198–1229