Variable threshold algorithm for division of labor analyzed as a dynamical system

Division of labor is a widely studied aspect of colony behavior of social insects. Division of labor models indicate how individuals distribute themselves in order to perform different tasks simultaneously. However, models that study division of labor from a dynamical system point of view cannot be found in the literature. In this paper, we define a division of labor model as a discrete-time dynamical system, in order to study the equilibrium points and their properties related to convergence and stability. By making use of this analytical model, an adaptive algorithm based on division of labor can be designed to satisfy dynamic criteria. In this way, we have designed and tested an algorithm that varies the response thresholds in order to modify the dynamic behavior of the system. This behavior modification allows the system to adapt to specific environmental and collective situations, making the algorithm a good candidate for distributed control applications. The variable threshold algorithm is based on specialization mechanisms. It is able to achieve an asymptotically stable behavior of the system in different environments and independently of the number of individuals. The algorithm has been successfully tested under several initial conditions and number of individuals

Modeling the formation of R\&D alliances: An agent-based model with empirical validation

We develop an agent-based model to reproduce the size distribution of R\&D alliances of firms. Agents are uniformly selected to initiate an alliance and to invite collaboration partners. These decide about acceptance based on an individual threshold that is compared with the utility expected from joining the current alliance. The benefit of alliances results from the fitness of the agents involved. Fitness is obtained from an empirical distribution of agent's activities. The cost of an alliance reflects its coordination effort. Two free parameters $a_{c}$ and $a_{l}$ scale the costs and the individual threshold. If initiators receive $R$ rejections of invitations, the alliance formation stops and another initiator is selected. The three free parameters $(a_{c},a_{l},R)$ are calibrated against a large scale data set of about 15,000 firms engaging in about 15,000 R\&D alliances over 26 years. For the validation of the model we compare the empirical size distribution with the theoretical one, using confidence bands, to find a very good agreement. As an asset of our agent-based model, we provide an analytical solution that allows to reduce the simulation effort considerably. The analytical solution applies to general forms of the utility of alliances. Hence, the model can be extended to other cases of alliance formation. While no information about the initiators of an alliance is available, our results indicate that mostly firms with high fitness are able to attract newcomers and to establish larger alliances

A macroscopic analytical model of collaboration in distributed robotic systems

In this article, we present a macroscopic analytical model of collaboration in a group of reactive robots. The model consists of a series of coupled differential equations that describe the dynamics of group behavior. After presenting the general model, we analyze in detail a case study of collaboration, the stick-pulling experiment, studied experimentally and in simulation by Ijspeert et al. [Autonomous Robots, 11, 149-171]. The robots' task is to pull sticks out of their holes, and it can be successfully achieved only through the collaboration of two robots. There is no explicit communication or coordination between the robots. Unlike microscopic simulations (sensor-based or using a probabilistic numerical model), in which computational time scales with the robot group size, the macroscopic model is computationally efficient, because its solutions are independent of robot group size. Analysis reproduces several qualitative conclusions of Ijspeert et al.: namely, the different dynamical regimes for different values of the ratio of robots to sticks, the existence of optimal control parameters that maximize system performance as a function of group size, and the transition from superlinear to sublinear performance as the number of robots is increased

IFSIM Handbook

This handbook explains the simulation model IFSIM. IFSIM is an agent based simulation model written in JAVA. The model is constructed for analyzing demographic and economic issues. The aim of the model is to include the main consumption and production patterns over the life-cycle and thus being able to test demo-economic interactions.agent-based modelling; simulation model; JAVA; demogrphy; economy; demo-economic interactions

GPU Implementation of DPSO-RE Algorithm for Parameters Identification of Surface PMSM Considering VSI Nonlinearity

In this paper, an accurate parameter estimation model of surface permanent magnet synchronous machines (SPMSMs) is established by taking into account voltage-source-inverter (VSI) nonlinearity. A fast dynamic particle swarm optimization (DPSO) algorithm combined with a receptor editing (RE) strategy is proposed to explore the optimal values of parameter estimations. This combination provides an accelerated implementation on graphics processing unit (GPU), and the proposed method is, therefore, referred to as G-DPSORE. In G-DPSO-RE, a dynamic labor division strategy is incorporated into the swarms according to the designed evolutionary factor during the evolution process. Two novel modifications of the movement equation are designed to update the velocity of particles. Moreover, a chaotic-logistic-based immune RE operator is developed to facilitate the global best individual (gBest particle) to explore a potentially better region. Furthermore, a GPU parallel acceleration technique is utilized to speed up parameter estimation procedure. It has been demonstrated that the proposed method is effective for simultaneous estimation of the PMSM parameters and the disturbance voltage (Vdead) due to VSI nonlinearity from experimental data for currents and rotor speed measured with inexpensive equipment. The influence of the VSI nonlinearity on the accuracy of parameter estimation is analyzed

Development of novel orthogonal genetic circuits, based on extracytoplasmic function (ECF) σ factors

The synthetic biology field aims to apply the engineering 'design-build-test-learn' cycle for the implementation of synthetic genetic circuits modifying the behavior of biological systems. In order to reach this goal, synthetic biology projects use a set of fully characterized biological parts that subsequently are assembled into complex synthetic circuits following a rational, model-driven design. However, even though the bottom-up design approach represents an optimal starting point to assay the behavior of the synthetic circuits under defined conditions, the rational design of such circuits is often restricted by the limited number of available DNA building blocks. These usually consist only of a handful of transcriptional regulators that additionally are often borrowed from natural biological systems. This, in turn, can lead to cross-reactions between the synthetic circuit and the host cell and eventually to loss of the original circuit function. Thus, one of the challenges in synthetic biology is to design synthetic circuits that perform the designated functions with minor cross-reactions (orthogonality). To overcome the restrictions of the widely used transcriptional regulators, this project aims to apply extracytoplasmic function (ECF) σ factors in the design novel orthogonal synthetic circuits. ECFs are the smallest and simplest alternative σ factors that recognize highly specific promoters. ECFs represent one of the most important mechanisms of signal transduction in bacteria, indeed, their activity is often controlled by anti-σ factors. Even though it was shown that the overexpression of heterologous anti-σ factors can generate an adverse effect on cell growth, they represent an attractive solution to control ECF activity. Finally, to date, we know thousands of ECF σ factors, widespread among different bacterial phyla, that are identifiable together with the cognate promoters and anti-σ factors, using bioinformatic approaches. All the above-mentioned features make ECF σ factors optimal candidates as core orthogonal regulators for the design of novel synthetic circuits. In this project, in order to establish ECF σ factors as standard building blocks in the synthetic biology field, we first established a high throughput experimental setup. This relies on microplate reader experiments performed using a highly sensitive luminescent reporter system. Luminescent reporters have a superior signal-to-noise ratio when compared to fluorescent reporters since they do not suffer from the high auto-fluorescence background of the bacterial cell. However, they also have a drawback represented by the constant light emission that can generate undesired cross-talk between neighboring wells on a microplate. To overcome this limitation, we developed a computational algorithm that corrects for luminescence bleed-through and estimates the “true” luminescence activity for each well of a microplate. We show that the correcting algorithm preserves low-level signals close to the background and that it is universally applicable to different experimental conditions. In order to simplify the assembly of large ECF-based synthetic circuits, we designed an ECF toolbox in E. coli. The toolbox allows for the combinatorial assembly of circuits into expression vectors, using a library of reusable genetic parts. Moreover, it also offers the possibility of integrating the newly generated synthetic circuits into four different phage attachment (att) sites present in the genome of E. coli. This allows for a flawless transition between plasmid-encoded and chromosomally integrated genetic circuits, expanding the possible genetic configurations of a given synthetic construct. Moreover, our results demonstrate that the four att sites are orthogonal in terms of the gene expression levels of the synthetic circuits. With the purpose of rationally design ECF-based synthetic circuits and taking advantage of the ECF toolbox, we characterized the dynamic behavior of a set of 15 ECF σ factors, their cognate promoters, and relative anti-σs. Overall, we found that ECFs are non-toxic and functional and that they display different binding affinities for the cognate target promoters. Moreover, our results show that it is possible to optimize the output dynamic range of the ECF-based switches by changing the copy number of the ECFs and target promoters, thus, tuning the input/output signal ratio. Next, by combining up to three ECF-switches, we generated a set of “genetic-timer circuits”, the first synthetic circuits harboring more than one ECF. ECF-based timer circuits sequentially activate a series of target genes with increasing time delays, moreover, the behavior of the circuits can be predicted by a set of mathematical models. In order to improve the dynamic response of the ECF-based constructs, we introduced anti-σ factors in our synthetic circuits. By doing so we first confirmed that anti-σ factors can exert an adverse effect on the growth of E. coli, thus we explored possible solutions. Our results demonstrate that anti-σ factors toxicity can be partially alleviated by generating truncated, soluble variants of the anti-σ factors and, eventually, completely abolished via chromosomal integration of the anti-σ factor-based circuits. Finally, after demonstrating that anti-σ factors can be used to generate a tunable time delay among ECF expression and target promoter activation, we designed ECF/AS-suicide circuits. Such circuits allow for the time-delayed cell-death of E. coli and will serve as a prototype for the further development of ECF/AS-based lysis circuits