Research Labworks for MSc

Seeing is believing. This sentence is as true as it is tricky. Most cellular components and processes, crucial for the nuanced understanding of (human) life, are not observable by conventional light microscopy since Abbe’s Law describes their maximum resolution to roughly half the wavelength of the observed light. This law is literally set in stone in Jena. However, over the past 15 years several ways of cleverly circumventing this diffraction limit were developed and implemented, achieving three-dimensional resolutions down to the nanometer range, resulting in the ever-growing field of optical super-resolution microscopy, for which the 2014 Nobel Prize in Chemistry was awarded.

The aim of this projects is to introduce, understand and apply the principles of state of the art fluorescence microscopy techniques, used e.g. in a broad range of modern biomedical and cell-biological research. Students prepare their own, fluorescently labeled, biological samples and will image them on a variety of advanced microscopes with different (resolution) capabilities. The qualitative and quantitative comparison of acquired images will illustrate the advantages and limitations of the respective microscopy technique.

Goals and Context

• Principles and application of advanced fluorescence microscopy techniques
• Concept of diffraction-limited and super-resolution
• Preparation of fluorescently labeled, biological samples
• 3D & multi-colour imaging at the nanoscale

Methods

• Cell culture and wet lab
• Fluorescent labeling
• A selection of advanced fluorescence microscopy techniques from the IAOB toolbox:
  • Confocal Laser Scanning Microscopy
  • Array Scan Microscopy
  • Stimulated Emission Depletion (STED)
  • Structured Illumination Microscopy (SIM)
  • Single-Molecule Localization Microscopy (SMLM)
  • MINFLUX Nanoscopy
• Image analysis by Fiji/ImageJ

Prerequisites

• An open mind and motivation for independent thinking
• Students should be able to explain the general difference between confocal and widefield microscopy and have basic knowledge on the concepts of super-resolution microscopy (e.g. Abbe’s diffraction limit)
• You should know the basic principles of fluorescence

A good preparation for the course is the biophysics lecture from Prof. C. Eggeling

Person in charge: Christian Franke & Katharina Reglinski

Supervisors: Christian Franke & Katharina Reglinski         

Venue: Microscopy Labs of the IOAB in the ZAF and Abbeanum or at the IPHT (Beutenberg)

The topic is suitable for two groups with 1-2 students each.

In the realm of advanced scientific research, the exploration of precise measurement techniques and the development of stable optical systems have emerged as crucial endeavors. These fields have witnessed remarkable progress, enabling breakthroughs in various scientific disciplines and pushing the boundaries of our understanding. Precise measurement techniques, coupled with ultra-stable optical systems, have revolutionized fields such as quantum optics, spectroscopy, and fundamental physics research. These techniques allow us to probe the fundamental properties of matter and light with unprecedented accuracy and precision. Additionally, they enable the detection and measurement of elusive phenomena such as gravitational waves, opening up new avenues for exploring the mysteries of the universe. At the heart of these precise measurement techniques and stable optical systems lie advanced stabilization methods for optical cavities and lasers. Optical cavities, with their ability to enhance light-matter interactions, play a crucial role in achieving high-precision measurements. Stabilizing these cavities ensures their reliability and accuracy, enabling precise control over photon generation and manipulation. Our focus will extend beyond specific applications and delve into the general principles and techniques involved in stabilizing these optical systems. We will explore advanced stabilization methods such as the Side-of-Fringe (SOF) locking technique and the Pound-Drever-Hall (PDH) locking technique, which are widely applicable in diverse scientific settings.

 Teaching Goals and Content

• Understand the principles and importance of optical cavities in current technologies.
• Design and construction of an optical cavity.
• Calculations of the mode-matching optics of a cavity by using ABCD matrix.
• Explore the Side-of-Fringe (SOF) locking technique for cavity stabilization.
• Explore the Pound-Drever-Hall (PDH) locking technique for stabilizing optical cavities by using radiofrequency techniques.
• Compare and contrast the SOF and PDH locking techniques in terms of performance and applicability.
• Analyze the stability and reliability of the optical cavity using these locking techniques.

 Experimental Techniques and Equipment

• Optical alignment of optical cavities.
• Continuous wave pump lasers at suitable wavelengths.
• Photodetectors for monitoring the cavity's reflected and transmitted light.
• Electro-optic modulators for phase modulation in the PDH technique.
• Lock-in amplifiers for demodulation and proportional-integral (PID systems) for feedback control.
• Data acquisition systems for recording and analyzing the locking signals.

Contact:

Supervisor:    M.Sc. Nayana Jalimarad

Place:              Fraunhofer IOF institute

For this experiment two students are recommended.

Nanoimprint lithography (NIL) is a method for the fast formation of nanostructures by replication. A flexible mold is derived from an electron-beam patterned master substrate and is used to imprint the structure into a UV-curable resist. Consequently, nanostructures can be replicated several times using the same mold. Therefore, NIL offers great potential for producing optical components, such as waveguides, LEDs, and photovoltaics. However, manufacturing large-area patterns of nano-size structures remains challenging, as both structural fidelity and optical performance need to be maintained. 

In this project, students will manufacture optical nanostructures. Characterization will be done by Scanning Electron Microscopy and interferometry. We want to investigate the influence of different imprint materials and vary process parameters to link the quality of the nanostructures with material properties. In the end, the goal is to understand the underlying processes like capillary flow in nano-cavities and polymerization dynamics.  

Objectives

•  Fabrication of nanostructures and related lab skills
•  Material properties of UV-curable photo resist
•  Understanding the processes behind the fabrication, such as capillary flow 

Objectives 

Supervisor: Tom Kretzschmar & Robert Leitel 

Venue: Fraunhofer IOF (Beutenberg) 

Since the lab work is done in a clean room, this project is suitable for one student. Supervision 
is possible in German and English. 

Nowadays the generation of ultra-short laser pulses with a duration down to some femto seconds is state of the art. Such pulses find their application not only in the field of scientific research to investigate ultra-fast processes, to perform ultra-precise spectroscopy, or to generate extreme electrical and magnetic fields through ultra-high light intensities, but they are also applied in material processing, medicine, especially in ophthalmology. Nevertheless, the generation and metrology of ultra-short pulses require complex measurement techniques. The basics to understand the underlying effects of pulse generation, stretching and compression as well as their measurement will be taught here. Some of these effects are based on non-linear optics and frequency conversion, that requires phase matching to get reasonable efficiencies. Second harmonic generation and two-photon absorption are used for pulse characterization by auto-correlation here. The limitations of the auto-correlation for the reconstruction of the temporal behavior of the laser field will be investigated in more detail.   

Teaching goals and content 

• Working principle and properties of solid-state lasers (Ti:sapphire)
• Cavity stability and longitudinal cavity modes
• Dependence of output power on pump power
• Generation of femtosecond pulses by Kerr-lens mode-locking
• Compensation of group velocity dispersion in optical cavities
• Impact of spectral phase on pulse duration and temporal pulse shape
• Measurement of band-width and duration of laser pulses
• Application of Fourier-Transform to explain pulse stretching and compression
• Interferometric and intensity auto-correlation and their limitations for pulse characterization
• Measurement of group velocity dispersion (GVD) of several materials

Experimental techniques and equipment

• diode-pumped, frequency-doubled 5W Nd:YV0₄-laser as pump source
• homemade Ti:sapphire femtosecond laser with prism GVD compensation
• external prism pulse compressor
• optical spectrometer
• second harmonic generating auto-correlator
• photodiodes, powermeter and oscilloscope

Contact:

Supervisor:   Dr. Joachim Hein

Place:  F-Praktikum

For this experiment two students are recommended.

Flat photonics have emerged in the last few years as a disruptive technology for the manipulation of optical wavefronts. The big advantages of flat photonics are the compactness and the absence of aberration due to curved interfaces, an inherent limit in standard lenses. The concept is based upon the transverse structuring of the material, inducing a local phase delay independent from the thickness. By changing the phase across the beam cross-section, the optical propagation can be sculpted at will, going well beyond the functionality of standard lenses.

The goal here is to characterize photonic devices in glass obtained by structuring locally the material with intense pulsed beams. The large intensity of the writing beam makes the glass locally anisotropic. The control on the local anisotropy permits to control the phase delay (i.e., the optical path), allowing to write a phase hologram featuring a large degree of tunability.

The main aim of the work is to fully characterize the optical propagation after the device. To accomplish the goal, an automatized characterization set-up capable of measuring the beam profile at different distances is required. The work will include writing a Python code capable of moving a translation stage and integrate this library with the currently available software controlling an in-house made polarimeter. Once the setup is ready, the candidate will characterize beam deflectors, lenses and gratings based upon flat optics.

Teaching goals and content

•  Wavefront manipulation via holograms
•  Measurement automatization based on Python
•  Integration between different systems
•  Acquiring hands-on expertise in estimating the accuracy of a measurement
•  Learning how an imaging system works

Prerequisites

•  Fundamental optics, especially Gaussian beams and diffraction
•  Confidence with lab work
•  Basic knowledge of Python
•  Interest in photonics and modern optics

Supervisor:         Dr. Jisha Chandroth Pannian / Dr. Alessandro Alberucci

Place:                   Institute of Applied Physics (IAP, Beutenberg)

The topic is suitable for one or two students.  

Fiber Bragg gratings (FBG) play a key role in modern fiber optics. They consist of a modulated refractive index in the fiber core and act as narrow-bandwidth in-fiber reflectors. Their application spans from cavity mirrors or dispersion control in fiber lasers, signal filtering in quantum optics as well as astro photonics to integrated strain and temperature sensing.

Commonly, FBGs are realized so-called single mode fibers, where only the fundamental mode is guided within the fiber core, offering straight forward characterization. However, especially in the application of (high power) lasers, FBGs are also realized in the cladding of the fiber. However, the fiber cladding guides hundreds of modes, which cause interference and disturbance of the spectral measurement, hindering the full characterization of the FBG.

The main goal of this project is the realization of a measurement system for spectral characterization of multimode optical fibers. The fluctuations of the spectral signal are to be mitigated by mechanical perturbations. The spectral measurement is realized, integrating a motorized fiber bend modulator. Different configurations are compared, to optimize the measurement. Finally, FBG realized in the fiber cladding are measured.

Teaching goals and content

•  Basics of FBGs their inscription by femtosecond pulsed laser
•  Fiber handling and preparation
•  Setup of a spectral transmission measurement of a multimode fiber
•  Realization and control of the fiber bend modulator
•  Basic signal processing and analysis

Prerequisites

•  Basics in optics
•  Minimal experimental skills
•  Basic knowledge in programming, ideally in Python\Matlab\LabView
•  Interest in integrated fiber optics and their application 

Supervisor: M.Sc. Ria Krämer

Place:           Institute of Applied Physics (IAP, Beutenberg)

Transition metal dichalcogenides (TMDs) such as MoS₂, exhibits strong second harmonic generation (SHG) in their monolayer form due to breaking of their inversion symmetry [1]. On the other hand, their inversion symmetry is restored in even lumber of layers which cancels out the SHG originating from each odd and even number of layers. However, a polytype of the material-3R MoS₂, possess ABC stacking and exhibit stronger SHG as it adds up constructively with their number of layers [2].

A Different scenario emerges for polar metals (Ga/In), as metals are lossy and do not exhibit strong 2^nd order nonlinearity. Moreover, they are not stable in the 2D regime.  However, stable metals can be achieved in the 2D regime by confining them between SiC substrate and epitaxial graphene [3]. This eventually induces strong structural polarity which drives unusually strong 2^nd order nonlinearity arising from asymmetric electronic states and interband transitions [4].

Both of these material systems are candidates for generating robust 2^nd order nonlinear signal down to atomic level thickness but have completely different electronic environment. In semiconducting 3R MoS₂, the 2^nd order nonlinearity originates from non-centrosymmetric stacking and strong light-matter interaction. On the other hand, polar metals combine inversion symmetry breaking with metallic conductivity and free charge carriers. Although, both these systems exhibit out-of-plane nonlinear response, 10% of symmetry breaking in the out-of-plane direction in polar metals leads to enhancement of SHG [4].

In this lab project, students fabricate 3R MoS₂ through mechanical exfoliation and dry transfer, and characterize them with 2^nd order nonlinear spectroscopy. They first determine the layer dependent SHG response of 3R MoS₂, then measure and compare with Indium and Gallium based 2D polar metals. Finally, they measure the out-of-plane SHG response of 2D polar metals.

Objectives

•  Basics of nonlinear spectroscopy
•  Comparison of 2^nd order nonlinear response from layer dependent 3R MoS₂ and polar metals.
•  Comparing in-plane and out-of-plane SHG response of polar metals.

Experimental techniques

•  Mechanical exfoliation of 2D materials and optical identification of monolayers
•  Deterministic dry transfer of 2D flakes (PDMS stamping)
•  In-plane and out-of-plane nonlinear spectroscopy at room temperature
•  Spectral fitting and simple data analysis (Python or Origin)

Contact:

Supervisor: M.Sc. Rahil Rezwan, M.Sc. Muhammad Hussain

Venue: GUFOS, IFK (Room E0114)

The topic can be worked on by one or two students. Supervision is possible in English.

References

[1] Malard, Leandro M., et al. "Observation of intense second harmonic generation from MoS 2 atomic crystals." Physical Review B—Condensed Matter and Materials Physics 87.20 (2013): 201401.

[2] Zhao, Mervin, et al. "Atomically phase-matched second-harmonic generation in a 2D crystal." Light: Science & Applications 5.8 (2016): e16131-e16131.

[3] Nisi, Katharina, et al. "Light–matter interaction in quantum confined 2D polar metals." Advanced Functional Materials 31.4 (2021): 2005977.

[4] Steves, Megan A., et al. "Unexpected near-infrared to visible nonlinear optical properties from 2-D polar metals." Nano letters 20.11 (2020): 8312-8318.

Learning target and topics

• Thin metal layers: deposition, characterization of the layer properties and structure
• High vacuum technology
• Introduction and application of various analysis methods
  •  Scanning Electron Microscopy (SEM) and Energy Dispersive X-Ray Analysis (EDX)
  •  Scanning Tunneling or Atomic Force Microscopy (STM, AFM)
  •  AugerElectronSpectroscopy (AES)
  •  X-ray diffractometry

Experimental equipment

•  Sputter coating system from Oxford Instruments
•  Thermal evaporation system (self-made)
•  Mass Spectrometer for residual gas analysis
•  Scanning Electron Microscope
•  Atomic Force Microscope
•  Scanning Tunneling Microscope
•  Auger Electron Spectrometer

Supervisor:   MSc. Markus Walther & Dr. Thomas Siefke

Venue:           F-Praktikum, IFK and IOQ

The topic is suitable for one or two students.

Single crystalline metal layers on natural mica are often used in electronic devices such as transistors, solar cells, and sensors, due to their high electrical conductivity and mechanical stability. Additionally, they can be used as a substrate for growing other single crystalline materials, such as semiconductors, which can be used in electronic devices as well. The high thermal and chemical stability of natural mica also makes it an ideal substrate for a wide range of applications, such as in the aerospace and automotive industries. Overall, the cost-effective fabrication of single crystalline metal layers on natural mica can have a significant impact on the development of new technologies and the improvement of existing ones.

The experiment aims to fabricate and investigate the properties of single crystalline metal layers using a thermal evaporation method. In this process, the metal material will be thermally evaporated onto a substrate of natural mica under specific conditions, such as temperature, pressure, and evaporation rate, to achieve single crystalline growth. The substrate will be carefully chosen, cleaned and prepared to ensure optimal growth conditions.

The characterization of the fabricated metal layers will be done using a combination of techniques including atomic force microscopy (AFM) and x-ray diffraction studies (XRD). The AFM will be used to observe the surface morphology of the metal layers, including the thickness, uniformity, and surface roughness. The XRD will be used to determine the crystal structure of the metal layers, including the crystal size, lattice spacing, and crystal orientation, as well as to identify any defects or impurities in the crystal structure.

The goal of the experiment is to understand how the thermal evaporation fabrication method and process conditions affect the properties of single crystalline metal layers and how such layers can be used in various applications such as electronics, catalysis, and sensing. The experiment will also help in understanding the relationship between the growth conditions and the crystal structure and will provide a better understanding of the fundamental physics of metal growth.

The main goals of this experiment are:

• Fabrication of single crystalline metal layers using thermal evaporation
• Investigation of the structural and morphological properties

Prerequisites:

• Familiarity with basic laboratory techniques
• Basic understanding of crystal growth and crystal structure

Methods:

• Thermal evaporation setup
• Atomic force microscopy (AFM)
• X-ray diffraction studies (XRD)

Contact:

Supervisor: Dr. Maximilian Schaal, Dr. Marco Grünewald

Language: German or English

Venue: F-Praktikum and labs of the IOQ

The topic is suitable for one or two students.

Micro- and nanotechnology forms the basis for a growing number of everyday objects and current scientific research. Many physical systems require a direct examination or at least a basic understanding of this technology chain.

The theoretical foundations are already taught at the FSU as part of the Micro/Nanotechnology lecture in the Physics or Photonics Master's programme and the associated seminar. Practical training has not yet been provided. This gap is to be closed by expanding the programme of the lab course.

The aim of this offer is to gain initial experience with an existing lithography line in the clean room and to jointly develop a concept for how this can be used for future teaching.

Contact:

Supervisor:   MSc. Andres Saenz Perez, Dr. Thomas Siefke

Venue:           Clean room of the IFK and F-Praktikum

The topic is suitable for one or two students.

According to de Broglie matter has not only particle but also wave character. It was shown that electrons, due to their rest mass, already exhibit wavelengths of around 1 angstrom at acceleration voltages of about 150 V, which is in the range of atomic distances in solids. Crystals therefore represent natural diffraction gratings for accelerated electrons, just as they do for X-rays of similar wavelengths. However, due to the strong inelastic interaction between electrons and atoms, the inelastic mean free path of electrons in solids ranges from less than 1 to several 100 nm which is thus considerably smaller than for X-rays. This makes electron diffraction especially suited for the investigation of crystalline surfaces and thin layers.

The aim of this projects is to understand principles of a special type of electron diffraction, namely X-ray photoelectron diffraction (XPD). This method enables an element specific analysis of the structure of a crystalline surface. For comparison, low-energy electron diffraction (LEED) will also be performed as a widely used characterization method for inorganic compounds. Students will learn how to prepare their own samples, starting from cleaning single-crystal surfaces, followed by the deposition of films via molecular beam epitaxy as well as their structural characterization by means of LEED and XPD. All preparation and analyzing steps are performed under ultrahigh vacuum (UHV) conditions.

Goals and context

• principles and application of electron diffraction in two dimensions (2D)
• concept of reciprocal space
• preparation of atomically clean single crystals and two dimensional materials
• highly-ordered ultrathin layers by molecular beam epitaxy
• vacuum technology (pumps, gauges, rest gas analysis etc.)

Methods

• UHV chambers with:
  • Photoelectron spectroscopy setup (X-ray source, hemispherical analyzer)
  • MCP-LEED (electron gun, phosphor screen, micro channel plates, camera)
  • sputter gun and sample heater
  • vacuum pumps (roughing, turbo, ion getter, and titanium pump)
• metal single crystals as sample substrates

Contact:

Supervisor: Dr. Maximilian Schaal & Dr. Felix Otto    

Venue: Labs of AG Fritz (ZAF)

The topic is suitable for two students.

Monolayer transition metal dichalcogenides (TMDs) such as MoSe₂ and WSe₂ are direct bandgap semiconductor materials, with optical emission primarily originating from excitons [1]. Their optical bandgap is tunable, it can be tuned ranging from approximately 1.56 eV (for x = 0, pure MoSe₂) to 1.65 eV (for x = 1, pure WSe₂) by alloying the those TMDs through variations in elemental composition (Mo and W), as in Mo_1-xW_xSe₂ [2]. Alloying is a straightforward chemical knob for band structure engineering.

This tunability becomes significantly more interesting when two monolayers are stacked to form a van der Waals heterostructure. In such a heterostructure, the conduction and valence bands of the two layers do not align, forming the expected type-II alignment. Electrons transfer to one layer and holes to the other within picoseconds after excitation. A photoluminescence (PL) spectrum directly reveals two key phenomena: the strong quenching of the bright emission from each individual monolayer, and the emergence of a new, lower-energy emission line corresponding to interlayer exciton, wherein the electron and hole reside in different layers [3,4]. The energy this interlayer exciton serves as a direct fingerprint of the band offset between the two materials. A recent first-principles study [5] calculated the exact systems investigated here Mo_0.75W_0.25Se₂/WSe₂, Mo_0.75W_0.25Se₂/MoSe₂, and, as a reference, MoSe₂ /WSe₂ and predicted concrete numbers for their band gaps and band offsets. The central claim is that the alloy layer inserts a tunable intermediate energy level into the MoSe₂-WSe₂ heterostructure, allowing the band alignment to be designed by choosing the composition x.

In this lab project, students build these heterostructures through mechanical exfoliation and dry transfer, and characterize them entirely with photoluminescence spectroscopy. They first determine the composition x of their alloy flakes from the monolayer PL, then measure how the interlayer exciton energy changes when the alloy is combined with pristine WSe₂ or with MoSe₂, and finally compare the resulting band offsets with the theoretical prediction.

Objectives

•  Basics of PL spectroscopy
•  Type-II band alignment and charge transfer in van der Waals heterostructures
•  Comparing an experimental result with a theoretical prediction

Experimental techniques

•  Mechanical exfoliation of 2D materials and optical identification of monolayer
•  Deterministic dry transfer of 2D flakes (PDMS stamping)
•  Photoluminescence spectroscopy at room temperature
•  Spectral fitting and simple data analysis (Python or Origin)

Contact:

Supervisor: M.Sc. Muhammad Hussain

Venue: GUFOS, IFK (Room E0114)

The topic can be worked on by one or two students. Supervision is possible in English.

References

[1] G. Wang et al., Colloquium: Excitons in atomically thin transition metal dichalcogenides, Rev. Mod. Phys. 90, 021001 (2018).

[2] Hussain, Muhammad, et al. "Nonlinear optical properties of mono and multilayer MoWSe2 alloys." Advanced Optical Materials 13.29 (2025)

[3] P. Rivera et al., Observation of long-lived interlayer excitons in monolayer MoSe₂–WSe₂ heterostructures, Nat. Commun. 6, 6242 (2015).

[4] L. A. Jauregui et al., Electrical control of interlayer exciton dynamics in atomically thin heterostructures, Science 366, 870 (2019).

[5] J. Ma et al., Photoelectric properties of alloyed Mo₁₋ₓWₓSe₂/XSe₂ (X = Mo, W) heterojunctions: a first-principles study, J. Phys. Chem. C 129, 16295 (2025).

Thin layers are layers with thicknesses in the micrometer and nanometer range. Their physical parameters such as electrical conductivity often deviates from that of the bulk material, allowing for altered, tailored properties and new functionalities. In addition, the material savings are often of great economic importance. Well known is the application in the field of protection against environmental conditions, e.g. against corrosion or oxidation. However, thin layers are most important in microelectronics, where almost all components are manufactured using thin-film technology. In optics, thin layers and layer stacks are used to influence the reflection and transmission behavior, but also the polarization. In particular, layer systems play a prominent role in X-ray optics.

In the internship, metallic layers are usually deposited and characterized by different methods. Concrete topics and goals, amongst others taken from current research projects, are proposed by the supervisor at the beginning of the internship, but can be discussed and adapted depending on the interests.

Learning goals and content:

• Deposition of thin metal layers by means of various coating methods (sputter coating, thermal evaporation)
• Characterization of the layer properties (e.g., composition, roughness, crystalline properties) depending on substrate properties and coating parameters (e.g. chamber pressure, residual gas composition, process times, substrate heating)
• Introduction and application of various analysis methods
  • Scanning Electron Microscopy (SEM) and Energy Dispersive X-Ray Analysis (EDX)
  • Scanning Tunneling or Atomic Force Microscopy (STM, AFM)
  • Auger Electron Spectroscopy (AES)
  • X-ray diffractometry (in cooperation with the X-ray group)

Experimental equipment:

• Sputter coating system from Oxford Instruments
• Thermal evaporation system (self-made)
• Mass Spectrometer for residual gas analysis
• Quartz layerthickness monitor
• Scanning Electron Microscope
• Atomic Force Microscope
• Scanning Tunneling Microscope
• Auger Electron Spectrometer

Contact:

Supervisor:  MSc. Markus Walther & Dr. Thomas Siefke

Venue:           F-Praktikum

The topic is suitable for one or two students.

Self-assembled protein nanofibers are emerging as highly promising building blocks for next-generation biomaterials, combining unique structural, mechanical, and bioactive properties. Importantly, these properties are strongly influenced by the environmental conditions and molecular mechanisms governing fibril formation. A detailed understanding of the self-assembly process is therefore essential for the controlled design and reliable application of protein nanofibers in biomedical materials.

The aim of this project is to investigate how self-assembly mechanisms and kinetics influence the formation and morphology of protein nanofibers. UV-Vis spectroscopy will be used to monitor and quantify the fibrillation process under different environmental conditions. In parallel, Atomic Force Microscopy (AFM) will provide nanoscale insights into the nanostructure of protein nanofibers. The overall goal is to develop a deeper understanding of protein nanofiber self-assembly and establish reproducible protocols for their controlled production, providing a foundation for future biomaterial applications.

Goals and context

•  Investigation of the underlying molecular mechanism of protein self-assembly
•  Analysis and understanding of the kinetics of the self-assembly process
•  Characterization of self-assembled protein nanostructures
•  Investigation of how environmental conditions affect the kinetics and morphology of protein nanofibers
•  Development of reproducible protocols for controlled protein nanofiber production

Methods

•  Synthesis and characterization of self-assembled protein aggregates
•  UV-Vis spectroscopy to investigate the kinetics of the self-assembly process
•  Atomic Force Microscopy (AFM) measurements to resolve the nanostructure of protein nanofibers
•  Scanning Electron Microscopy (SEM) for structural characterization at a larger size
•  Quantitative data analysis and interpretation

Prerequisites

•  Interest in soft matter physics and materials science

Contact

Person in charge: Prof. Dr. Klaus D. Jandt

Supervisor: MSc Linus Reck

Venue: OSIM, Löbdergraben 32

The topic is suitable for two students (pair).

The self-assembly process of proteins is of great importance in nature, enabling the protein to assume a unique structure, giving it properties necessary for specific tasks. The adopted conformation itself is highly dependent on the physical environment and can therefore be manipulated by it, making the selective formation of many different nanostructures possible.

One of the most investigated structures many proteins can assume is that of a long and extremely thin fiber, often connected with exceptional mechanical properties with the most famous example being spider silk, which attracted much attention in materials science.

In addition, protein nanofibers possess innate high biocompatibility and biodegradability with some being endowed with antimicrobial and/or bone promoting properties. These properties can be leveraged by developing novel protein nanofiber coatings which can be used for giving medical implants antimicrobial properties and accelerate bone growth improving initial and long-term success.

The aim of this project is to investigate the conditions for fiber formation, or their surface attachment behavior, and characterize the resulting nanofiber network. The aim of this project may be discussed and adjusted.

Goals and Context

•  Creation of a protein nanofiber coating via self-assembly
•  Applying this coating onto a substrate
•  Characterize the nanofiber coating
•  Identify impact of environmental parameters on fiber structure or attachment behavior
•  Investigate structure-property relationships of materials
•  Insight into novel surface engineering strategies

Methods

•  Advanced literature research
•  Analysis of nanofiber coating using atomic force microscopy (AFM)
•  Investigation of formation kinetics using UV-VIS spectroscopy
•  Water contact angle (WCA) analysis
•  Ethanol-induced self-assembly

Prerequisites

•  Interest in materials and cross disciplinary science

Contact

Person in Charge: Prof. Dr. Klaus D. Jandt

Supervisor: M. Sc. Nils Wolf

Venue: OSIM, Löbdergraben 32

This topic is suitable for one or two students.

Ultra-High-Molecular-Weight Polyethylene (UHMWPE), well known for its outstanding mechanical properties such as high durability and chemical resistance, is used for a multitude of applications from conveyor systems to orthopedic joint replacements. Yet these very same properties make it difficult to fabricate, which represents a challenge when developing novel applications.

Within this work the modification of UHMWPE surfaces through thermal-nanoimprint lithography will be the focus. During this process the material is heated up until it reaches a point at which it can be deformed through the use of a mold and the application of high pressures.

 Consequently, a heating press will be used within this project to imprint a defined surface structure into the polymer surface. Afterwards, atomic force microscopy and water contact angle measurements will be used to characterize the resulting surface structure and evaluate the success of the modification.

Goal and context

•  Creation of nanostructured polymer surfaces
•  Surface characterization
•  Insight into research and development of novel materials
•  Structure-property relationships of materials

Methods

•  Literature research
•  Thermal nanoimprinting of UHMWPE with a heated press
•  Surface characterization with an atomic force microscope (AFM)
•  Water contact angle (WCA) measurements

Prerequisites

•  Interest in solid states physics and material science

Contact

Person in charge: Prof. Dr. Klaus D. Jandt

Supervisor: M.Sc. Ernst A. Weiß

Venue: OSIM, Löbdergraben 32

The Topic is suitable for one student

Goals and context

This lab project provides a comprehensive introduction to atomistic quantum-mechanical simulations, specifically utilizing density-functional theory (DFT), for investigating the properties of nanomaterials. DFT enables parameter-free simulations and analysis of material characteristics, offering a powerful complement to experiments.

In recent years, low-dimensional semiconductors, such as transition metal dichalcogenide monolayers, have garnered significant attention due to their exceptional optical properties and potential for next-generation optoelectronic applications. Their mechanical flexibility further allows for the creation of van der Waals heterostructures by combining single layers of the same or different materials. This versatility opens up a vast landscape of novel materials with tunable characteristics that can be efficiently disclosed from first principles.

This project will provide basic knowledge and practical skills to conduct ab initio simulations on low-dimensional materials using DFT. Key tasks include structure optimization, calculations of electronic properties (including quantum effects), and comparison against available experimental data. Beyond running calculations, basic programming skills (preferentially in Python) will be trained to prepare or customize post-processing and visualization scripts.

The specific research focus will be tailored to align with the interests of the participating students, ensuring an engaging and personalized learning experience.

Methods

•  Density functional theory

Prerequisites

•  Knowledge of quantum mechanics and elements of programming are requested
•  Knowledge of solid-state theory and Python are an asset.

Organization

Person in charge: Prof. Dr. Caterina Cocchi

Supervisor: Dr. M. Sufyan Ramzan, Prof. Dr. Caterina Cocchi

Place: IFTO, Abbeanum

Possible topics within this project are:

• Entanglement and its entropy measures in quantum mechanics
• Supersymmetric quantum mechanics
• Magnetic monopoles and quantization of electric charge
• Magnetic monopoles in theoretical condensed matter physics: From the Berry phase in quantum mechanics to the field theoretical description of Weyl semimetals
• Do particles exist interpolating between a fermionic and a bosonic behaviour? Anyons and their description in terms of Chern-Simons theory.
• Hawking radiation and evaporating quantum black holes*
  
  *basic knowledge of general relativity and quantum field theory required.

Contact

Please contact Prof. Dr. Martin Ammon and/or Prof. Dr. Holger Gies

Venue: Theoretisch-Physikalisches Institut, Fröbelstieg 1 (Abbeanum)

One or two students may work on this topic per term.

Goals and context

Computational Fluid Dynamics (CFD) is a central part of computational physics and has been a driver for the development of modern numerical methods. It involves solving flow mechanical problems that cannot be solved analytically and are expensive to study experimentally by integrating generally nonlinear, partial differential equations.

In this project, the students will apply numerical methods to solve the Navier-Stokes-Equations for the case of an incompressible fluid to study flow within a cavity and flow around obstacles.

Methods

Timestepping schemes for integration of hyperbolic equations as well as a relaxation scheme for solving elliptic equations will be employed to solve the Navier-Stokes-Equations numerically on a staggered grid in two dimensions. The stability and convergence behavior of these schemes will be examinated.

The students will use C/C++, Python or Matlab to implement these methods.

Prerequisites

•  Basic knowledge of partial differential equations
•  Basic knowledge of numerical methods
•  Familiarity with at least one of the suggested programming languages

Contact:

Person in charge: Prof. Dr. Bernd Brügmann

Supervision: M. Sc. Guilherme Leite Bruzão 

Place:  Abbeanum, Fröbelstieg 1 or PAF Computerpool

Per term, one or two students may work on the topic

Quantum computations in a harmonic-oscillator basis aims to expand the unknown (nuclear) wave function, for instance of a deuteron, into a discrete set of well-defined and orthonormal oscillator eigenstates. To this end, one typically separates the center-of-mass motion and describes the relative motion of a two-particle system in terms of harmonic-oscillator (radial) wave functions and angular-momentum states. The Schrö-dinger equation is then transformed into a matrix eigenvalue problem by computing Hamiltonian matrix elements in this basis and diagonalizing the resulting finite matrix.

While the oscillator basis cannot reproduce the correct asymptotic tail of the wave functions with a small number of states, a systematic enlargement of the basis enables one to control convergence. Moreover, the analytic properties of HO functions simplify the evaluation of kinetic-energy and interaction matrix elements, which is one reason why this basis is widely used in nuclear-structure theory and elsewhere.

This project aims to understand and to implement how simple quantum computations can be done, either on a real quantum computer or some classical counterpart. We also wish to analyze the efficiency of such a scheme.

Goals of the project

•  Derive and implement the radial harmonic-oscillator wave functions and verify their orthonormality numerically.
•  Construct and diagonalize the kinetic-energy operator in a truncated harmonic-oscillator basis.
•  Implement a simple model interaction (e.g., a Gaussian potential) and compute the deuteron ground-state energy variationally.
•  Decompose the two-particle Hamiltonian into quantum circuits and use openFermions (software) to determine expectation values.

Prerequisites:

•  basic knowledge of quantum mechanics
•  programming skills (Python, Julia)

Contact:

Supervision:  Prof. Stephan Fritzsche, Theoretisch-Physikalisches Institut

Where: Theoretisch-Physikalisches Institut & Helmholtz-Institut Jena, Frauenhoferstr. 8.

Per term, one or two students may work on the project

Goals and context

The strong coupling of light to quantum systems relies on the confinement of electromagnetic fields to sub-wavelength volumes. This can be achieved by hybrid nanophotonic quantum systems, in which photonic nanostructures support tightly confined electromagnetic resonances. Computer simulations are an essential part of this research since the fabrication of nanoscopic structures is challenging and the experimental characterization of optical fields at the few photon level with nanometer resolution is equally complicated. Therefore, reliable simulation methods are required to calculate the electromagnetic response of nanostructured matter in advance. Since we are dealing with structures in the sub-wavelength range, "rigorous" methods are needed, which solve Maxwell´s equations without any approximation. Different approaches have explored for certain classes of nanophotonic structures (micro and nano cavities, metasurfaces, nanoantennas).

Methods

The students will implement and use a rigorous numerical method (FDTD or FEM) for the solution of electrodynamic problems. They will either use one of the existing professional implementations of such methods or will be working on their own implementation in a programming language suitable for high-performance computing. The method will be used to simulate the behavior of a nanophotonic structure and to investigate the coupling to quantum systems.

Programming can be done in any language preferred by the students, but Python and Matlab are supported by existing implementations.

Prerequisites

• Basic knowledge of electrodynamics and related partial differential equations
• Basic knowledge of optics
• Basic knowledge of numerical methods
• Familiar with at least one programming language supporting numerical simulations (preferred Python or Matlab)

Contact:

Person in charge: Prof. Dr. Thomas Pertsch

Supervisor: Dr. Ángela Barreda

Place: Abbe Center of Photonics, Campus Beutenberg

Per term, one group of one or two students may work on the topic.

Goals and context

Quantum computers promise a runtime advantage compared to their classical counterparts for certain tasks. However, currently existing quantum devices operate with moderate numbers of qubits and are prone to errors due to experimental noise and decoherence. To show that quantum computers provide an actual advantage requires outperforming the best algorithms for simulating quantum dynamics on classical computer, which led to a race between scaling up quantum hardware and improving classical simulation algorithms.

The goal of this project is to build a classical emulator of quantum circuits and to use it to simulate one of the major quantum algorithms. Also, you will explore how to model noise and errors in quantum devices. The focus of the project can be adapted depending on pace and interests of the students.

Methods

•  Quantum gates, quantum circuit model, quantum algorithms
•  Open system dynamics simulation through quantum channels/Lindblad mater equation
•  Numerical methods for linear algebra: Sparse matrices, eigenvalue problems
•  Numerical solution of ordinary differential equations, numerical integrators
•  Visualization tools for numerical data
•  Use of libraries for quantum circuit emulation like qiskit, qutip etc.

Instructions will be provided in Jupyter notebooks with code examples in Python. If preferred, another programming language can be used.

Prerequisites

•  Solid knowledge quantum mechanics
•  Basic knowledge of numerical methods
•  Familiarity with Python programming language and use of numpy/scipy libraries (or another programming language suitable for numerical simulation such as Julia, Matlab,...)
•  Basic knowledge of quantum optics is useful

Organization

Person in charge: Prof. Dr. Martin Gärttner

Supervisor: M.Sc. Ege Görgün

Place: IFTO, Abbeanum

Per term, one group of one or two students may work on the topic.

Goals and context

• Basic concept of hyperbolic partial differential equations (PDEs) and the initial-boundary value problem (IVBP)
• Finite differencing methods for derivative approximation
• Method-of-line for time-domain PDEs with Runge-Kutta timesteps
• Numerical implementation of methods to solve multi-D PDEs
• Concepts of numerical stability and convergence

Methods

The students will solve the IBVP with the wave equation in 1+1 and 2+1 dimensions (one time dimension and one and two spatial dimensions) numerically. The project has different sequential steps:

• Wave equation and reduction to first order system
• Characteristic analysis and well-posedness
• Finite differencing approximation of derivatives and convergence
• Runge-Kutta time integrators
• Solution of IBVP withthe 1+1 wave equation and periodic boundaries using the method of lines
• Stability and convergence
• IBVP with open boundaries and Sommerfeld boundary conditions
• Wave equation with a potential: the Regge-Wheeler equation, scattering of graviational waves off a black hole and quasi-normal modes
• More spatial dimensions: the 2+1 wave equation

Students can code in their preferred language, although Python is strongly recommended (open sources, simple and optimal for visualizations).

Prerequisites

• Basic knowledge of partial differential equations
• Basic programming skills

Contact:

Person of charge: Prof. Dr. S. Bernuzzi

Supervision: M. Sc. Anuraag Reddy Devarakonda

Place: Abbeanum, Fröbelstieg 1 or PAF Computerpool

Per term, one or two students may work on the topic.

We study solar and lunar eclipse predictions and observations for different reasons:

(i) The Earth rotation period increases with time by ca. 1.7-1.8 milli-seconds per century,which is less than expected purely from tidal interaction with the moon; other causes areunder dispute. An empirical method to measure such changes over at least three millennia iscomparing historical occultation observations (e.g. time and location of solar and lunareclipses) with calculated predictions.

(ii) We will determine certain eclipse parameters for different kinds (e.g. total or partial) ofobserved, predicted, and non-detected eclipses like magnitude, duration, height abovehorizon, time of day or night etc. – for both solar and lunar eclipses. We can then study howeclipse theories, predictions, and observations have improved over the centuries for differentcultures: Babylonia, East Asia, India, Arabia/Persia, Mediterranean Antiquity (Latin/Greek),and medieval Europe.

Each group will select a certain culture and time window to compare all solar and/or lunareclipses according to modern predictions with the real observational records (available inEnglish translation). Depending on language skills, it is recommended to also consider theoriginal reports and to study how different cultures have recorded details like contact timesand eclipse magnitude.

With this project, students can understand the physical causes for the different kinds ofeclipses, can learn how one can predict eclipse details like time, magnitude, and location onEarth, can comprehend the historical development of eclipse theories for different cultures, and will contribute to quantify for the Earth rotation period offsets.

Supervisor

Prof. Dr. Ralph Neuhäuser

Astrophysical Institute FSU Jena, ralph.neuhaeuser@uni-jena.de

One or two students can work on this project.

Resources

Richard Stephenson, 2009, Historical Eclipses and Earth's Rotation, Cambridge Univ. Press
https://eclipse.gsfc.nasa.gov/solar.html
https://eclipse.gsfc.nasa.gov/lunar.html
https://www.eclipsewise.com 

Supernova remnants (SNRs) are extended nebulae formed by the violent explosion of stars. Their optically visible emission comes mainly from shock-heated gas, producing bright filamentary structures in emission lines such as Halpha, [O III], and [S II] in their spectra . Optical studies of SNRs provide unique information on the shock physics, chemical abundances of the interstellar medium, and the dynamical evolution of the explosion debris. While X-ray and radio observations probe the high-energy plasma and relativistic particles, optical observations offer direct measurements of ionisation states, densities, and velocities. Narrow-band imaging allows us to map the morphology of the filaments, while spectroscopy provides line ratios to diagnose shock conditions, electron densities, and shock velocities.

This lab exercise focuses on the optical analysis of supernova remnants through both archival data and new observations. Students will learn how to process and analyse photometric and spectroscopic data of SNRs using IRAF and Python (Astropy, specutils, photutils). In addition to data reduction and interpretation, emphasis will be placed on conducting a lab project using public datasets and, when possible, telescope observations.

Tasks

•  Selection of a supernova remnant for study from available catalogs (e.g., Greens SNR catalog)
•  Reduction and calibration of spectroscopic data and measurement of emission line fluxes and construction of diagnostic line ratio maps ([S II]/Halpha, [O III]/Hbeta)
•  Extraction of physical parameters such as electron density, temperature, and shock velocity from spectra
•  Photometric analysis of filamentary structures to estimate surface brightness and compare with models
•  Doppler shift measurements of emission lines to obtain expansion velocities

Contact:

Supervisor: Günay Paylı

The tasks can be worked on by up 1 or 2 students

Contents and learning objectives

Since the discovery of the first binaries, visual, photometric and spectrometric observations have shown that most stars observable in the night sky are indeed stellar systems of two or even more stars. These binary or multiple star systems, which are bound together by their gravitational force, follow the laws of celestial mechanics, which were first empirically described by Kepler and then later astrophysically explained by Newton. Thanks to the classical mechanics, it is possible with observations to precisely determine the properties of the stars in these stellar systems, in particular their masses.

Since the mass of stars determines their evolution significantly, the observation and characterization of binary star systems is astrophysically very important. While wide binaries can still be observed directly with a telescope, more closer systems can be investigated spectroscopically by means of the Doppler effect. The movement of the components around their center of gravity reveals itself as a shift of the spectral lines in the common spectrum of the stellar system. The precise analysis of the radial velocities of the stars yields an exact characterization of the orbital parameters of the stellar system (e.g. period and orbital eccentricity) as well as its mass function or the mass ratio of its components.

In this project the students use the observing method described above for the detection and characterization of spectroscopic binary stars in order to determine the properties of these systems, as well as their actual orbital parameters. The students learn the important basics for the reduction and analysis of spectroscopic data of stars, which they themselves have taken with the modern instruments, operated at the University Observatory in Großschwabhausen.

Technology

The spectroscopic observations are carried out by the students at night at the University Observatory in Großschwabhausen (see Fig.2) with the Échelle spectrograph FLECHAS, which is operated at the 90cm reflector telescope of the observatory.

Supervisor: Dr. Markus Mugrauer

Location (night observation): University Observatory in Großschwabhausen

Location (data reduction and analysis): Astrophysical Institute, Schillergäßchen 2, Jena

Each spectroscopic binary system can be processed by one or two students. The specific task will be adjusted depending on the observed stellar system.

Comets are small bodies in the Solar System consisting mainly of ice and dust. As well as comets on periodic orbits (the first of which was discovered by E. Halley), there are also many non-periodic comets. Recently, even interstellar comets have been discovered flying through the solar system. As comets spend most of their time far from the Sun, in the dark and cold depths of the solar system, they remain unobservable. However, as they approach the Sun, they begin to evaporate in the sunlight, forming a coma (the 'head' of the comet) and, eventually, a tail, which makes them visible in the night sky. As comets consist of almost unchanged, frozen matter from the early stages of the solar system, studying them provides important insights into the nature of matter during the formation process of the solar system. By observing comets, it is possible to determine their orbital elements and thus their place of origin in the solar system. Additionally, the activity of comets can be studied as they pass through the inner solar system. 

Tasks: 

1. Observe new comets using the telescopes operated at the University Observatory in Großschwabhausen. 
2. Reduce and analyze all data, particularly with regard to astrometry (the position of the comets in sky), and photometry (the brightness of the comets).
3. Examine the morphological evolution of the comets over time, such as coma diameter and tail length.
4. Determine the orbital elements of the comets, as well as their absolute brightness dependant on the distance from the Sun.
5. Study the activity of the comets dependant on solar distance, and search for non-gravitational forces that alter their orbits.  

Technology

The imaging observations are carried out by the students at night at the University Observatory in Großschwabhausen with the CCD-cameras, which are operated at the individual telescopes of the observatory. 
 

Contact:

Supervisor: Dr. Markus Mugrauer 

Location (night observation): University Observatory in Großschwabhausen 

Location (data reduction and analysis): Astrophysical Institute, Schillergäßchen 2, Jena 

Each comet can be processed by one or two students. The specific tasks will be adjusted depending on the observed comet. 

Contents and learning objectives

Since the discovery of the first planet outside our solar system some 20 years ago, more than 1000 of these exoplanets have been detected around distant stars. Several dozens of planets could be imaged directly next to their host star, using modern observing techniques on large telescopes of the 8 to 10m class. The vast majority of exoplanets, however, were detected indirectly by accurate spectrophoto-metric measurement of the light of their host stars. The transit method is today the most successfully used method for the planet search.

In the transit method, the occultation of the host star by its exoplanet is observed. By means of precise photometric measurements, the light curve of the star is measured during the transit of the planet, which allows the determination of the orbital period, the inclination of the planetary orbital plane and the planetary radius.

From the combination of the obtained results with available spectroscopic measurements (msin (i), minimum mass of the planet), the mean density of the exoplanet can be determined, which allows conclusions about its internal structure.

In this project, the students should use the observing method described above for the detection of planets in order to determine the properties of exoplanets, as well as their actual orbital parameters. The students learn the important basics for the reduction and analysis of photometric data of stars, which they themselves have recorded with the modern instruments, operated at the University Observatory in Großschwabhausen. 

Technology

The photometric observations are carried out by the students at night at the University Observatory in Großschwabhausen (see Fig. 2) with the CCD-cameras, which are operated at the individual telescopes of the observatory.

Supervisor: Dr. Markus Mugrauer

Location (night observation): University Observatory in Großschwabhausen

Location (data reduction and analysis): Astrophysical Institute, Schillergäßchen 2, Jena

Each exoplanet can be processed by one or two students. The specific task will be adjusted depending on the observed exoplanet.