Derivative-Free Optimization of Rate Parameters of Capsid Assembly Models from Bulk in Vitro Data

A method for efficient Bayesian optimization of self-assembly systems from scattering data

BACKGROUND

The ability of collections of molecules to spontaneously assemble into large functional complexes is central to all cellular processes. Using the viral capsid as a model system for complicated macro-molecular assembly, we develop methods for probing fine details of the process by learning kinetic rate parameters consistent with experimental measures of assembly. We have previously shown that local rule based stochastic simulation methods in conjunction with bulk indirect experimental data can meaningfully constrain the space of possible assembly trajectories and allow inference of experimentally unobservable features of the real system.

RESULTS

In the present work, we introduce a new Bayesian optimization framework using multi-Gaussian process model regression. We also extend our prior work to encompass small-angle X-ray/neutron scattering (SAXS/SANS) as a possibly richer experimental data source than the previously used static light scattering (SLS). Method validation is based on synthetic experiments generated using protein data bank (PDB) structures of cowpea chlorotic mottle virus. We also apply the same approach to computationally cheaper differential equation based simulation models.

CONCLUSIONS

We present a flexible approach for the global optimization of computationally costly objective functions associated with dynamic, multidimensional models. When applied to the stochastic viral capsid system, our method outperforms a current state of the art black box solver tailored for use with noisy objectives. Our approach also has wide applicability to general stochastic optimization problems.