Conference-school in frame of MMCP2017

Lectures & Tutorials

Tutorial 1.

Mathematical modeling in radiation biophysics: DNA damage and repair

Dr. Oleg Belov
Laboratory of Radiation Biology, JINR
 

The tutorial covers the most popular methods currently used to simulate enzymatic processes associated with DNA damage and repair. The training will start with the overall brief information about DNA damage and repair. A couple of already existing models of DNA repair systems operating in bacterial and human cells will be reviewed and basic principles of modeling be shown. Simulation techniques based on usage of either systems of ordinary differential equations or stochastic approach (Gillespie algorithm) will be explained. Then, applicants will be trained in simulation of simple enzymatic processes of DNA repair using the Wolfram Mathematica software suite and some its biokinetics extensions.

 

Tutorial 2.

Simulation of radiation transport in biomolecules and cells with Geant4-DNA
Dr. Munkhbaatar Batmunkh, Dr. Oleg Belov
​Laboratory of Radiation Biology, JINR

 

The tutorial is focused on training the applicants in using some of biomedical examples of Geant4 to evaluate processes of radiation damage of biological molecules and cells. The training will provide brief information on basic principles of simulation of radiation transport with Geant4. Specific issues regarding modeling of radiation damage to biological matter will be discussed. A couple of newest Geant4 examples developed by authors and focused on simulation of radiation transport in neural cells will be explained in detail. Then, applicants will be encouraged to perform their own modeling of particle traversals to different biological objects with the examples provided.

 

Tutorial 3.

The particle physics data processing using of scientific software framework ROOT(PyROOT) 

Dr. Nazim Huseynov
​Laboratory of Nuclear Problems, JINR
 

ROOT is a software framework for data analysis, a powerful tool to cope with the demanding tasks Scientific data analysis. Among its features are an advanced graphical user interface, ideal for interactive analysis, An interpreter for the C++ programming language, for rapid and efficient prototyping and a persistence mechanism for C++ objects, used also to write every year petabytes of data recorded by the Large Hadron Collider experiments in CERN. This course of lectures illustrates are the main features of ROOT, relevant for the typical problems of data analysis: input and Plotting of data from measurements and fitting of analytical functions.

Tutorial 4.

Introduction to the Geant4 simulation toolkit 

Dr. A.S. Zhemchugov,
Dzhelepov Laboratory of Nuclear Problems, JINR
 

Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science. The lecture will give a brief introduction into the Geant4 functionality, followed by a hands-on session to demonstrate how to build and to run simple Geant4 examples.


Tutorial 5.

Simulation and reconstruction of MPD events in MpdRoot
Dr. K. Gertsenberger,
Veksler and Baldin Laboratory of High Energy Physics, JINR

 

Software for simulations, reconstruction and analysis of particle physics data is an essential part of each high-energy physics experiment. A new generation of the experiments for heavy-ion physics is expected to turn on in the nearest years at the Nuclotron based Ion Collider fAcility (NICA) in Dubna, Russia. The Baryonic Matter at the Nuclotron (BM@N) is a fixed target experiment, which was started in 2015 at the Nuclotron, and the MultiPurpose Detector (MPD) experiment, which will operate at the storage rings of the NICA facility. For both of the above experiments software frameworks are now under development: MpdRoot is intended for the MPD and BmnRoot for the BM@N. They are based on the FAIRroot package used by many experiments at GSI and CERN at the present moment. Simulation, reconstruction and physical analyses of simulated and experimental data will be shown. 

 

Lecture 1.

 

MpdRoot: framework for data processing of the MPD experiment at NICA

Dr. K. Gertsenberger,
Veksler and Baldin Laboratory of High Energy Physics, JINR

 

Lecture 2.

Parallel Programming Technologies for Applied Problems Solution 

Dr. D.V.Podgainy, Dr. O.I. Streltsova, M.I. Zuev
Laboratory of Information Technologies, JINR

Lecture 3.

Heavy Ion Collisions and Relativistic Hydrodynamics 

Prof. Kalinovsky Yu. L.
​Laboratory of Information Technologies, JINR
 

We consider  the basics of relativistic hydrodynamics and their application to modeling of physical processes in heavy ion collisions. We  also discuss  the basic methods and problem solving  algorithms  arising in the analysis of data obtained in experiments on heavy  ion impact.

Lecture 4.

Intel® architecture and technologies for High Performance Computing 

Dr. Mester N.
​Intel Corporation