A Framework for Stochastic Optimization of Parameters for Integrative Modeling of Macromolecular Assemblies

Integrative modeling of macromolecular assemblies requires stochastic sampling, for example, via MCMC (Markov Chain Monte Carlo), since exhaustively enumerating all structural degrees of freedom is infeasible. MCMC-based methods usually require tuning several parameters, such as the move sizes for coarse-grained beads and rigid bodies, for sampling to be efficient and accurate. Currently, these parameters are tuned manually. To automate this process, we developed a general heuristic for derivative-free, global, stochastic, parallel, multiobjective optimization, termed StOP (Stochastic Optimization of Parameters) and applied it to optimize sampling-related parameters for the Integrative Modeling Platform (IMP). Given an integrative modeling setup, list of parameters to optimize, their domains, metrics that they influence, and the target ranges of these metrics, StOP produces the optimal values of these parameters. StOP is adaptable to the available computing capacity and converges quickly, allowing for the simultaneous optimization of a large number of parameters. However, it is not efficient at high dimensions and not guaranteed to find optima in complex landscapes. We demonstrate its performance on several examples of random functions, as well as on two integrative modeling examples, showing that StOP enhances the efficiency of sampling the posterior distribution, resulting in more good-scoring models and better sampling precision.

Effect of process parameters of mashing on consumer properties and processability of polymalt extracts production process

The development of the technology of viscous polymalt extracts using bare-grained oats will provide the population with a functional food ingredient and products with specified consumer properties. Existing techniques for the production of extracts did not affect the study of temperature conditions and the duration of the process at the mashing stage, using bare-grained oats in its composition. Crops of Belarusian breeding were used as raw materials: barley (H. vulgare), bare-grained oats (A. sativa), wheat (Tr. aestivum) grain. Optimization of parameters in the production of polymalt wort based on barley, oat and wheat malt was carried out by regression analysis and weight coefficients. Dependencies of physico-chemical indices of oat-malt and polymalt worts on temperature and duration of mashing are established. These dependencies predict content of dry substances, maltose, amine nitrogen, protein and acidity in the process of production of worts. Optimal technological parameters were selected at the stage of barley-wheat-oat polymalt wort mashing, which made it possible to increase the dry substances by 12.5%, maltose – by 21.3%, protein – by 16.2% and filtration rate – by 25.0%. The maximum solid content 14.4%, maltose 11.4 g·(100·сm-3)-1, protein 1.22%, in polymalt wort achieved under the following modes: (3 ±1)°C for 30 minutes, (44±1)°C for 50 minutes, (53±1)°C for 60 minutes, (63±1)°C for 50 minutes, (72±1)°C for 20 minutes and (78±1)°C for 60 minutes.

Results of identification and optimization of the parameters of axial piston pump

In the development of applicative software for mathematical modelling, identification, and optimization of parameters of axial piston pumps, special attention is paid to the real need of the engineers' practice. We used the original graphical 2D and 3D software for the application in real-time with a simultaneous presentation and processing in 24 windows of high resolution. Here it is mentioned that during optimization and identification of axial piston pump's parameters, we automatically form and present several hundreds of the complex 2D diagrams, which enables to intervene at any point in the study of hydrodynamic processes by the change of input data, where the following flow of identification and optimization is changed.