Ensuring the positive definiteness and avoiding ill conditioning of the Hessian update in the
stochastic Broyden-Fletcher-Goldfarb-Shanno (BFGS) method are significant in solving …

Mechanistic dynamic models have become an essential tool for understanding biomolecular
networks and other biological systems. Biochemical stochasticity can be extremely important …

Motivation Recent work has demonstrated the feasibility of using non-numerical, qualitative
data to parameterize mathematical models. However, uncertainty quantification (UQ) of such …

The cell cycle of Caulobacter crescentus involves the polar morphogenesis and an
asymmetric cell division driven by precise interactions and regulations of proteins, which …

QNSTOP consists of serial and parallel (OpenMP) Fortran 2003 codes for the quasi-Newton
stochastic optimization method of Castle and Trosset for stochastic search problems. A …

Progress in experimental techniques enables a more accurate quantification of genes,
mRNA, and proteins at the single cell level. Provided with limited time series data from …

Caulobacter crescentus goes through a classic dimorphic cell division cycle to adapt to the
stringent environment and reduce intraspecific competition. Caulobacter mother cell gives …

The yeast centrosome or Spindle Pole Body (SPB) is an organelle situated in the nuclear
membrane, where it nucleates spindle microtubules and acts as a signalling hub. The SPB …

Multisite phosphorylation plays an important role in regulating switch-like protein activity and
has been used widely in mathematical models. With the development of new experimental …

Numerous challenges arise in modeling and simulation as biochemical networks are
discovered with increasing complexities and unknown mechanisms. With the improvement …