A software system for modeling evolution in a population of organisms with vision, interacting with each other in 3D simulator

Development of computer models imitating the work of the nervous systems of living organisms, taking into account their morphology and electrophysiology, is one of the important and promising branches of computational neurobiology. It is often sought to model not only the nervous system, but also the body, muscles, sensory systems, and a virtual three-dimensional physical environment in which the behavior of an organism can be observed and which provides its sensory systems with adequate data streams that change in response to the movement of the organism. For a system of hundreds or thousands of neurons, one can still hope to determine the necessary parameters and get the functioning of the nervous system more or less similar to that of a living organism – as, for example, in a recent work on the modeling of the Xenopus tadpole. However, of greatest interest, both practical and fundamental, are organisms that have vision, a more complex nervous system, and, accordingly, significantly more advanced cognitive abilities. Determining the structure and parameters of the nervous systems of such organisms is an extremely difficult task. Moreover, at the cellular level they change over time, these including changes under the influence of the streams of sensory signals they perceive and the life experience gained, including the consequences of their own actions under certain circumstances. Knowing the structure of the nervous system and the number of nerve cells forming it, at least approximately, one can try to optimize the initial parameters of the model through artificial evolution, during which virtual organisms will interact and survive, each under the control of its own version of the nervous system. In addition, in principle, the rules by which the brain changes during the life of the organism can also evolve. This work is devoted to the development of a neuroevolutionary simulator capable of performing simultaneous functioning of virtual organisms that have a visual system and are able to interact with each other. The amount of computational resources required for the operation of models of the physical body of an organism, the nervous system and the virtual environment was estimated, and the performance of the simulator on a modern desktop computing system was determined depending on the number of simultaneously simulated organisms

OpenWorm: an open-science approach to modeling Caenorhabditis elegans.

OpenWorm is an international collaboration with the aim of understanding how the behavior of Caenorhabditis elegans (C. elegans) emerges from its underlying physiological processes. The project has developed a modular simulation engine to create computational models of the worm. The modularity of the engine makes it possible to easily modify the model, incorporate new experimental data and test hypotheses. The modeling framework incorporates both biophysical neuronal simulations and a novel fluid-dynamics-based soft-tissue simulation for physical environment-body interactions. The project's open-science approach is aimed at overcoming the difficulties of integrative modeling within a traditional academic environment. In this article the rationale is presented for creating the OpenWorm collaboration, the tools and resources developed thus far are outlined and the unique challenges associated with the project are discussed

OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans

The adoption of powerful software tools and computational methods from the software industry by the scientific research community has resulted in a renewed interest in integrative, large-scale biological simulations. These typically involve the development of computational platforms to combine diverse, process-specific models into a coherent whole. The OpenWorm Foundation is an independent research organization working towards an integrative simulation of the nematode Caenorhabditis elegans, with the aim of providing a powerful new tool to understand how the organism's behaviour arises from its fundamental biology. In this perspective, we give an overview of the history and philosophy of OpenWorm, descriptions of the constituent sub-projects and corresponding open-science management practices, and discuss current achievements of the project and future directions. This article is part of a discussion meeting issue ‘Connectome to behaviour: modelling C. elegans at cellular resolution’

Probing the structural evolution of ruthenium doped germanium clusters: Photoelectron spectroscopy and density functional theory calculations

We present a combined experimental and theoretical study of ruthenium doped germanium clusters, RuGen- (n = 3-12), and their corresponding neutral species. Photoelectron spectra of RuGen- clusters are measured at 266 nm. The vertical detachment energies (VDEs) and adiabatic detachment energies (ADEs) are obtained. Unbiased CALYPSO structure searches confirm the low-lying structures of anionic and neutral ruthenium doped germanium clusters in the size range of 3 8, the Ru atom in RuGen-/0 clusters is absorbed endohedrally in the Ge cage. The theoretically predicted vertical and adiabatic detachment energies are in good agreement with the experimental measurements. The excellent agreement between DFT calculations and experiment enables a comprehensive evaluation of the geometrical and electronic structures of ruthenium doped germanium clusters

Influencing engineering education through the competency-based approach

The article poses a problem of engineering education and training of today, which are facing difficulties while developing an efficient competency-based approach realization. The authors concentrate on an urgent task of developing the integration competence of future engineers which is treated as a metadisciplinary competence providing students with ability and readiness to synthesize subject-oriented professional and social competences into a holistic system. The structure of integration competence is analyzed and the following components are determined: a value and motivation component; a practical activity component; a cognitive component; a self-analysis and self-assessment component. Among distinguishing features of the integration competence the authors define its instrumental character, metadisciplinary and universal properties as well as its nonalgorithmic character. It is shown that professionally oriented training is a core factor of integration competence development. Depending on elements being integrated, the main forms of integration of competences are determined. The model of competence integration presented in the article can serve as the basis for developing methods and conditions for its systematic elaboration in university training. The results of this study can be useful for educators of different administrative levels, teaching-and-training schools which realize a competency-based approach in their teaching

Influencing engineering education through the competency-based approach

The article poses a problem of engineering education and training of today, which are facing difficulties while developing an efficient competency-based approach realization. The authors concentrate on an urgent task of developing the integration competence of future engineers which is treated as a metadisciplinary competence providing students with ability and readiness to synthesize subject-oriented professional and social competences into a holistic system. The structure of integration competence is analyzed and the following components are determined: a value and motivation component; a practical activity component; a cognitive component; a self-analysis and self-assessment component. Among distinguishing features of the integration competence the authors define its instrumental character, metadisciplinary and universal properties as well as its nonalgorithmic character. It is shown that professionally oriented training is a core factor of integration competence development. Depending on elements being integrated, the main forms of integration of competences are determined. The model of competence integration presented in the article can serve as the basis for developing methods and conditions for its systematic elaboration in university training. The results of this study can be useful for educators of different administrative levels, teaching-and-training schools which realize a competency-based approach in their teaching