Scaling theory of transport in complex networks

Transport is an important function in many network systems and understanding its behavior on biological, social, and technological networks is crucial for a wide range of applications. However, it is a property that is not well-understood in these systems and this is probably due to the lack of a general theoretical framework. Here, based on the finding that renormalization can be applied to bio-networks, we develop a scaling theory of transport in self-similar networks. We demonstrate the networks invariance under length scale renormalization and we show that the problem of transport can be characterized in terms of a set of critical exponents. The scaling theory allows us to determine the influence of the modular structure on transport. We also generalize our theory by presenting and verifying scaling arguments for the dependence of transport on microscopic features, such as the degree of the nodes and the distance between them. Using transport concepts such as diffusion and resistance we exploit this invariance and we are able to explain, based on the topology of the network, recent experimental results on the broad flow distribution in metabolic networks.Comment: 8 pages, 6 figure

Multi-FedLS: a Framework for Cross-Silo Federated Learning Applications on Multi-Cloud Environments

Federated Learning (FL) is a distributed Machine Learning (ML) technique that can benefit from cloud environments while preserving data privacy. We propose Multi-FedLS, a framework that manages multi-cloud resources, reducing execution time and financial costs of Cross-Silo Federated Learning applications by using preemptible VMs, cheaper than on-demand ones but that can be revoked at any time. Our framework encloses four modules: Pre-Scheduling, Initial Mapping, Fault Tolerance, and Dynamic Scheduler. This paper extends our previous work \cite{brum2022sbac} by formally describing the Multi-FedLS resource manager framework and its modules. Experiments were conducted with three Cross-Silo FL applications on CloudLab and a proof-of-concept confirms that Multi-FedLS can be executed on a multi-cloud composed by AWS and GCP, two commercial cloud providers. Results show that the problem of executing Cross-Silo FL applications in multi-cloud environments with preemptible VMs can be efficiently resolved using a mathematical formulation, fault tolerance techniques, and a simple heuristic to choose a new VM in case of revocation.Comment: In review by Journal of Parallel and Distributed Computin

Colwellia psychrerythraea Strains from Distant Deep Sea Basins Show Adaptation to Local Conditions

Many studies have shown that microbes, which share nearly identical 16S rRNA genes, can have highly divergent genomes. Microbes from distinct parts of the ocean also exhibit biogeographic patterning. Here we seek to better understand how certain microbes from the same species have adapted for growth under local conditions. The phenotypic and genomic heterogeneity of three strains of Colwellia psychrerythraeawas investigated in order to understand adaptions to local environments. Colwellia are psychrophilic heterotrophic marine bacteria ubiquitous in cold marine ecosystems. We have recently isolated two Colwellia strains: ND2E from the Eastern Mediterranean and GAB14E from the Great Australian Bight. The 16S rRNA sequence of these two strains were greater than 98.2% identical to the well-characterized C. psychrerythraea 34H, which was isolated from arctic sediments. Salt tolerance, and carbon source utilization profiles for these strains were determined using Biolog Phenotype MicoArrays. These strains exhibited distinct salt tolerance, which was not associated with the salinity of sites of isolation. The carbon source utilization profiles were distinct with less than half of the tested carbon sources being metabolized by all three strains. Whole genome sequencing revealed that the genomes of these three strains were quite diverse with some genomes having up to 1600 strain-specific genes. Many genes involved in degrading strain-specific carbon sources were identified. There appears to be a link between carbon source utilization and location of isolation with distinctions observed between the Colwellia isolate recovered from sediment compared to water column isolates

Complex networks theory for analyzing metabolic networks

One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of the organism, while networks are appropriate abstract description of all kinds of interactions. In the past few years, great achievement has been made in developing theory of complex networks for revealing the organizing principles that govern the formation and evolution of various complex biological, technological and social networks. This paper reviews the accomplishments in constructing genome-based metabolic networks and describes how the theory of complex networks is applied to analyze metabolic networks.Comment: 13 pages, 2 figure

A distributed stream temperature model using high resolution temperature observations

International audienceDistributed temperature data are used as input and as calibration data for an energy based temperature model of a first order stream in Luxembourg. A DTS (Distributed Temperature Sensing) system with a fiber optic cable of 1500 m was used to measure stream water temperature with 1 m resolution each 2 min. Four groundwater inflows were identified and quantified (both temperature and relative discharge). The temperature model calculates the total energy balance including solar radiation (with shading effects), longwave radiation, latent heat, sensible heat and river bed conduction. The simulated temperature is compared with the observed temperature at all points along the stream. Knowledge of the lateral inflow appears to be crucial to simulate the temperature distribution and conversely, that stream temperature can be used successfully to identify sources of lateral inflow. The DTS fiber optic is an excellent tool to provide this knowledge

Vibrational dynamics of a two-dimensional microgranular crystal

We study the dynamics of an ordered hexagonal monolayer of polystyrene microspheres adhered to a glass substrate coated with a thin aluminum layer. A laser-induced transient grating technique is employed to generate and detect three types of acoustic modes across the entire Brillouin zone in the Γ−K direction: low-frequency contact-based modes of the granular monolayer, high-frequency modes originating from spheroidal vibrations of the microspheres, and surface Rayleigh waves. The dispersion relation of contact-based and spheroidal modes indicates that they are collective modes of the microgranular crystal controlled by particle-particle contacts. We observe a spheroidal resonance splitting caused by the symmetry breaking due to the substrate, as well as an avoided crossing between the Rayleigh and spheroidal modes. The measurements are found to be in agreement with our analytical model.United States. Department of Energy (Grant DE-FG02-00ER15087)National Science Foundation (U.S.) (Grant CHE-1111557

A Taxonomy of Causality-Based Biological Properties

We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a theoretical point of view, biochemical reactions are abstractly represented as causal implications and the produced metabolites as causal consequences of the implication representing the corresponding reaction. The fact that a reactant is produced is represented by means of the chain of reactions that have made it exist. Such representation abstracts away from quantities, stoichiometric and thermodynamic parameters and constitutes the basis for the characterization of our properties. Moreover, we propose an effective method for verifying our properties based on an abstract model of system dynamics. This consists of a new abstract semantics for the system seen as a concurrent network and expressed using the Chemical Ground Form calculus. We illustrate an application of this framework to a portion of a real metabolic pathway