Parameter estimation and inference for stochastic reaction-diffusion systems: application to morphogenesis in D. melanogaster

Background: Reaction-diffusion systems are frequently used in systems biology to model developmental and signalling processes. In many applications, count numbers of the diffusing molecular species are very low, leading to the need to explicitly model the inherent variability using stochastic methods. Despite their importance and frequent use, parameter estimation for both deterministic and stochastic reaction-diffusion systems is still a challenging problem. Results: We present a Bayesian inference approach to solve both the parameter and state estimation problem for stochastic reaction-diffusion systems. This allows a determination of the full posterior distribution of the parameters (expected values and uncertainty). We benchmark the method by illustrating it on a simple synthetic experiment. We then test the method on real data about the diffusion of the morphogen Bicoid in Drosophila melanogaster. The results show how the precision with which parameters can be inferred varies dramatically, indicating that the ability to infer full posterior distributions on the parameters can have important experimental design consequences. Conclusions: The results obtained demonstrate the feasibility and potential advantages of applying a Bayesian approach to parameter estimation in stochastic reaction-diffusion systems. In particular, the ability to estimate credibility intervals associated with parameter estimates can be precious for experimental design. Further work, however, will be needed to ensure the method can scale up to larger problems

Constrained Nonlinear Model Predictive Control of an MMA Polymerization Process via Evolutionary Optimization

In this work, a nonlinear model predictive controller is developed for a batch polymerization process. The physical model of the process is parameterized along a desired trajectory resulting in a trajectory linearized piecewise model (a multiple linear model bank) and the parameters are identified for an experimental polymerization reactor. Then, a multiple model adaptive predictive controller is designed for thermal trajectory tracking of the MMA polymerization. The input control signal to the process is constrained by the maximum thermal power provided by the heaters. The constrained optimization in the model predictive controller is solved via genetic algorithms to minimize a DMC cost function in each sampling interval.Comment: 12 pages, 9 figures, 28 reference

Learning Dynamic Boltzmann Distributions as Reduced Models of Spatial Chemical Kinetics

Finding reduced models of spatially-distributed chemical reaction networks requires an estimation of which effective dynamics are relevant. We propose a machine learning approach to this coarse graining problem, where a maximum entropy approximation is constructed that evolves slowly in time. The dynamical model governing the approximation is expressed as a functional, allowing a general treatment of spatial interactions. In contrast to typical machine learning approaches which estimate the interaction parameters of a graphical model, we derive Boltzmann-machine like learning algorithms to estimate directly the functionals dictating the time evolution of these parameters. By incorporating analytic solutions from simple reaction motifs, an efficient simulation method is demonstrated for systems ranging from toy problems to basic biologically relevant networks. The broadly applicable nature of our approach to learning spatial dynamics suggests promising applications to multiscale methods for spatial networks, as well as to further problems in machine learning

A computationally efficacious free-energy functional for studies of inhomogeneous liquid water

We present an accurate equation of state for water based on a simple microscopic Hamiltonian, with only four parameters that are well-constrained by bulk experimental data. With one additional parameter for the range of interaction, this model yields a computationally efficient free-energy functional for inhomogeneous water which captures short-ranged correlations, cavitation energies and, with suitable long-range corrections, the non-linear dielectric response of water, making it an excellent candidate for studies of mesoscale water and for use in ab initio solvation methods.Comment: 6 pages, 5 figure