TY - GEN
T1 - Multiscale models for synthetic biology
AU - Kaznessis, Yiannis N.
PY - 2009/1/1
Y1 - 2009/1/1
N2 - Reacting systems away from the thermodynamic limit cannot be accurately modeled with ordinary differential equations. These continuous-deterministic modeling formalisms, traditionally developed and used by chemical engineers can be distinctly false if the number of molecules of reacting chemical species is very small, or if reaction events are very rare. Then stochastic-discrete representations are appropriate. Importantly, in cases where in a network of reactions there are some parts that must be modeled discretely and stochastically, yet others can be modeled continuously and deterministically, the need for development of multiscale models emerges naturally. In computational synthetic biology, such cases arise often. In this work we present the development of multiscale models for synthetic biology applications, demonstrating accuracy, computational efficiency and utility.
AB - Reacting systems away from the thermodynamic limit cannot be accurately modeled with ordinary differential equations. These continuous-deterministic modeling formalisms, traditionally developed and used by chemical engineers can be distinctly false if the number of molecules of reacting chemical species is very small, or if reaction events are very rare. Then stochastic-discrete representations are appropriate. Importantly, in cases where in a network of reactions there are some parts that must be modeled discretely and stochastically, yet others can be modeled continuously and deterministically, the need for development of multiscale models emerges naturally. In computational synthetic biology, such cases arise often. In this work we present the development of multiscale models for synthetic biology applications, demonstrating accuracy, computational efficiency and utility.
KW - Chemical langevin equations
KW - Kinetic monte carlo
KW - Stochastic simulations
KW - Synthetic biology
UR - http://www.scopus.com/inward/record.url?scp=77951009400&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=77951009400&partnerID=8YFLogxK
U2 - 10.1109/IEMBS.2009.5333516
DO - 10.1109/IEMBS.2009.5333516
M3 - Conference contribution
AN - SCOPUS:77951009400
SN - 9781424432967
T3 - Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009
SP - 6408
EP - 6411
BT - Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society
PB - IEEE Computer Society
T2 - 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009
Y2 - 2 September 2009 through 6 September 2009
ER -