Evaluating simulated annealing algorithms in the optimization of bacterial strains

In this work, a Simulated Annealing (SA) algorithm is proposed for a Metabolic Engineering task: the optimization of the set of gene deletions to apply to a microbial strain to achieve a desired production goal. Each mutant strain is evaluated by simulating its phenotype using the Flux-Balance Analysis approach, under the premise that microorganisms have maximized their growth along natural evolution. A set based representation is used in the SA to encode variable sized solutions, enabling the automatic discovery of the ideal number of gene deletions. The approach was compared to the use of Evolutionary Algorithms (EAs) to solve the same task. Two case studies are presented considering the production of succinic and lactic acid as the target, with the bacterium E. coli. The variable sized SA seems to be the best alternative, outperforming the EAs, showing a fast convergence and low variability among the several runs and also enabing the automatic discovery of the ideal number of knockouts.FEDER.Portuguese Foundation for Science and Technology (FCT) - POSC/EIA/59899/2004

Interpreting the regulatory interplay in E. coli metabolic pathways

Many regulatory processes in the cell are based on the control of gene expression through the interaction of transcription factors. However, enzymatic regulation often overlays transcriptional regulation and even, in some metabolic pathways, enzymatic regulation prevails. The present study addresses the regulatory network of Escherichia coli and offers a global view of the regulation of its metabolic pathways. It identifies the regulatory mechanisms responsible for key metabolic activities and details the structures behind such mechanisms. This knowledge is considered of relevance to further studies on the bacteria’s system and its industrial application, namely for understanding the signal cascades comprised in the responses to various environmental stresses.FCT funded MIT-Portugal Program in Bioengineering (MIT-Pt/BSBB/ 0082/2008); PhD grants from FCT (ref. SFRH/BD/22863/2005 and SFRH/BD/41763/2007)

Evaluating evolutionary algorithms and differential evolution for the online optimization of fermentation processes

Although important contributions have been made in recent years within the field of bioprocess model development and validation, in many cases the utility of even relatively good models for process optimization with current state-of-the-art algorithms (mostly offline approaches) is quite low. The main cause for this is that open-loop fermentations do not compensate for the differences observed between model predictions and real variables, whose consequences can lead to quite undesirable consequences. In this work, the performance of two different algorithms belonging to the main groups of Evolutionary Algorithms (EA) and Differential Evolution (DE) is compared in the task of online optimisation of fed-batch fermentation processes. The proposed approach enables to obtain results close to the ones predicted initially by the mathematical models of the process, deals well with the noise in state variables and exhibits properties of graceful degradation. When comparing the optimization algorithms, the DE seems the best alternative, but its superiority seems to decrease when noisier settings are considered.Fundo Europeu de Desenvolvimento Regional (FEDER)Fundação para a Ciência e a Tecnologia (FCT

Exploring Replica-Exchange Wang-Landau sampling in higher-dimensional parameter space

We considered a higher-dimensional extension for the replica-exchange Wang-Landau algorithm to perform a random walk in the energy and magnetization space of the two-dimensional Ising model. This hybrid scheme combines the advantages of Wang-Landau and Replica-Exchange algorithms, and the one-dimensional version of this approach has been shown to be very efficient and to scale well, up to several thousands of computing cores. This approach allows us to split the parameter space of the system to be simulated into several pieces and still perform a random walk over the entire parameter range, ensuring the ergodicity of the simulation. Previous work, in which a similar scheme of parallel simulation was implemented without using replica exchange and with a different way to combine the result from the pieces, led to discontinuities in the final density of states over the entire range of parameters. From our simulations, it appears that the replica-exchange Wang-Landau algorithm is able to overcome this difficulty, allowing exploration of higher parameter phase space by keeping track of the joint density of states.Comment: Proceedings of CCP2014 will appear in Journal of Physics: Conference Series (JPCS), published by the IO

2D pattern evolution constrained by complex network dynamics

Complex networks have established themselves along the last years as being particularly suitable and flexible for representing and modeling several complex natural and human-made systems. At the same time in which the structural intricacies of such networks are being revealed and understood, efforts have also been directed at investigating how such connectivity properties define and constrain the dynamics of systems unfolding on such structures. However, lesser attention has been focused on hybrid systems, \textit{i.e.} involving more than one type of network and/or dynamics. Because several real systems present such an organization (\textit{e.g.} the dynamics of a disease coexisting with the dynamics of the immune system), it becomes important to address such hybrid systems. The current paper investigates a specific system involving a diffusive (linear and non-linear) dynamics taking place in a regular network while interacting with a complex network of defensive agents following Erd\"os-R\'enyi and Barab\'asi-Albert graph models, whose nodes can be displaced spatially. More specifically, the complex network is expected to control, and if possible to extinguish, the diffusion of some given unwanted process (\textit{e.g.} fire, oil spilling, pest dissemination, and virus or bacteria reproduction during an infection). Two types of pattern evolution are considered: Fick and Gray-Scott. The nodes of the defensive network then interact with the diffusing patterns and communicate between themselves in order to control the spreading. The main findings include the identification of higher efficiency for the Barab\'asi-Albert control networks.Comment: 18 pages, 32 figures. A working manuscript, comments are welcome

Information dynamics shape the networks of Internet-mediated prostitution

Like many other social phenomena, prostitution is increasingly coordinated over the Internet. The online behavior affects the offline activity; the reverse is also true. We investigated the reported sexual contacts between 6,624 anonymous escorts and 10,106 sex-buyers extracted from an online community from its beginning and six years on. These sexual encounters were also graded and categorized (in terms of the type of sexual activities performed) by the buyers. From the temporal, bipartite network of posts, we found a full feedback loop in which high grades on previous posts affect the future commercial success of the sex-worker, and vice versa. We also found a peculiar growth pattern in which the turnover of community members and sex workers causes a sublinear preferential attachment. There is, moreover, a strong geographic influence on network structure-the network is geographically clustered but still close to connected, the contacts consistent with the inverse-square law observed in trading patterns. We also found that the number of sellers scales sublinearly with city size, so this type of prostitution does not, comparatively speaking, benefit much from an increasing concentration of people

Data integration issues in the reconstruction of the genome-scale metabolic model of Zymomonas mobillis

Genome-scale model reconstruction represents a major tool in the field of Metabolic Engineering .This paper reports on a study about data integration issues in the process of genome- scale reconstruction of the metabolic model of the bacterium Zymomonas mobilis, a promising organism for bioethanol production. Data is retrieved from the Entrez Gene, KEGG, BioCyc and Brenda databases, and the several processes involved in data integration from these sources are described, as well as the data quality issues.Fundação para a Ciência e a Tecnologia (FCT) - POCI/BIO/60139/2004, PhD grant ref. SFRH/BD/41763/200

Poynting's theorem for planes waves at an interface: a scattering matrix approach

We apply the Poynting theorem to the scattering of monochromatic electromagnetic planes waves with normal incidence to the interface of two different media. We write this energy conservation theorem to introduce a natural definition of the scattering matrix S. For the dielectric-dielectric interface the balance equation lead us to the energy flux conservation which express one of the properties of S: it is a unitary matrix. For the dielectric-conductor interface the scattering matrix is no longer unitary due to the presence of losses at the conductor. However, the dissipative term appearing in the Poynting theorem can be interpreted as a single absorbing mode at the conductor such that a whole S, satisfying flux conservation and containing this absorbing mode, can be defined. This is a simplest version of a model introduced in the current literature to describe losses in more complex systems.Comment: 5 pages, 3 figures, submitted to Am. J. Phy