Mathematical models in biology: From molecules to life

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Volumn 3, Issue 3, 2011, Pages 314-322

  Kaznessis, Yiannis N ^a  

^a University of Minnesota   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; BIOLOGICAL MODEL; HUMAN; METHODOLOGY; REVIEW; SYSTEMS BIOLOGY; THERMODYNAMICS;

ANIMALS; HUMANS; MODELS, BIOLOGICAL; SYSTEMS BIOLOGY; THERMODYNAMICS;

EID: 79960325264     PISSN: 19395094     EISSN: 1939005X     Source Type: Journal    
DOI: 10.1002/wsbm.142     Document Type: Review

References (58)

1. Humphreys P. Extending Ourselves. Oxford: Oxford University Press; 2004.
2. Schwede T, Peitsch MC. Computational Structural Biology: Methods and Applications. Singapore: World Scientific; 2008.
3. Broglia RA, Serrano L, Tiana G. Protein Folding and Drug Design (International School of Physics Enrico Fermi). Bologna, Italy: IOS Press; 007.
4. Becker OM, Karplus M. Guide to Biomolecular Simulations (Focus on Structural Biology). Berlin: Springer; 2005.
5. Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nat Struct Biol 2002, 9:646-652.
6. Pastor RW, Venable RM, Feller SE. Lipid bilayers, NMR relaxation, and computer simulations. Acc Chem Res 2002, 35:438-446.
7. Harris SA. Modelling the biomechanical properties of DNA using computer simulation. Philos Transact A Math Phys Eng Sci 2006, 364:3319-3334.
8. Wong CF,McCammon AJ. Protein simulation and drug design. Adv Protein Chem 2003, 66:87-121.
9. Duan YH, Reddy BVB, Kaznessis YN. Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions. Prot Sci 2005, 12:316-328.
10. Bolintineanu D, Hazrati E, Davis HT, Lehrer RI, Kaznessis YN. Antimicrobial mechanism of pore-forming protegrin peptides: 100 pores to kill E. coli. Peptides 2010, 31:1-8.
11. Warshel A, Parson WW. Dynamics of biochemical and biophysical reactions: insight from computer simulations. Q Rev Biophys 2001, 34:563-679.
12. Adcock SA, McCammon JA. Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev 2006, 106:1589-1615.
13. Chipot C, Phorille A. Free Energy Calculations. Berlin: Springer; 2007.
14. Ricklin D, Hajishengallis G, Yang K, Lambris JD. Complement: a key system for immune surveillance and homeostasis. Nat Immunol 2010, 11:785-797.
15. Mastellos D, Andronis C, Persidis A, Lambris JD. Novel biological networks modulated by complement. Clin Immunol 2005, 115:225-235.
16. Stephanopoulos G, Aristidou AA, Nielsen J. Metabolic Engineering: Principles and Methodologies. New York: Academic Press; 1998.
17. Smolke C, ed. The Metabolic Pathway Engineering Handbook: Fundamentals. Boca Raton, Florida: CRC Press; 2009.
18. Gilbert SF. Developmental Biology. Sunderland, MA: Sinauer Associates; 2010.
19. Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000, 403:335-338.
20. Gardner TS, Cantor CR, Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature 2000, 403:339-342.
21. Kaern M, Blake WJ, Collins JJ. The engineering of gene regulatory networks. Annu Rev Biomed Eng 2003, 5:179-206.
22. Andrianantoandro E, Basu S, Karig DK, Weiss R. Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2:2006.0028.
23. Keasling J. The promise of synthetic biology. Bridge Natl Acad Eng 2005, 35:18-21.
24. Alon U. Biological networks: the tinkerer as an engineer. Science 2003, 301:1866-1867.
25. Serrano L. Synthetic biology: promises and challenges. Mol Syst Biol 2007, 3:158.
26. Drubin DA, Way JC, Silver PA. Designing biological systems. Genes Dev 2007, 21:242-254.
27. Ramalingam KI, Tomshine J, Maynard JA, Kaznessis YN. Forward engineering of synthetic bio-logical AND gates. Biochem Eng J 2009, 47:38-47.
28. Nurse P. Life, logic and information. Nature 2008, 454:424-426.
29. Weeding E, Houle J, Kaznessis YN. SynBioSS designer: aweb-based tool for the automated generation of kinetic models for synthetic biological constructs. Brief Bioinform 2010, 11:394-402.
30. Hill AD, Tomshine JR, Weeding EM, Sotiropoulos V, Kaznessis YN. SynBioSS: the synthetic biology modeling suite. Bioinformatics 2008, 24:2551-2553.
31. Jacob F, Monod J. Biochemical and geneticmechanisms of regulation in the bacterial cell. Bull Soc Chim Biol (Paris) 1964, 46:1499-1532.
32. Jacob F, Monod J. Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 1961, 3:318-356.
33. Tuttle L, Salis H, Tomshine J, Kaznessis YN. Modeldriven design principles of gene networks: the oscillator. Biophys J 2005, 89:3873-3883.
34. Tomshine J, Kaznessis YN. Optimization of a stochastically simulated gene network model via simulated annealing. Biophys J 2006, 91:3196-3205.
35. Salis H, Kaznessis YN. Computer-aided design of modular protein devices: Boolean AND gene activation. Phys Biol 2006, 3:295-310.
36. Sotiropoulos V, Kaznessis YN. Synthetic tetracyclineinducible regulatory networks: computer-aided design of dynamic phenotypes. BMC Syst Biol 2007, 1:7.
37. Salis H, Kaznessis YN. Stochastic simulations of gene regulatory modules. Comput Chem Eng 2005, 29:577-588.
38. Kaznessis Y. Multi-scale models for gene network engineering. Chem Eng Sci 2006, 61:940-953.
39. McQuarrie DA. Stochastic approach to chemical kinetics. J Appl Probab 1967, 4:413-447.
40. Oppenheim I, Shuler KE. Master equations and Markov processes. Phys Rev 1965, 138:1007-1011.
41. Van Kampen NG. Stochastic Processes in Physics and Chemistry. Revised and enlarged ed. Amsterdam: Elsevier; 2004.
42. Gardiner CW. Handbook of Stochastic Methods for Physics, Chemistry and Natural Sciences. 3rd ed. Berlin: Springer; 2004.
43. Gillespie DT. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J Comp Phys 1976, 22:403-434.
44. Gillespie DT. Exact stochastic simulation of coupled chemical reactions. J Phys Chem 1977, 81:2340-2361.
45. Haseltine EL, Rawlings JB. Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics. J Chem Phys 2002, 117:6959-6969.
46. Gibson MA, Bruck J. Efficient exact stochastic simulation of chemical systems with many species and many channels. J Phys Chem2000, 104:1876-1889.
47. Cao Y, Li H, Petzold L. Efficient formulation of the stochastic simulation algorithm for chemically reacting systems. J Chem Phys 2004, 121:4059-4067.
48. Chatterjee A, Mayawala K, Edwards JS, Vlachos DG. Time accelerated Monte Carlo simulations of biological networks using the binomial {tau}-leap method. Bioinformatics 2005, 21:2136-2137.
49. Salis H, Kaznessis YN. Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions. J Chem Phys 2005, 054103:122.
50. Salis H, Kaznessis YN. An equation-free probabilistic steady state approximation: dynamic application to the stochastic simulation of biochemical reaction networks. J Chem Phys 2005, 123:214106.
51. Sotiropoulos V, Kaznessis YN. An adaptive time step scheme for a system of SDEs with multiple multiplicative noise. Chemical Langevin equation, a proof of concept. J Chem Phys 2008, 128:014103.
52. Sotiropoulos V, Contou-Carrere M-N, Daoutidis P, Kaznessis YN. Model reduction of multiscale chemical Langevin equations: a numerical case study. IEEE/ACM Trans Comp Biol Bioinf 2009, 6:470.
53. Kaznessis Y. Models for synthetic biology. BMC Syst Biol 2007, 1:47.
54. Salis H, Sotiropoulos V, Kaznessis YN. Multiscale Hy3S: hybrid stochastic simulations for supercomputers. BMC Bioinform 2006, 7:93.
55. Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U. COPASI-a COmplex PAthway SImulator. Bioinformatics 2006, 22:3067-3074.
56. de Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol 2002, 9:67-103.
57. Goutsias J, Lee NH. Computational and experimental approaches for modeling gene regulatory networks. Curr Pharm Des 2007, 13:1415-1436.
58. Stelling J, Gilles ED. Mathematical modeling of complex regulatory networks. IEEE Trans Nanobiosci 2004, 3:172-179.