Model-based Simulation of a Hydraulic Closed-loop Rotary Transmission with Automatic Control

Model-based simulation of a hydraulic closed-loop rotary transmission with automatic control of hydraulic pump and hydraulic motor is considered in the paper. The approach is based on multi-pole modelling and intelligent simulation. In the paper the functional scheme of the transmission is proposed and multi-pole models of components are introduced. Mathematical multi-pole models of components for steady state conditions and for dynamic transient responses are presented. A high-level graphical environment CoCoVila (compiler compiler for visual languages) is used as a tool for describing models and performing simulations. Object-oriented multi-pole models, visual programming environment, automatic program synthesis and distributed computing are as original approach in simulation of fluid power systems.

Configuring a virtual prototype of a BiSCARA robot

The paper presents the configuring of a virtual prototype BiSCARA robot generated on the basis of a fully developed kinematic model of the robot. The virtual CAD model developed in this way will enable its implementation in the Python graphical environment as an integral part of the open architecture control system developed on the basis of the presented kinematic model. The developed kinematic model included solving the inverse and direct kinematic problem, determining the Jacobian matrix and workspace analysis. Verification of the kinematic model, i.e. the configured virtual prototype of the robot, was performed by simulations of the end-effector tip movement according to the given program in a CAD / CAM environment.

STR: A Mathematica package for the method of uniqueness

We present Star–Triangle Relations (STRs), a Mathematica® package designed to solve Feynman diagrams by means of the method of uniqueness in any Euclidean space-time dimension. The method of uniqueness is a powerful technique to solve multi-loop Feynman integrals in theories with conformal symmetry imposing some relations between the powers of propagators and the space-time dimension. In our algorithm, we include both identities for scalar and Yukawa type integrals. The package provides a graphical environment in which it is possible to draw the desired diagram with the mouse input and a set of tools to modify and compute it. Throughout the use of a graphic interface, the package should be easily accessible to users with little or no previous experience on diagrams computation. This manual includes some pedagogical examples of computation of Feynman graphs as the scalar two-loop kite master integral and a fermionic diagram appearing in the computation of the spectrum of the [Formula: see text]-deformed [Formula: see text] SYM in the double scaling limit.

Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation

This work seeks to remedy two deficiencies in the current nucleic acid nanotechnology software environment: the lack of both a fast and user-friendly visualization tool and a standard for structural analyses of simulated systems. We introduce here oxView, a web browser-based visualizer that can load structures with over 1 million nucleotides, create videos from simulation trajectories, and allow users to perform basic edits to DNA and RNA designs. We additionally introduce open-source software tools for extracting common structural parameters to characterize large DNA/RNA nanostructures simulated using the coarse-grained modeling tool, oxDNA, which has grown in popularity in recent years and is frequently used to prototype new nucleic acid nanostructural designs, model biophysics of DNA/RNA processes, and rationalize experimental results. The newly introduced software tools facilitate the computational characterization of DNA/RNA designs by providing multiple analysis scripts, including mean structures and structure flexibility characterization, hydrogen bond fraying, and interduplex angles. The output of these tools can be loaded into oxView, allowing users to interact with the simulated structure in a 3D graphical environment and modify the structures to achieve the required properties. We demonstrate these newly developed tools by applying them to design and analysis of a range of DNA/RNA nanostructures.

Design, optimization, and analysis of large DNA and RNA nanostructures through interactive visualization, editing, and molecular simulation

This work seeks to remedy two deficiencies in the current nucleic acid nanotechnology software environment: the lack of both a fast and user-friendly visualization tool and a standard for common structural analyses of simulated systems. We introduce here oxView, a web browser-based visualizer that can load structures with over 1 million nucleotides, create videos from simulation trajectories, and allow users to perform basic edits to DNA and RNA designs. We additionally introduce open-source software tools for extracting common structural parameters to characterize large DNA/RNA nanostructures simulated using the coarse-grained modeling tool, oxDNA, which has grown in popularity in recent years and is frequently used to prototype new nucleic acid nanostructural designs, model biophysics of DNA/RNA processes, and rationalize experimental results. The newly introduced software tools facilitate the computational characterization of DNA/RNA designs by providing multiple analysis scripts, including mean structures and structure flexibility characterization, hydrogen bond fraying, and interduplex angles. The output of these tools can be loaded into oxView, allowing users to interact with the simulated structure in a 3D graphical environment and modify the structures to achieve the required properties. We demonstrate these newly developed tools by applying them to in silico design, optimization and analysis of a range of DNA and RNA nanostructures.

SOFTWARE IMPLEMENTATION OF THE TASKS OF THE OPEN REGIONAL ROBOTICS CHALLENGE "FAIRYTALE TOURNAMENT"

The article presents some solutions to the tasks "Ilya Muromets" and "Goldfish" those were done by the participants of the open regional robotics challenge "Fairytale tournament". The tasks can be used while teaching robotics at school. Schoolchildren may have different levels of training. The design of the robot to solve the tasks done with LEGO MINDSTORMS NXT and LEGO MINDSTORMS EV3 is offered. The solutions are done in Lego MINDSTORMS Education EV3 graphical environment.

MLC parameters from static fields to VMAT plans: an evaluation in a RT-dedicated MC environment (PRIMO)

Background PRIMO is a graphical environment based on PENELOPE Monte Carlo (MC) simulation of radiotherapy beams able to compute dose distribution in patients, from plans with different techniques. The dosimetric characteristics of an HD-120 MLC (Varian), simulated using PRIMO, were here compared with measurements, and also with Acuros calculations (in the Eclipse treatment planning system, Varian). Materials and methods A 10 MV FFF beam from a Varian EDGE linac equipped with the HD-120 MLC was used for this work. Initially, the linac head was simulated inside PRIMO, and validated against measurements in a water phantom. Then, a series of different MLC patterns were established to assess the MLC dosimetric characteristics. Those tests included: i) static fields: output factors from MLC shaped fields (2 × 2 to 10 × 10 cm2), alternate open and closed leaf pattern, MLC transmitted dose; ii) dynamic fields: dosimetric leaf gap (DLG) evaluated with sweeping gaps, tongue and groove (TG) effect assessed with profiles across alternate open and closed leaves moving across the field. The doses in the different tests were simulated in PRIMO and then compared with EBT3 film measurements in solid water phantom, as well as with Acuros calculations. Finally, MC in PRIMO and Acuros were compared in some clinical cases, summarizing the clinical complexity in view of a possible use of PRIMO as an independent dose calculation check. Results Static output factor MLC tests showed an agreement between MC calculated and measured OF of 0.5%. The dynamic tests presented DLG values of 0.033 ± 0.003 cm and 0.032 ± 0.006 cm for MC and measurements, respectively. Regarding the TG tests, a general agreement between the dose distributions of 1–2% was achieved, except for the extreme patterns (very small gaps/field sizes and high TG effect) were the agreement was about 4–5%. The analysis of the clinical cases, the Gamma agreement between MC in PRIMO and Acuros dose calculation in Eclipse was of 99.5 ± 0.2% for 3%/2 mm criteria of dose difference/distance to agreement. Conclusions MC simulations in the PRIMO environment were in agreement with measurements for the HD-120 MLC in a 10 MV FFF beam from a Varian EDGE linac. This result allowed to consistently compare clinical cases, showing the possible use of PRIMO as an independent dose calculation check tool.

Numerical simulation of the stress-strain state of complex-reinforced elements

The article describes a developed technique of a numerical simulation of the stress-strain state of complex-reinforced elements, which allows you to create models of double-span continuous. The performed experimental and theoretical studies allowed us to carry out the testing of the developed design model and to justify the reliability of the proposed numerical simulation methodology. The results of the experimental studies were compared with those of the theoretical studies. The theoretical calculus algorithm was developed by using the finite element method. Theoretical calculations were performed by using the mathematical-graphical environment software system LIRA-SOFT and the mathematical and computer program MATLAB. On the basis of the experimental research, the iso-fields of displacements and stresses in the materials of an eccentrically compressed beam with a small bend of the slab were constructed, which collapse behind the inclined narrow strip of concrete and displacements and stresses in the materials of the eccentrically stretched beam, which is destroyed due to the yield of the upper mounting armature.

Python in proteomics

Python is a versatile scripting language that is widely used in industry and academia. In bioinformatics, there are multiple packages supporting data analysis with Python that range from biological sequence analysis with Biopython to structural modeling and visualization with packages like PyMOL and PyRosetta, to numerical computation and advanced plotting with NumPy/SciPy. In the proteomics community, Python began to be widely used around 2012 when several mature Python packages were published including pymzML, Pyteomics and pyOpenMS. This has led to an ever-increasing interest in the Python programming language in the proteomics and mass spectrometry community. The number of publications referencing or using Python has risen eight fold since 2012 (compared with the same time period before 2012), with multiple open-source Python packages now supporting mass spectrometric data analysis and processing. Computing and data analysis in mass spectrometry is very diverse and in many cases must be tailored to a specific experiment. Often, multiple analysis steps have to be performed (identification, quantification, post-translational modification analysis, filtering, FDR analysis etc.) in an analysis pipeline, which requires high flexibility in the analysis. This is where Python truly shines, due to its flexibility, visualization capabilities and the ability to extend computation with a large number of powerful libraries. Python can be used to quickly prototype software, combine existing libraries into powerful analysis workflows while avoiding the trap of re- inventing the wheel for a new project. Here, we will describe data analysis with Python using the pyOpenMS package. An extended documentation and tutorial can also be found online at https://pyopenms.readthedocs.io. To allow the reader to follow all steps in the tutorial, we will also describe the installation process of the software. Our installation is based on Anaconda, an open- source Python distribution that includes the Spyder integrated development environment (IDE) that allows development with pyOpenMS in a graphical environment.