Spatiotemporal modeling of microbial metabolism

Background Microbial systems in which the extracellular environment varies both spatially and temporally are very common in nature and in engineering applications. While the use of genome-scale metabolic reconstructions for steady-state flux balance analysis (FBA) and extensions for dynamic FBA are common, the development of spatiotemporal metabolic models has received little attention. Results We present a general methodology for spatiotemporal metabolic modeling based on combining genome-scale reconstructions with fundamental transport equations that govern the relevant convective and/or diffusional processes in time and spatially varying environments. Our solution procedure involves spatial discretization of the partial differential equation model followed by numerical integration of the resulting system of ordinary differential equations with embedded linear programs using DFBAlab, a MATLAB code that performs reliable and efficient dynamic FBA simulations. We demonstrate our methodology by solving spatiotemporal metabolic models for two systems of considerable practical interest: (1) a bubble column reactor with the syngas fermenting bacterium Clostridium ljungdahlii; and (2) a chronic wound biofilm with the human pathogen Pseudomonas aeruginosa. Despite the complexity of the discretized models which consist of 900 ODEs/600 LPs and 250 ODEs/250 LPs, respectively, we show that the proposed computational framework allows efficient and robust model solution. Conclusions Our study establishes a new paradigm for formulating and solving genome-scale metabolic models with both time and spatial variations and has wide applicability to natural and engineered microbial systems

Multifidelity Computing for Coupling Full and Reduced Order Models

Hybrid physics-machine learning models are increasingly being used in simulations of transport processes. Many complex multiphysics systems relevant to scientific and engineering applications include multiple spatiotemporal scales and comprise a multifidelity problem sharing an interface between various formulations or heterogeneous computational entities. To this end, we present a robust hybrid analysis and modeling approach combining a physics-based full order model (FOM) and a data-driven reduced order model (ROM) to form the building blocks of an integrated approach among mixed fidelity descriptions toward predictive digital twin technologies. At the interface, we introduce a long short-term memory network to bridge these high and low-fidelity models in various forms of interfacial error correction or prolongation. The proposed interface learning approaches are tested as a new way to address ROM-FOM coupling problems solving nonlinear advection-diffusion flow situations with a bifidelity setup that captures the essence of a broad class of transport processes

A stigmergy-based analysis of city hotspots to discover trends and anomalies in urban transportation usage

A key aspect of a sustainable urban transportation system is the effectiveness of transportation policies. To be effective, a policy has to consider a broad range of elements, such as pollution emission, traffic flow, and human mobility. Due to the complexity and variability of these elements in the urban area, to produce effective policies remains a very challenging task. With the introduction of the smart city paradigm, a widely available amount of data can be generated in the urban spaces. Such data can be a fundamental source of knowledge to improve policies because they can reflect the sustainability issues underlying the city. In this context, we propose an approach to exploit urban positioning data based on stigmergy, a bio-inspired mechanism providing scalar and temporal aggregation of samples. By employing stigmergy, samples in proximity with each other are aggregated into a functional structure called trail. The trail summarizes relevant dynamics in data and allows matching them, providing a measure of their similarity. Moreover, this mechanism can be specialized to unfold specific dynamics. Specifically, we identify high-density urban areas (i.e hotspots), analyze their activity over time, and unfold anomalies. Moreover, by matching activity patterns, a continuous measure of the dissimilarity with respect to the typical activity pattern is provided. This measure can be used by policy makers to evaluate the effect of policies and change them dynamically. As a case study, we analyze taxi trip data gathered in Manhattan from 2013 to 2015.Comment: Preprin

Empirical Formulation of Highway Traffic Flow Prediction Objective Function Based on Network Topology

Accurate Highway road predictions are necessary for timely decision making by the transport authorities. In this paper, we propose a traffic flow objective function for a highway road prediction model. The bi-directional flow function of individual roads is reported considering the net inflows and outflows by a topological breakdown of the highway network. Further, we optimise and compare the proposed objective function for constraints involved using stacked long short-term memory (LSTM) based recurrent neural network machine learning model considering different loss functions and training optimisation strategies. Finally, we report the best fitting machine learning model parameters for the proposed flow objective function for better prediction accuracy.Peer reviewe

A simple spatiotemporal evolution model of a transmission power grid

In this paper, we present a model for the spatial and temporal evolution of a particularly large human-made network: the 400-kV French transmission power grid. This is based on 1) an attachment procedure that diminishes the connection probability between two nodes as the network grows and 2) a coupled cost function characterizing the available budget at every time step. Two differentiated and consecutive processes can be distinguished: a first global space-filling process and a secondary local meshing process that increases connectivity at a local level. Results show that even without power system engineering design constraints (i.e., population and energy demand), the evolution of a transmission network can be remarkably explained by means of a simple attachment procedure. Given a distribution of resources and a time span, the model can also be used to generate the probability distribution of cable lengths at every time step, thus facilitating network planning. Implications for network's fragility are suggested as a starting point for new design perspectives in this kind of infrastructures.Peer ReviewedPostprint (author's final draft