TSSP ExSci 2024 projects

The main component of the summer program is an active participation in the selected Science research project offered by the staff members of the Nicolaus Copernicus University, please see the topics and their descriptions below. Interested students are welcome to contact possible advisors for more details concerning the foreseen projects and discuss the dates that the project could be undertaken.

Mathematics and computer sciences:

Robotics:

Physics:


Mathematics and computer sciences

Applications of Probability in Reliability Theory


The aim of the project is to apply probability methods in describing reliability properties of some technical devices. Firstly, we briefly recall some important properties of random variables and random vectors. In particular, we focus on order statistics which play a major role in statistical inference and reliability theory. Then we start with recalling relevant concepts and facts from the reliability theory of coherent systems, which provide useful mathematical models for sophisticated technical devices composed of simple elements. We will consider a well-known k-out-of-n system, which functions as long as at least k of its n components function. The special cases are the series (k=n) and the parallel systems (k=1). After introducing the basic ideas, we will concentrate on reliability properties of binary systems, where both the system and its components can be only in two possible states: perfect functioning or complete failure. This includes studying the properties of the random variable which represent the number of failed components in the system under various conditions. This quantity is very important in real life situations, since it gives an idea of how many spares should be available to replace all failed components and to rejuvenate the others. It can be useful in the system optimal design. If time permits, we will also consider more flexible multi-state modeling, when the system has a wide range of performance levels, from perfect functioning to the complete failure. At the end we present interesting open problems related to the topic of the project.

Supervisor: Agnieszka Goroncy (gemini[at]mat.umk.pl)
Co-supervisors:Krzysztof Jasiński (krzys[at]mat.umk.pl)
Time: 24 June – 21 July 2024 (+/- one-week shift possible)

^ ^ ^ ^ ^

Exploring Vulnerabilities in LLMs (like Copilot or ChatGPT) through Prompt Manipulation


This project focuses on assessing the susceptibility of code generation by Large Language Models (LLMs), such as ChatGPT and Copilot, to adversary attacks, with a specific concentration on manipulating prompts. The primary objectives involve replicating literature findings and conducting preliminary research to comprehend and mitigate security risks associated with intentionally manipulating LLM prompts to generate potentially harmful or undesirable software snippets.

Summer Project Objectives: Adversary attacks in this context involve experimenting with generating biased or misleading prompts to steer LLM-generated code in undesirable directions, emphasizing the potential impact on code quality and security. Mining Software Repositories (MSR) techniques will complement this exploration.

While programming skills are essential, prior experience in adversarial attacks or LLMs is not mandatory. Tutorials at the project's commencement will equip participants with the necessary knowledge to actively contribute to exploring security challenges in code generation by LLMs, with a specific emphasis on prompt manipulation.

Supervisor: Piotr Przymus (eror[at]mat.umk.pl , piotr.przymus[at]gmail.com)
Time: 1 - 31 July 2024 (+/- one-week shift possible)

^ ^ ^ ^ ^

Robotics

Controlling robot arm and gripper using hand movements and gestures


The project concerns developing and implementing a human-robot interface. The interface should be implemented on a computer. The task of the interface is to determine position, orientation and hand gestures in 3D space using 2D cameras. Based on this data, the interface should send commands to the robot controller so that the gripper attached to the robot tracks the movements of the system operator's hands and fingers. The constructed system is intended to be used to move objects.

Supervisor: Sławomir Mandra (manslaw[at]fizyka.umk.pl)
Time: 1 - 31 July 2024 (+/- one-week shift possible)

^ ^ ^ ^ ^

Physics

Source of ultracold atoms for optical clocks and quantum computers


Ultracold atom based optical clocks and quantum computers are in forefront of quantum innovation. For instance, optical clocks with neutral cold atoms allow for absolute precision on the order of 10-18, unmatched by any other device. However, ultracold atomic experiments are composed of complex setups which require team work and broad knowledge for operation. Laboratory work includes broad range of design, simulations, theoretical and experimental work with ultracold qubits, active and passive optical clocks, construction of an ultra- stable laser, methods for cooling of atoms, searching of dark matter and other topological defects and studies of fundamental physics with atom-light interaction. Currently the largest limitation is continuous operation of ultracold atom machines that would significantly improve its performance. The main activity of the internship is related to investigation of methods for continuous source of ultracold atoms that are spatially transferred and cooled inside a hollow-core fibre and frequency modulated dipole trap light. Development of a compact source of laser-cooled atoms can be used not only for optical clocks and quantum computers but other atomic sensors as well. All projects are conducted with a cooperation with the leading quantum metrology groups like NIST (USA), LNE-SYRTE (France), University of Amsterdam (the Netherlands) or University of Bonn (Germany) and industry Menlo (Germany) or AQT (Austria). The specific tasks will be adopted to student's interests and skills.

Supervisor: Sławomir Bilicki (slawko[at]fizyka.umk.pl)
Time: 1 - 31 July 2024 (+/- one-week shift possible)

^ ^ ^ ^ ^

Active superradiant optical atomic clock for investigation QED and fundamental physics


Performance of all state-of-the-art optical atomic clocks is limited by an optical frequency oscillator, namely a clock laser used to probe the ultra-narrow optical atomic transition. The clock laser is necessary as optical clocks are passive devices (Rev. Mod. Phys. 87, 637 (2015)), where the extremely narrow atomic transition – the clock transition – needs to be interrogated with external laser field. The proposed research program is connected with construction of a novel superrdiant continuos optical clock. The main two goals of proposed internship are to gain experience in research team work and learn about optical atomic clock operation and construction. The involved student will mostly work on construction of a new type of clock –an active optical clock. The internship can be focused either on:
Supervisor: Marcin Bober (bober[at]fizyka.umk.pl)
Time: 1 - 31 July 2024 (+/- one-week shift possible)

^ ^ ^ ^ ^

The influence of photooxidation on exciton delocalization and the resonance Raman spectra of organic co-polymers


The power conversion efficiencies of organic photovoltaics (OPVs) have steadily increased over the last decade, reaching efficiencies on par with comercial solar technologies. The biggest drawback of OPVs remains their poor operational stability [1], in large part as a result of photochemical reactions with oxygen or water molecules trapped during fabrication, or which diffuse through imperfect plastic encapsulation. In this project, we will determine the spectroscopic fingerprints of photo-induced oxygen degradation for the PM6 and D18 organic co-polymers used in the OPV active layer [2]. We will consider monomers, built by combining molecular building blocks with donor (D) and acceptor (A) character into the D-A monomer unit, as well as dimers. For these molecules, we will investigate exciton delcalization using time dependent density functional theory, as well as calculate the resonance Raman (RR) spectra of pristine molecules and possible photooxidation products. RR is of particular interest for D- A co-polymers because it correlates with the (de)localization of excitons [3], which crucial for OPV functioning. By comparing oxidation products to pristine oligomers, we will be able to determine the influence of photooxidation on exciton delocalization, as well as its fingerprints in resonance Raman spectroscopy.

References:

[1] J. Luke, et al., Nat. Rev. Mater. 8, 839–852 (2023),
https://doi.org/10.1038/s41578-023-00606-5
[2] Wang, et al., Joule 7, 810–829 (2023),
https://doi.org/10.1016/j.joule.2023.03.002
[3] W. A. Saidi, P. Norman, Carbon 67, 17–26 (2014),
https://doi.org/10.1016/j.carbon.2013.09.045

Supervisor: Iulia Emilia Brumboiu (iubr[at]umk.pl)
Time: 1 - 31 July 2024 (+/- one-week shift possible)

^ ^ ^ ^ ^

New light-controlled materials for soft robotics


Soft robotics focuses on mimicking living organisms in applications of man-made devices in which the rigid parts can be replaced by susceptible soft materials. Among many possible materials that can be used in this, the light-responsive polymers are particularly interesting. Access to control of such materials is through photoactivation that is remote and non-destructive. Light acts as stimulus for photosensitive polymers that undergo macroscopic deformation in response to it. It is well known, that azobenzene polymers possess that behavior due to their cis-trans isomerization that happens under light stimuli. The goal of this project is to investigate new azo-compounds modified with substituents of different nature to better understand the mechanisms of photoactivation and their use in soft robotics. Within the project, the photophysical and photomechanical properties of new azo-compounds will be studied. The proposed project includes four research tasks:
  1. linear optics measurement (absorption spectra);
  2. validation of proper response of material to light stimulus (photoizomerization measurements);
  3. building the set-up to control the modification of material behavior with light;
  4. study of the change in the shape of material under the influence of light.
The result of this project will be to obtain a group of materials showing visible photomechanical changes. A publication in a high-level journal on the obtained results is expected.

Supervisor: Beata Derkowska (beata[at]fizyka.umk.pl)
Time: 1 - 31 July 2024 (+/- one-week shift possible)

^ ^ ^ ^ ^

Interplay of periodic lattice distortions and spin density waves in bulk Cr


Understanding the nature of magnetism has always been a great challenge in the field of condensed matter physics. In the transition metal series, Cr stands out for exhibiting an itinerant antiferromagnetic character which leads to the formation of spin-density waves (SDWs) at low temperatures [1]. Electronic structure calculations based on density functional theory (DFT) are usually very useful to understand the microscopic mechanisms behind the magnetic coupling, but, in the case of Cr, they fail to reproduce the SDW ground state, favoring instead a simple anti-ferromagnetic configuration [2]. A few possible reasons have been suggested to explain this discrepancy between theory and experiment, as e.g., the shortcomings of semi-local DFT functionals or an inappropriate treatment of the lattice degrees of freedom. The primary objective of this project is to explore the influence of periodic lattice distortions (PLDs, also known as strain waves) on the stability of SDWs in bulk Cr. To this aim, structural optimization of large supercells of bcc Cr will be performed, exploring different combinations of initial atomic positions and their correspondence to SDWs. The calculations will be performed with the Vienna ab-initio simulation package (VASP) [3], which offers a smooth learning path for a student. Overall, the analysis of the changes induced by PLDs on total energies and spectral properties will provide extensive information on the SDW formation, favoring potential applications in magneto-optical devices and spintronics.

[1] Reviews of Modern Physics 60, 209 (1988)
[2] Physical Review B 65,184432 (2002)
[3] Computational Material Science 6, 15 (1996)

Supervisor: Igor Di Marco (igor.dimarco[at]umk.pl)
Co-supervisor: Shivalika Sharma (shivalika.sharma[at]umk.pl)
Time: 1 - 31 July 2024 (+/- one-week shift possible)

^ ^ ^ ^ ^

The luminance for two-photon visual perception


This internship aims to explore two-photon vision: visual perception of pulsed infrared laser beams due to two- photon absorption and consecutive isomerization of visual pigments. The planned tasks involve the measurement of the brightness of two-photon stimuli of several different wavelengths (from the range 850-1300 nm) by comparing them to the visible stimuli of similar color, of known luminance. The existing optical system for two-photon vision with adopted psychophysical procedures will be used. The gathered data will be essential for calibrating adaptive optics two-photon visual simulators and future projects involving two-photon-based augmented reality displays.

Supervisor: Katarzyna Komar (kkomar[at]fizyka.umk.pl)
Time: 1 - 31 July 2024 (+/- one-week shift possible)

^ ^ ^ ^ ^

Advanced linear and nonlinear cavity-enhanced frequency comb spectroscopy


Laboratory of Ultrafast and Ultrasensitive Spectroscopy develops new linear and nonlinear spectroscopy techniques. One of our current projects is the development of cavity-enhanced two-dimensional infrared spectroscopy of gas-phase samples (CE-2DIR). Time-resolved nonlinear spectroscopy techniques, such as 2DIR spectroscopy, are routinely used to study ultrafast dynamics. Owing to the limited sensitivity of these techniques, they are most commonly applied to optically thick samples, such as solid and liquid solutions, to acquire low resolution spectra. Compared to gas-phase measurements, a solvent environment strongly influences the studied dynamics, making accurate theoretical predictions difficult. The aim of this project is to develop a new experimental technique which increases sensitivity as well as resolution, enabling application of 2DIR spectroscopy to weakly absorbing systems.

As pioneers of instrumental-line-shape-free frequency comb spectroscopy, we continuously apply the technique to new molecular systems. Our current projects include: measuring intensities of CO ν1 and ν3 modes transitions with accuracy better than 1% to demonstrate the remote accurate temperature measurements (this project is supported by HORIZON EUROPE EMPIR grant); studying photolysis-induced chemical reaction kinetics; developing new methods of calibrating astronomical spectrographs with optical frequency combs.

Depending on the progress in implementing the projects and student’s interests, specific research tasks may include:
Supervisor: Piotr Masłowski (pima[at]fizyka.umk.pl)
Co-supervisor: Grzegorz Kowzan (gkowzan[at]umk.pl)
Time: 15 July - 11 August 2024 (+/- one-week shift possible)

^ ^ ^ ^ ^

Dimensionality reduction for exploring conformational landscapes and motions from experiments and molecular dynamics using Python


The project's primary goal is to extend the capabilities of the ProDy API by integrating tools for efficient dimensionality reduction. ProDy, a versatile and widely-used open-source Python package (>2.3 downloads) for protein structural dynamics analysis, provides a rich set of functionalities for molecular dynamics (MD) trajectories and experimental data (e.g., cryoEM, NMR). The proposed enhancements will introduce the integration of dimensionality reduction techniques, such as KernelPCA, ICA, and tICA, into the ProDy framework. By incorporating these capabilities, the scientific community gains access to a powerful toolkit facilitating in-depth exploration of conformational landscapes and motions in protein structures. This integrated solution is poised to benefit computational biology, biophysics, and pharmacy by enabling a comprehensive analysis of MD simulations and experimental data. The following tasks will be performed within the framework of the project:
  1. Familiarization with the ProDy package to enhance the understanding of the development environment. The knowledge will be utilized to develop the code effectively.
  2. Implementation of dimensionality reduction methods within the ProDy environment, including KernelPCA, ICA, tICA, and more.
  3. Tests of the developed code on various systems (MD trajectories, PDB ensembles) to validate its efficacy.
  4. Gain proficiency in using GitHub to share the code with ProDy developers.
Supervisor: Karolina Mikulska-Rumińska (karolamik[at]fizyka.umk.pl)
Time: 1 - 31 July 2024 (+/- one-week shift possible)

^ ^ ^ ^ ^

Thermoelectric properties of ZnO: Sb


The goal of the project is to determine the figure of merit of ZnO: Sb in the direction parallel to the surface, including the measurement of thermal conductivity, electrical conductivity and Seebeck coefficient. To achieve this goal, it is necessary to:
  1. measure thermal conductivity using thermo-reflection,
  2. measure electrical conductivity using 4 probe methods,
  3. measure Seebeck coefficient.
Supervisor: Michał Pawlak (mpawlak[at]umk.pl)
Time: 1 - 31 July 2024 (+/- one-week shift possible)

^ ^ ^ ^ ^

Exploring the Unseen: Computer Analysis of the Vitreous Body data to Enhance Throughput


This project focuses on image analysis using Optical Coherence Tomography (OCT), specifically targeting the vitreous body, the largest yet elusive tissue of the eye. Despite the detailed images provided by OCT, imaging the vitreous structure poses challenges due to its low scattering nature, dynamic changes, and its relatively large size for traditional OCT scans. To address these limitations, our proposed solution involves developing a Python-based software program. This program will automatically align and stitch together multiple OCT scans captured at various angles and depths, forming a comprehensive panoramic view spanning from the retina to the crystalline lens. The software's workflow begins with preprocessing individual OCT scans to correct distortions or artifacts. Utilizing image processing techniques, including feature detection and registration, the program aligns and stitches the scans together. The stitched OCT images will then be compared with data obtained through Ultrasonography (USG). While USG provides a broader view using high-frequency sound waves, its resolution is lower compared to OCT. This project aims to overlay the high-resolution OCT scans onto the coarse USG images, offering a unique synthesis that combines the 'big picture' from USG with the superior resolution and detailed insights of OCT. This synthesized tool will provide more comprehensive understanding of the vitreous body's structure, providing ophthalmologists with valuable insights into its morphology.

Supervisor: Daniel Rumiński (drdr[at]fizyka.umk.pl)
Time: 24 June - 24 July 2024 (+/- one-week shift possible)

^ ^ ^ ^ ^

Quasi -2D and 2D chemistry


Quantum confinement substantially alters the electronic structure of quantum systems (e.g., atoms, molecules, and solids) as compared to their corresponding free-state counterparts. This is exhibited in the changes in electronic energy levels, electronic shell filling, and orbitals, which, in consequence, affect their physical as well as chemical properties such as energetics, reactivity, response properties, etc. Therefore, the chemistry of confinement systems may drastically change. Within this project, the student will be involved in the development of numerical code that is able to perform quantum chemistry calculations within these two confinement regimes.

Potential candidates should be well-motivated to pursue scientific work. Good mathematical skills and basic knowledge of quantum chemistry and the Linux operating system will be more than welcome.

+ preparation of computational setup
+ analysis of the results

Supervisor: Szymon Śmiga (szsmiga[at]fizyka.umk.pl)
Time: 1 - 31 July 2024 (+/- one-week shift possible)

^ ^ ^ ^ ^

Bridging the knowledge gap: computational insights into sulfonylurea inhibition across KATP channel diversity


ATP-activated potassium channels (KATP) are complex protein structures found throughout our bodies. The three crucial KATP channel isoforms – pancreatic, cardiac, and vascular - differ in the components from which they are constructed. Nevertheless, all of them can be inhibited by sulfonylurea drugs, widely used in diabetes treatment. Despite their considerable similarity, individual KATP isoforms differ in their sensitivity to the sulfonylurea’s inhibition. We still need to figure out why and we will do this with the help of numerical modelling.

The project's goal is to directly compare all three major channel isoforms-pancreatic, cardiac and vascular- upon sulfonylurea inhibition. A participant in the summer research program will learn to build models of molecular systems based on existing structures and homology models. We will use bioinformatics tools to compare sequences and identify essential motifs and ligands binding sites. Then, we will use classical and enhanced molecular dynamics methods to determine hot spots in the ligand binding in the systems and understand their structural differences.

No prior knowledge in molecular dynamics is required; however, programming skills in Python will be very helpful for participants to fully engage with the computational aspects of the project.

Supervisor: Katarzyna Walczewska-Szewc (kszewc[at]fizyka.umk.pl)
Time: 1 - 31 July 2024 (+/- one-week shift possible)

^ ^ ^ ^ ^