Spring 2021 Program

This is the programme of the Sitola seminar in spring 2021. Presentations for the current semester are available here.

• 3.3.2021
  Mgr. Martin Friák, Ph.D.
  Applications of quantum computers in chemistry, physics and materials science
  Abstract: One of the most important applications of quantum computing is solving classically intractable problems in chemistry, physics, and materials science. As calculations on classical (super-)computers are currently reaching their limits, emerging quantum technologies may help answer unresolved questions related to high-temperature superconductivity, new batteries, transition metal catalysis, or biochemical reactions and drug design. Therefore, significant attention has been recently paid to quantum-computer calculations of the electronic structure of materials. While the corresponding progress has been impressive, numerous major challenges remain. Albeit promising, quantum computers are still in their infancy. Currently, there are only a few working prototypes worldwide with very limited performance. As quantum computers are fundamentally different from classical ones, many basic algorithms need to be developed.
  The talk will summarize the current status of quantum-computer calculations in chemistry, including increasing academic and industrial activities worldwide. Next, the prominent aspects of these calculations will be illustrated on calculations of selected small systems such as the H- ion or the H₂ molecule. For these, we have recently performed an extensive set of calculations on quantum processors and their classical simulators using the IBM Quantum Experience platform. Further, special attention will be paid to the impact that (i) different set-ups of quantum circuits, (ii) applied computational methods, and (iii) real (i.e., noisy) realizations of quantum processors have on the calculated results. The talk will close with an outlook on quantum computing in physics and materials science.
• 10.3.2021
  Search at Sitola: overview presentations about search methodologies in Sitola
  Hana Rudová: Problem-specific search

• 17.3.2021
  RNDr. Miloš Liška, Ph.D.
  Are videoconferences safe?
  Abstract: With the onset of COVID-19 pandemics, video communication has become a staple in our personal and business interactions. A trend is to provide videoconferencing platforms as simple and easy to use as possible without bothering users with a plethora of different settings and options. That being said, the question is if videoconferences, as we know and use them today, are secure and safe.
  In this talk, we first provide an overview of videoconferencing platforms and tools provided by CESNET and generic concepts of security and safety in terms of these tools. In the second part of the talk, we show examples of how not to set up and use videoconferences. The talk will be concluded with a walkthrough of best practices and options to make videoconferencing safe.
• 24.3.2021
  Search at Sitola: overview presentations about search methodologies in Sitola
  Jiří Filipovič: Using searching algorithms in projects of the HPC group
• 21.4.2021
  RNDr. Vladimír Míč, Ph.D., RNDr. Tomáš Raček
  Protein chain similarity search
  Abstract: Proteins are essential parts of every living organism. As their 3D structure largely influences their function, biologists are interested in finding similar protein subunits in different proteins, even from other species. In this talk, we will present our 1-month-old, still unpublished web application for efficient search in the world’s largest protein database for the first time. We will describe the standardized similarity measure for these protein subunits and then discuss the challenges of the similarity searching in this very recent complex data. We will also briefly sketch our approaches to address these challenges. Finally, we will conclude the talk with a comparison of our approach and the currently used one to illustrate that our search is about 20 times faster (including the visualizations) while decreasing the average searching accuracy to 94%.
• 28.4.2021
  Ing. Jana Hozzová, Ph.D.
  How we have made our data publicly available, slides in PDF
  Abstract: This year, our research group published a dataset via the Mendeley repository and Data in Brief article. It was the first time we made available such a comprehensive dataset with associated scripts, and we gathered a few pieces of information, tips, recommendations, and experiences worth sharing. In this talk, I will cover the whole process from deciding to publish data, choosing a way to do so, preparing and polishing them, documenting their details to actually making them publicly available.
• 5.5.2021
  Marek-Martin Matyska
  Data driven game design
  Abstract: The talk will provide an introduction to the various types of data sets that we collect and utilize while we develop our games, how do they differ, and what kind of challenges/advantages they bring to the table. We will also open up the moral issues of utilizing big data and how does it affect the entire application ecosystem.
• 12.5.2021
  prof. RNDr. Jiří Barnat, Ph.D.
  RoFI — Open-hardware platform of distributed metamorphic robots
  Abstract: In the talk, we will introduce metamorphic robots. In particular, we will talk about a modular metamorphic RoFI platform that is being developed at FI MU. Besides the general view on the platform, we will also present some concrete goals to achieve with the platform as well as problems to be solved. Due to the nature of the RoFIbots, the platform is a nice experimental environment for ad-hoc networking, reconfiguration plan scheduling, etc., which might be of interest to Sitola Laboratory members.
• 19.5.2021
  Discussion about the future Sitola
  
• 26.5.2021
  Bc. Aneta Moravčíková (30 minutes)
  Decentralized data distribution with financial incentives
  Abstract: This talk presents an extension of the BitTorrent protocol that enables collecting rewards for torrent seeding. After users download their desired data, the BitTorrent protocol does not offer any additional benefit for users to keep seeding individual torrents. We introduce a solution that includes incentives in the form of cryptocurrency micropayments carried over Bitcoin’s Lightning Network. Micropayments should motivate the users to keep the shared content available for long-term periods.

  Mgr. Michal Pajtinka (20 minutes)
  Algorithms for detection of geometrical arrangement of molecular fragments
  Abstract: Researchers often depend entirely on structural data of biomolecules from publicly available databases in processes such as drug design. To gain results of in silico calculations corresponding to reality, the correctness of the input data is crucial. In Protein Data Bank (PDB), the most popular database for structural data of biomacromolecules, entries are being automatically validated for maximum reliability. This validation includes information about missing atoms, atom bond length outliers, unexpected bond angles, wrong chirality, and similar issues. Nevertheless, the validation system is still under active development, and some problems are not being checked at all — among other things, shapes of some molecular fragments (rings, scaffolds). Previous research shows that some rings have their atoms geometrically arranged in an energetically unfavorable manner in up to 25% of their occurrences. However, how to handle this problem?

• 2.6.2021 (120 minutes)
  Second discussion about the future Sitola
  
• 16.6.2021
  State exam rehearsals (master)
  Jan Dvořák: Vizualization of AI algorithms for computer games
  Vedoucí: Hana Rudová
  Oponent: David Kuťák

  Aneta Moravčíková: Decentralized data distribution with financial incentives
  Vedoucí: Michal Zima
  Oponent: Lukáš Ručka

  David Kočnar: Swap
  Vedoucí: Eva Hladká
  Oponent: Barbora Bühnová

• 23.6.2021
  State exam rehearsals (bachelor)
  Josef Handl: Příprava balíku Scipion pro běh v kontejneru a cloudovém prostředí
  Vedoucí: Aleš Křenek
  Oponent: Miroslav Ruda

  Mikoláš Stuchlík: Idiomatické rozhraní jazyka Swift pro práci s knihovnou GTK+
  Vedoucí: Michal Zima
  Oponent: Lukáš Ručka

Contact: Hana Rudová