OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production

Computational tools have been widely adopted for strain optimisation in metabolic engineering, contributing to numerous success stories of producing industrially relevant biochemicals. However, most of these tools focus on single metabolic intervention strategies (either gene/reaction knockout or amplification alone) and rely on hypothetical optimality principles (e.g., maximisation of growth) and precise gene expression (e.g., fold changes) for phenotype prediction. This paper introduces OptDesign, a new two-step strain design strategy. In the first step, OptDesign selects regulation candidates that have a noticeable flux difference between the wild type and production strains. In the second step, it computes optimal design strategies with limited manipulations (combining regulation and knockout) leading to high biochemical production. The usefulness 1and capabilities of OptDesign are demonstrated for the production of three biochemicals in E. coli using the latest genome-scale metabolic model iML1515, showing highly consistent results with previous studies while suggesting new manipulations to boost strain performance. Source code is available at https://github.com/chang88ye/OptDesign.

Impact of Strong Wind and Optimal Estimation of Flux Difference Integral in a Lattice Hydrodynamic Model

A modified lattice hydrodynamic model is proposed, in which the impact of strong wind and the optimal estimation of flux difference integral are simultaneously analyzed. Based on the control theory, the stability condition is acquired through linear analysis. The modified Korteweg-de Vries (mKdV) equation is derived via nonlinear analysis, in order to express a description of the evolution of density waves. Then, numerical simulation is conducted. From the simulation results, strong wind can largely influence the traffic flow stability. The stronger the wind becomes, the more stable the traffic flow is, to some extent. Similarly, the optimal estimation of flux difference integral also contributes to stabilizing traffic flow. The simulation results show no difference compared with the theoretical findings. In conclusion, the new model is able to make the traffic flow more stable.

Validation of AERONET-Estimated Upward Broadband Solar Fluxes at the Top-Of-The-Atmosphere with CERES Measurements

The AERONET (Aerosol Robotic Network) global network provides estimations of broadband solar radiative fluxes at the surface and at the TOA (Top-Of-the-Atmosphere). This paper reports on the validation of AERONET flux estimations at the TOA with the CERES (Clouds and the Earth’s Radiant Energy System) instrument. The validation was made at eight AERONET sites worldwide with at least seven years of Level 2.0 and Version 3 data and representatives of mineral dust, biomass burning, background continental, and urban-industrial aerosol regimes. To co-locate in time and space the AERONET and CERES fluxes, several criteria based on time and distance differences and cloud coverage were defined. When the strictest criterion was applied to all sites, the linear relationship between the observed and estimated fluxes (y = 1.04x – 3.67 Wm−2) was very close to the 1:1 ideal line. The correlation coefficient was 0.96 and nearly all points were contained in the ±15% region around the 1:1 line. The average flux difference was –2.52 Wm−2 (–0.84% in relative terms). AERONET overestimations were observed at two sites and were correlated with large aerosol optical depth (AOD) (>0.2) Underestimations were observed at one desert site and were correlated with large surface albedos (>0.2).

The flux difference memory integral effect on two-lane stability in the lattice hydrodynamic model

In this paper, the flux difference memory integral (FDMI) effect is introduced into the lattice hydrodynamic model for a two-lane freeway. The FDMI effect plays an important role on the linear stability condition, from theoretic analysis, in a two-lane system. The FDMI effect including the intensity reaction coefficient and the integral historical time are investigated on two lanes via simulation. From numerical simulation, both lane changing rate and FDMI effect strengthening the stability of traffic flow on two lanes is determined.