A Machine Learning Approach to Predict Metabolic Pathway Dynamics from Time Series Multiomics Data

New synthetic biology capabilities hold the promise of dramatically improving our ability to engineer biological systems. However, a fundamental hurdle in realizing this potential is our inability to accurately predict biological behavior after modifying the corresponding genotype. Kinetic models have traditionally been used to predict pathway dynamics in bioengineered systems, but they take significant time to develop, and rely heavily on domain expertise. Here, we show that the combination of machine learning and abundant multiomics data (proteomics and metabolomics) can be used to effectively predict pathway dynamics in an automated fashion. The new method outperforms a classical kinetic model, and produces qualitative and quantitative predictions that can be used to productively guide bioengineering efforts. This method systematically leverages arbitrary amounts of new data to improve predictions, and does not assume any particular interactions, but rather implicitly chooses the most predictive ones

Semigroup analysis of structured parasite populations

Motivated by structured parasite populations in aquaculture we consider a class of size-structured population models, where individuals may be recruited into the population with distributed states at birth. The mathematical model which describes the evolution of such a population is a first-order nonlinear partial integro-differential equation of hyperbolic type. First, we use positive perturbation arguments and utilise results from the spectral theory of semigroups to establish conditions for the existence of a positive equilibrium solution of our model. Then, we formulate conditions that guarantee that the linearised system is governed by a positive quasicontraction semigroup on the biologically relevant state space. We also show that the governing linear semigroup is eventually compact, hence growth properties of the semigroup are determined by the spectrum of its generator. In the case of a separable fertility function, we deduce a characteristic equation, and investigate the stability of equilibrium solutions in the general case using positive perturbation arguments.Comment: to appear in Mathematical Modelling of Natural Phenomen

Smoke Studies of Secondary Flows in Bends, Tandem Cascades, and High-turning Configurations

Flow-visualization studies, using smoke, were made of the secondary flows in rectangular bends, tandem cascades, and high-turning configurations. The roll-up of the wall boundary layer of a rectangular bend forms a passage vortex near the suction surface similar to that previously observed for cascades. The vortex so formed then shifts out into the main stream. Because of leading-edge effects, the boundary-layer flows in bends were found to be sufficiently different from the flows in blade rows to make direct application of bend results to blade rows inadvisable. Passage vortices are shown, in the tandem-cascade study, to resist turning with the main stream through which they pass and to disturb the flow in subsequent blade rows. This disturbance may explain in part the appreciable size of the losses sometimes attributed to secondary flows in turbomachines despite the fact that the energy involvement in vortex formation is slight. Tip-flow studies of high-turning blades with relative motion between blades and end wall indicated that if the relative sizes of the passage vortex forces, the tip clearance forces, and the blade-scraping effects are properly controlled, it may be possible to improve the blade-tip loading characteristics in turbomachine

A Visualization Study of Secondary Flows in Cascades

Flow-visualization techniques are employed to ascertain the streamline patterns of the nonpotential secondary flows in the boundary layers of cascades, and thereby to provide a basis for more extended analyses in turbomachines. The three-dimensional deflection of the end-wall boundary layer results in the formation of a vortex within each cascade passage. The size and tightness of the vortex generated depend upon the main-flow turning in the cascade passage. Once formed, a vortex resists turning in subsequent blade rows, with consequent unfavorable angles of attack and possible flow disturbances on the pressure surfaces of subsequent blade rows when the vortices impinge on these surfaces. Two major tip-clearance effects are observed, the formation of a tip-clearance vortex and the scraping effect of a blade with relative motion past the wall boundary layer. The flow patterns indicate methods for improving the blade tip-loading characteristics of compressors and of low- and high-speed turbulence

Human Computer Interaction, Art and Experience

With contributions from artists, scientists, curators, entrepreneurs and designers engaged in the creative arts, this book is an invaluable resource for both researchers and practitioners, working in this emerging field

A biomechanical model of anther opening reveals the roles of dehydration and secondary thickening

Understanding the processes that underlie pollen release is a prime target for controlling fertility to enable selective breeding and the efficient production of hybrid crops. Pollen release requires anther opening, which involves changes in the biomechanical properties of the anther wall. In this research, we develop and use a mathematical model to understand how these biomechanical processes lead to anther opening