TY - GEN
T1 - Multiscale models for synthetic biology
AU - Kaznessis, Yiannis N.
AU - Sotiropoulos, Vassilios
AU - Hill, Anthony
AU - Tomshine, Jonathan
AU - Volzing, Katherine
AU - Barrett, John S
AU - Weeding, Emma
PY - 2008
Y1 - 2008
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 multiscae 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 multiscae 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=62649141937&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=62649141937&partnerID=8YFLogxK
M3 - Conference contribution
AN - SCOPUS:62649141937
SN - 1601320558
SN - 9781601320551
T3 - Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008
SP - 835
EP - 837
BT - Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008
T2 - 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008
Y2 - 14 July 2008 through 17 July 2008
ER -