Physics/Mathematics Research at RUG

Action Spectroscopy of Gas-Phase Biomolecules

What is the topic of your research group?

Our research focuses on understanding the structure and dynamics of biomolecules using advanced photon-based techniques. We investigate how isolated and microsolvated biomolecules interact with light, with the goal of uncovering fundamental mechanisms that govern molecular structure, function, and reactivity. To achieve this, we perform state-of-the-art experiments at large-scale photon facilities and collaborate closely with theorists and computational scientists. Students will conduct their project in our research group at DESY in Hamburg while being supervised through my affiliation with the University of Groningen.

What can students expect to do when doing a project in your group?

Students will work with us in the lab at DESY Hamburg, participating in beamtime (if available) and lab experiments. As an experimental group, we design, build, and operate our own instruments to prepare and study molecules in the gas phase, often in combination with large-scale facilities such as synchrotrons and X-ray free-electron lasers, but also with table-top lasers in the lab. Depending on the project, students may help develop experimental setups, participate in measurements at DESY, prepare samples, analyze experimental data, and contribute to the interpretation of the results. Throughout the project, students will work closely with researchers from different disciplines in an international and collaborative research environment.

What could be topics of interest for students in which they can do a project?

• Testing new ion trapping and activation modes.
• Setting up ion mobility schemes.
• Commissioning a new hydration electrospray ionization source.
• Developing and building experimental setups.
• Conducting ultraviolet (UV) action spectroscopy experiments in the lab.
• Data analysis for X-ray and laser-based experiments.
• Structural changes induced by hydration, protonation, and ligands.
• Radiation damage.
• Proton migration.
• Energy transfer in biomolecules.
• Non-covalent interactions in biomolecules.

The exact Bachelor's or Master's project can be tailored to the student's interests and background.

What courses are related to your research field?

• Atomic and (Bio-)Molecular Interactions
• Atoms and Molecules
• Quantum Mechanics
• Optical Spectroscopy
• Physics Instrumentation and Technology
• Computational Physics
• Physics Lab
• Spectroscopic Tools for Life Sciences

What can students learn when doing a project in your research group?

In a project with our group, students learn how to design and perform cutting-edge spectroscopy experiments on gas-phase biomolecules and interpret the resulting mass spectra in terms of molecular structure and dynamics. They gain hands-on experience with large-scale photon facilities at DESY and develop strong skills in quantitative data analysis, while working on real research questions that are highly valuable for a future research career in molecular physics, physical chemistry, or spectroscopy.

Contact Information

Sadia Bari: sadia.bari@desy.de

Micromechanics | Onck Group

What is the topic of your research group?

Research in our group aims at understanding the micromechanical and functional behavior of biomimetic materials and biological processes based on an accurate description of the underlying physical mechanisms. Computational techniques (mostly molecular dynamics, but also Monte Carlo techniques, finite element methods and solid-fluid interaction approaches) are being used to explicitly account for the physical mechanisms at the relevant length scales. We increasingly make use of machine learning to parameterize the model parameters of the computational approaches.

The research can be grouped into two main topics:

1. Bio-inspired responsive materials (lab-on-chip and soft-robotic systems).
2. Biophysics (nuclear transport, condensates, neurodegenerative diseases, and cancer, often in collaboration with the UMCG).

What can students expect to do when doing a project in your group?

We use computational methods to simulate the processes we are interested in. This means we do programming and scripting to operate the software and solvers developed in the group. We run jobs on a range of HPC supercomputers of the Zernike Institute (Nieuwpoort), the University of Groningen (Habrok), and we use the national supercomputing facilities at SURF Sara in Amsterdam. We handle big data on a daily basis to extract physical insights.

Practically, you will get a desk in the group with a high-speed workstation. You will be assigned a daily supervisor (PhD student or postdoc) and will attend weekly meetings with the group leader and daily supervisor. A system administrator is available to assist with computer and software challenges.

What would be topics of interest for students in which they can do a project?

Students are invited to contact the group leader to discuss possible topics within the two research lines mentioned above. Roughly, topics are available on (i) the design of bio-inspired responsive materials, (ii) curiosity-driven biophysical research, and (iii) molecular understanding of cancer (leukemia and cancer metastasis) and neurodegenerative diseases (ALS, Alzheimer’s, Parkinson’s, and Huntington’s disease). The latter topics are carried out in close collaboration with the UMCG, aimed at translating new molecular insights into therapeutic approaches.

What courses are related to your research field?

Numerical Analysis, Physics of Fluids (BSc level), and Computational Physics (MSc level).

What can students learn when doing a project in your research group?

Students will learn to run massively parallel jobs on supercomputers, handle big data, employ high-end visualization, and utilize machine learning. In short, students will get training in ‘computational microscopy’ to go where no experimental techniques have gone before.

Contact Information

Patrick Onck: p.r.onck@rug.nl

Project 1: Exploring the role of mechanics in cancer cell migration: a computational analysis

Supervisor: Xiaoguang Li, PhD candidate, and Prof.dr.ir. Patrick R. Onck

Project Details:

Zernike Institute for Advanced Materials, Faculty of Science and Engineering, University of Groningen

Approximately 90% of cancer related deaths are associated with metastasis. Cancer metastasis depends not only on active cell migration but also on the ability of the nucleus to deform and respond to mechanical cues. Although computational studies have highlighted the importance of nuclear mechanics in migration, force transmission from the active cell boundary to the nucleus is often treated indirectly rather than through explicit intracellular structures. Here we present a 2D Cellular Potts model that explicitly represents the cell membrane, nuclear envelope, membrane-embedded linker proteins, and connecting semiflexible filaments as distinct mechanical elements. Within this framework, proteins act as mobile anchoring sites that move with the evolving cell and nuclear membranes. Filaments preserve the expected force-extension relation while their conformations evolve under Monte Carlo thermal fluctuations, allowing intracellular force transmission to emerge from stochastic filament mechanics. Taken together, this computational model provides a mechanistic description of how active membrane dynamics, linker protein distribution, and filamental mechanics jointly organize nuclear positioning and intracellular force transmission during invasive migration.

Based on this computational framework, the following research topics can be explored:

• Intracellular force transmission and nuclear positioning in confinement and during intravasation;
• Study the emergent cytoskeletal network during migration.

Project 2: How do viruses enter the nucleus? Molecular dynamics of constriction and dilation of nuclear pores.

Supervisor: Mohammad Habibi, PhD candidate, and Prof.dr.ir. Patrick R. Onck

Project Details:

The nuclear pore complex (NPC) is essential for eukaryotic cell function because it regulates macromolecular exchange between the nucleus and cytoplasm. A large fraction of NPC components are FG-repeat nucleoporins (FG-Nups), intrinsically disordered proteins that form the selective barrier within the central transport channel. A major open question in nuclear transport is how this barrier is shaped by large-scale structural changes in the NPC scaffold. Constricted and dilated NPC states have been proposed to regulate the dimensions of the central channel, but it remains unclear how these states affect FG-Nup organization and transport efficiency. Resolving this in the human NPC is especially important because human pores differ substantially from yeast in composition, architecture, and glycosylation, and are directly relevant to mammalian cell physiology and disease.

The human NPC is also directly relevant to viral infection, in particular HIV, which must transport its capsid through the nuclear pore to establish infection in cells. HIV is known to exploit human nucleoporins during nuclear entry, making the organization and dynamics of FG-Nups in the human pore biologically important beyond transport. A mechanistic description of how scaffold dilation, glycosylation reshape the FG-Nup barrier could therefore also provide a useful framework for understanding how HIV engages the human NPC.

The 1-bead-per-amino-acid (1BPA) coarse-grained molecular dynamics model developed by our group has been widely used to investigate the conformational and dynamic properties of yeast FG-Nups during nuclear transport (1).

This master project will use 1BPA coarse-grained model of the human NPC in constricted and dilated states and use them to determine how scaffold remodelling affects FG-Nup organization and Importin-β transport. In a single Master project, these aims can be achieved by focusing on equilibration of the human FG-Nup assemblies, and a first comparative analysis of Importin-β and HIV interactions and transport in constricted versus dilated pores. More realistically, the full scope is best divided over two master projects: a first project centered on validating and equilibrating the human NPC scaffold, FG-Nup assemblies in different structural states, and transport simulations with Importin-β and the extension to O-glycosylation and a second project centered on and HIV-related transport questions. Together, these studies will create a mechanistic and predictive framework for understanding how structural remodelling controls selective nuclear transport in the human NPC.

Project 3: Towards the origin of life: how can replicators catalyze droplet-formers?

Supervisor: Ahmad Dibajeh, PhD candidate

Project Details:

In the effort to study the origin of life, chemists have synthesized self-replicating and droplet-forming molecules to mimic the necessary building blocks of life. By combining these two systems with a dye molecule that releases oxygen to fuel droplet and fibril forming reactions, proto-metabolism can be achieved on a local scale [1]. Therefore, to understand and design the local catalytic effects of light-induced oxygen release, multi-scale molecular dynamics (MD) simulations can be employed as a computational microscope to examine the conditions under which replicators and droplets can co-partition. By varying the acceleration of partitioning near fibrils based on their propensity to attach to dye molecules, our aim is to predict conditions under which light-induced proto-metabolism can enable the mixing of compartmentalization, self-replication, and metabolism: the three necessary ingredients for life based on the Chemoton model [2]. As a BSc or MSc research project, we are looking for a student to build the self-replicating fibrils in coarse grained MD, where all-atom data is available.

Project 4: Phase separation-controlled gene transcription in leukemia: A computational approach

Supervisor: Ilse Visser, PhD candidate, and Prof.dr.ir. Patrick R. Onck

Project Details:

Zernike Institute for Advanced Materials, Faculty of Science and Engineering, University of Groningen

Leukemia is the 10th deadliest cancer worldwide [2]. Liquid-liquid phase separation (LLPS) has been linked to the pathology of acute myeloid leukemia (AML) [3]. However, the link between pathological condensates and AML is still largely unknown [3]. The project you will be joining is an interdisciplinary collaboration between the University of Groningen and the University Medical Center Groningen, investigating the connection between aberrant oncogene-driven condensates and the effect on gene expression in AML.

The project specifically focuses on studying the composition, formation and dynamics of AML-associated condensates. You will investigate this via zoomed in (investigating the composition and dynamics of a single oncogene-driven condensate) and/or zoomed out (big-data screening to discover novel condensate compositions) approaches. For this, you will be using computational tools and molecular dynamics simulations in a high-performance supercomputing environment. This project combines concepts of physics, biology, chemistry and computer science. You will have the opportunity to work in an interdisciplinary group with a variety of newly developed big data-driven tools and resources.

Experimental Particle Physics with the LHCb Experiment

LHCb Experiment

The Large Hadron Collider beauty, or LHCb, experiment at CERN is a high energy physics experiment dedicated to the study of subatomic particles containing beauty quarks. It tests the Standard Model (SM) of particle physics through high precision measurements of decay rates and asymmetries.

In the LHCb group at the Van Swinderen Institute, we search for physics beyond the SM by analysing the collected data and studying the performance of LHCb’s vertex locator, and we prepare for the future by contributing towards its next upgrade.

Join one of our Ongoing Research Projects:

Project 1: First measurement of the decay Bc→τν

• The decay rate of Bc→τν provides a powerful test of the SM, but is experimentally extremely challenging due to the neutrinos which cannot be detected.
• You will understand how a particle physics analysis is performed, process and plot data, study kinematic distributions, optimize selections, and evaluate your results.

Project 2: First search for the lepton flavour violating decay Λb→Λτμ

• Lepton flavour violation is a forbidden process in the SM, however, it has been observed in neutrino oscillations. Do we also see it in decays of Λb baryons?
• You will understand how a particle physics analysis is performed, process and plot data, study kinematic distributions, optimize selections, and evaluate your results.

Project 3: Performance study of LHCb’s Vertex Locator

• The VELO plays a crucial role in the identification of b-hadrons and measuring the properties of their decay. Understanding its performance is needed to control systematic uncertainties.
• You will understand how a high energy physics detector is used to measure particles, how we go from electrical signals to hits to particle tracks, and what information we can extract.

Project 4: Development of a new data acquisition strategy using the FELIX read-out card

• After the future upgrade, LHCb will operate at an order of magnitude higher luminosities, and thus create higher data rates. We are developing the corresponding data acquisition system.
• You will learn hardware programming, design and implement new components for the data acquisition, and test them in simulation and on the FELIX card.

Project 5: Development of new silicon pixel detectors with picosecond timing capabilities

• After the future upgrade, LHCb will operate at an order of magnitude higher luminosities, and thus create higher data rates. We are developing the next generation particle detectors.
• You will understand how a high energy physics detector is used to measure particles, how we go from electrical signals to hits to particle tracks, and what information we can extract.

Project 6: Phenomenology of CP violation in B meson decays

• To compare high precision experimental measurements with the theory predictions, we need to include subleading effects in our interpretation of the results.
• You will understand the subtleties and challenges involved in interpreting experimental measurements in terms of the theory parameters when going beyond leading approximation.

Interested? Get in touch to know more about these opportunities

Contact: Ann-Kathrin Perrevoort (a.perrevoort@rug.nl) & Kristof De Bruyn (k.a.m.de.bruyn@rug.nl)

Computational Spectroscopy | Jansen Group

Research Group: Computational Spectroscopy

What is the topic of your research group?

Our research group studies the dynamics of complex molecular and condensed-phase systems using computational and theoretical physics methods. We investigate how microscopic molecular motion and quantum effects give rise to experimentally observable spectra, with particular focus on ultrafast infrared and visible spectroscopy. The research combines molecular dynamics, statistical mechanics, quantum dynamics, and numerical modelling to understand systems ranging from liquids and biomolecules to light-harvesting materials and nanoscale systems. A major goal is to connect fundamental physical theory with state-of-the-art spectroscopic experiments and connect structural information with functional consequences.

What can students expect to do when doing a project in your group?

Students can expect to work on computational physics projects involving simulations, theoretical modelling, and scientific programming. Projects may involve molecular dynamics simulations, modelling quantum or vibrational dynamics, analysing multidimensional spectroscopic signals, or developing numerical algorithms and simulation software. Many projects combine physics concepts with high-performance computing and data analysis. Projects may have an individual character and/or involve the contribution to and use of one of our publicly available (GitHub) physics codes that are written in a collaborative effort.

What would be topics of interest for students in which they can do a project?

Possible project topics include nonlinear spectroscopy, quantum dynamics, exciton transport, molecular simulations, statistical mechanics, and computational modelling of complex systems. Students may study ultrafast energy transfer in photosynthetic systems, hydrogen-bond dynamics in liquids, vibrational dynamics in biomolecules, or optical properties of novel materials such as perovskites and molecular aggregates. Other projects may focus on scientific software development, numerical methods, stochastic modelling, or machine learning approaches for spectroscopy and molecular simulations.

What courses are related to your research field?

On Bachelor level: Quantum Physics 2, Optical Spectroscopy.

On Master level: Ultrafast Time-Resolved Spectroscopy, Computational Physics, Statistical Mechanics.

What can students learn when doing a project in your research group?

Students learn how modern computational physics methods can be used to understand complex molecular and condensed-phase systems. They gain practical experience with scientific programming, simulations, numerical modelling, and using large scale computer facilities. In addition, students develop skills in independent research, scientific communication, and problem solving in interdisciplinary physics research for example involving collaborating with experimental groups.

Contact information

Thomas La Cour Jansen: t.l.c.jansen@rug.nl

Website: https://www.rug.nl/research/zernike/theory-of-condensed-matter/jansen-group/

Dynamical Systems, Geometry, and Mathematical Physics

Research Group Details

The research activities of the group Dynamical Systems, Geometry, and Mathematical Physics cover a broad and diverse spectrum of subjects in the fields of fundamental and applied dynamical systems theory, classical, statistical, and quantum mechanics, and their interfaces in the light of dynamics. Applications to life sciences, meteorology, physics, and chemistry play a crucial role.

What can students expect to do when doing a project in your group?

Students can expect to conduct literature studies, prove theorems, and investigate particular dynamical systems through analytical methods or numerical simulations.

What could be topics of interest for students in which they can do a project?

• Dynamical systems
• Geometry
• Algebraic topology
• Knot theory
• Hamiltonian systems
• Problems arising from mathematical physics

What courses are related to your research field?

• Analysis on Manifolds (WBMA013-05)
• Algebraic Topology (WBMA058-05)
• Geometry (WBMA034-05)
• Dynamical Systems (WBMA031-05)
• Project Chaos Theory (WBMA025-05)

What can students learn when doing a project in your research group?

Students can learn to conduct a research project on a topic at the intersection of different branches of mathematics. An important aspect of this is presenting research results clearly, both in written and oral form, to experts and non-experts.

Contact information

Contact: A.E. Sterk: a.e.sterk@rug.nl

Theoretical cosmology and quantum gravity

What is the topic of your research group?

Twofold: one research line focusses on modelling the Big Bang, and the other investigates general aspects of quantum field theories and gravitational theories.

What can students expect to do when doing a project in your group?

Literature study, analytical calculations, occasionally a numerical code.

What would be topics of interest for students in which they can do a project?

Models of inflation, models of gravity, quantum field theory.

What courses are related to your research field?

RQM, Symmetries in physics, Lie groups, General relativity, Quantum field theory.

What can students learn when doing a project in your research group?

Lots of beautiful theories and their interrelations.

Contact information

Diederik Roest: d.roest@rug.nl

Theoretical particle physics

What is the topic of your research group?

Tests of the Standard Model, in particular tests of symmetries; effective field theory; QCD and hadron/nuclear physics; applications in astrophysics; fundamental quantum mechanics.

What can students expect to do when doing a project in your group?

Theory development, using mathematical physics, quantum mechanics, or quantum field theory, and when required coding, e.g. in mathematica; the connection to current experiments.

What would be topics of interest for students in which they can do a project?

Violation of parity, time reversal, baryon & lepton number; baryo- & leptogenesis; quantum computing, ...

What courses are related to your research field?

Quantum field theory, advanced quantum mechanics, mathematical methods of physics, general relativity, ...

What can students learn when doing a project in your research group?

Cutting-edge particle physics and quantum mechanics; how to use their brain.

Contact information

Rob Timmermans: r.g.e.timmermans@rug.nl

Cold Molecules

What is the topic of your research group?

We build table-top experiments to explore the limits of our knowledge of the physical universe. We do this through very precise measurements. In these measurements we put small quantum systems like atoms and molecules in a carefully controlled state using lasers, electric and magnetic fields, and explore their quantum structure. When we compare these measurements with equally precise theory (usually provided by our theory-friends in the institute :-)) we learn about the fundamental interactions and symmetries that are at the basis of particle physics. Recently we have also started doing experiments with optically levitated nanospheres (about the size of the corona-virus) to explore gravity and to make novel sensors.

What can students expect to do when doing a project in your group?

We are an experimental group - so you can do experiments! We design, built and operate our own experimental setups, which can be rather large (our molecule decelerator is 4,5 meters long!) or rather small (the nanosphere optical levitation setup easily fits on a single table). Of course, for the design, operation and interpretation of those experiments we rely heavily on theory and various computer codes, such as python, but also CAD drawing programs. Some projects are more heavily focused on the technical aspects of our experiments, some more on the use of computer simulations to interpret our data, and others more an exploration of theory and literature that is needed to design and plan future experiments.

What would be topics of interest for students in which they can do a project?

Typically, students join a research team that works for example on the molecule decelerator, the electron-EDM project, the cryogenic source, the laser cooling of molecules, or the nano-particle project. Within that team (typically 1-2 PhD students, a bachelor student and a master student) they explore a current research topic in the research group, that fits with their interest and capabilities. Because of the broad range of possible projects, from technical to fundamental, we have had students from both applied physics and physics. We also regularly host foreign engineering students for a research project.

What courses are related to your research field?

Electricity and magnetism - Waves and optics - Atoms and molecules - Particle physics

What can students learn when doing a project in your research group?

You can learn what it is like to do research in a research group: that means working together in a diverse team with different backgrounds, points of view and nationalities. You will practice the communication of scientific results in oral presentations and a project report. You will learn how to search, read and interpret scientific literature (publications) in an efficient way. And you will discover the exciting details that are important when you try to use quantum objects and lasers in your research!

Contact information

Steven Hoekstra: s.hoekstra@rug.nl

Research group webpage

Computational spectroscopy

What is the topic of your research group?

We study quantum, structural and dynamical properties that can be studied by applying light pulses to the sample and how this information can be used for new applications. The quantum properties include delocalization over nanosize structures and quantum transport. The structural properties range from the structure of proteins to packing of molecules in photovoltaic devices and artificial light-harvesting antenna. The dynamical properties could be the rotation of organic molecules in perovskites, the fast transfer of electronic excitation through super efficient natural light-harvesting systems, or slow aggregation processes. Interesting applications include better solar cells, or new types of devices.

What can students expect to do when doing a project in your group?

Depending on the topic of the research the students may be exposed to one or more of the actions below.

1. Writing their own computer code or contributing to one of the codes developed in the group
2. Performing molecular dynamics simulations (gromacs) to investigate the structure and/or dynamics of a system
3. Perform electronic structure calculations to learn about the vibrational or electronic states that one can excite with light
4. Perform spectral simulations with code developed in the group to interpret and/or predict spectra of systems of interest

What would be topics of interest for students in which they can do a project?

1. Quantum Dynamics/Quantum Coherence/Quantum Delocalization
2. Ultrafast Dynamics
3. Light harvesting systems
4. Protein structure and dynamics
5. Solvation, noise, and disorder

What courses are related to your research field?

Ultrafast time-resolved spectroscopy, statistical mechanics, quantum mechanics

What can students learn when doing a project in your research group?

1. Dynamics in open quantum systems
2. Molecular Dynamics
3. Programming (as python/c/MATLAB)
4. Large scale computations on large computer clusters

Contact information

Research group webpage

Twitter

Bio-Inspired Circuits and Systems (BICS)

What is the topic of your research group?

We aim to identify the principles of neural computation and implement them in fully parallel and low-power neuromorphic systems that offer the opportunity to overcome the limitations of traditional digital architectures. Hereby we develop physical models of recurrent neural networks with learning synapses and biological inspired sensor systems, which allow us to validate current theories of learning and perception.

Two main streams can be identified in our research activities: (i) neuromorphic systems and theories for brain inspired computation (learning, cortical inspired neural architectures); (ii) neuromorphic sensing and actuating.

What can students expect to do when doing a project in your group?

The BICS group can offer a variety of different projects. In the neuromorphic systems and theories for brain inspired computation research stream students can investigate algorithms and hardware implementations of online learning as well as neural architectures. Students will carry out this research by means of classical neuromorphic approaches (e.g. design and simulation of novel circuits and architectures in integrated circuit (IC) design software), through the exploitation of material properties (e.g. simulation of novel nano-electronic “memristive” device models in IC design software) and through modeling and simulation of spiking neural networks. Within the neuromorphic sensing and actuating research stream students can develop spiking neural network models and neuromorphic electronic circuits to build compact autonomous sensory and sensory-motor systems specialized for interacting with the environment and solving specific real-world tasks.

The properties of new neural network models can be first evaluated in spiking neural network simulators (BRIAN2, Nengo, nest, neurorobotics-platform) with python front-end. After a first proof of concept the approach can be implemented on already existing neuromorphic hardware systems (Loihi, DYNAP-SE, SpiNNaker) and tested with real world input from event-based sensors (Dynamic Vision Sensor, Neuromorphic Auditory Sensor). A closed loop evaluation on a robotic platform can be performed for some projects to proof their real world applicability.

Summarizing, our research group can offer a variety of different projects from neural network model simulation to circuit design, system integration and experimental validation.

What would be topics of interest for students in which they can do a project?

1. Learning
   • Learning in memristive systems
   • Recurrent competitive networks
   • Attractor networks
2. Neuromorphic touch
   • Neural networks for encoding and decoding touch stimuli
   • Receptive fields optimization for tactile sensing
3. Fly-inspired motion vision
   • Contrast normalization with the Time-Difference-Encoder
   • Collision avoidance on a robotic platform
4. Neuromorphic acoustic perception
   • Keyword spotting on Loihi
   • Sound-source-localization with the Time-Difference-Encoder
   • Implementation of an auditory sensor model into the neurorobotics platform
5. Interaction interface circuits (chip design)
   • Motor and actuator controllers for spiking systems (PWM/PFM)
   • SSpike conversion for interfacing to simple real world control and digital sensing (LEDs, switches)
   • Cell library design, RAM and CAM design for IC
   • Novel spiking neuronal network on the fly spike mapping
   • Spike filtering systems for neural networks

What courses are related to your research field?

Neuromorphic circuit design

What can students learn when doing a project in your research group?

1. Analogue integrated circuit (IC) design with CADENCE
2. Spiking neural network modelling in BRIAN2, nengo, nest
3. Basic and advanced data analysis
4. Neuromorphic Hardware: Loihi DYNAP-SE SpiNNaker
5. Basics of asynchronous digital integrated circuit (IC) design

Contact information

Elisabetta Chicca: e.chicca@rug.nl

Surface Science

What is the topic of your research group?

Experimental investigation and controlled modification of the electronic properties of low-dimensional structures. The research is carried out with surface science tools, mainly scanning tunneling microscopy, atomic force microscopy, photoelectron spectroscopy. Subtopics are:

1. The controlled tuning of the structural and electronic properties of conducting surfaces by patterning the surface with periodic molecular structures.
2. Research into 2D materials and combining them with either another 2D material or molecules to tune their electronic properties.
3. On-surface synthesis of 1D and 2D molecular nanostructures from small organic building blocks.
4. Investigation of controlled switching of long range ordered molecular structures on surfaces by using the bias voltage.

What can students expect to do when doing a project in your group?

They will do experimental work, mainly using scannning tunneling or atomic force microscopy. They will prepare the samples and they will also carry out the measurements. An experienced PhD student will be their daily supervisor and with him/her they will learn how to set up and perform experiments and to do data analysis.

What would be topics of interest for students in which they can do a project?

The topics for Bachelor research will be mainly focused on topics 2 and 4 from above because these experiments can be carried out under ambient conditions. For Master research all topics listed above are possible. If students are interested in our research they should get in touch with me and arrange a (online) meeting to discuss the topics in more detail. Additionally, background information in the form of recent publications or Bachelor/Master theses will be given.

What courses are related to your research field?

On Bachelor level: nanophysics and -technology, nanoprobing and -fabrication, solid state physics. On Master level: surfaces and interfaces.

What can students learn when doing a project in your research group?

They will learn how to perform experimental work, they will learn about preparation of surfaces, performing scanning tunneling and/or atomic force microscopy, structural and electronic surface properties, 2D materials, graphene nanoribbons, data analysis with special software.

Contact information

Meike Stöhr: m.a.stohr@rug.nl

Theorethical Subatomic Physics

What is the topic of your research group?

My research is mainly focussed on particle collider phenomenology, which means trying to describe what happens in particle collisions and to see if there are any deviations from the expectations.

What can students expect to do when doing a project in your group?

First of all, I never suggest projects on my own research topic. I want to learn new things from the projects of bachelor and master students that go beyond my own expertise. The projects are always in theoretical or mathematical physics. The projects typically involve literature study and analytical calculations (reproducing or modifying calculations from the literature), but occasionally also numerical calculations (mostly in Mathematica, no long writing of code).

What would be topics of interest for students in which they can do a project?

There is a broad range of topics to choose from. I have supervised projects on all kinds of aspects of symmetry and conservation laws, quantum mechanics, quantum field theory, finite temperature field theory, beyond the Standard Model physics, like Grand Unified Theories, and some more mathematical topics, such as exceptional points and semi-classical methods. Students are welcome to suggest a topic of their interest in theoretical or mathematical physics.

What courses are related to your research field?

Quantum Physics 2, Relativistic Quantum Mechancis, Symmetry in Physics, Lie Groups in physics, Quantum Field Theory, Elementary Particles

What can students learn when doing a project in your research group?

Fundamental aspects of physics, in particular in theoretical particle or high- energy physics and mathematical physics, but sometimes also in quantum optics or condensed matter physics.

Contact information

Daniël Boer: d.boer@rug.nl

Theoretical and Computational Chemistry

What is the topic of your research group?

In our group we develop and apply hybrid quantum/classical methods to study light-induced processes and quantum effects in biomolecules and novel materials.

What can students expect to do when doing a project in your group?

• Perform calculations using Q-Chem, one of the world’s leading quantum chemistry software.
• Perform simulations using Gromacs, one of the world’s leading molecular dynamics.
• Work with various visualization and analyzes tools such as IQmol and VMD.
• Write their own computer code and join the method development team.
• Run simulations on large computer clusters.
• Interpret and present their results.

What would be topics of interest for students in which they can do a project?

• Photo-switchable molecular motors
• Singlet fission in molecular solids
• Intermolecular columbic decay
• Proton-coupled electron transfer
• Excited state processed at light-sensitive (bio)molecules
• Basic machine learning and neural network algorithms
• Method development for hybrid quantum/classical excited-state dynamics

What courses are related to your research field?

• Molecular quantum mechanics II
• Topics in Chemistry with Python
• Molecular Dynamics

What can students learn when doing a project in your research group?

• Gain knowledge on various electronic structure methods for ground and excited electronic states.
• Gain knowledge on various photo-processes such as, excited-state electron or proton transfer, excitation energy transfer, photoionization and electron attachment processes.
• Gain experience on quantum mechanics and molecular mechanics softwar.e
• Gain experience on various visualization and analysis tools.
• Gain basic programming and scripting skills.
• Gain experience working with large scale computer facilities.

Contact information

Shirin Faraji: s.s.faraji@rug.nl

Photophysics & OptoElectronics

What is the topic of your research group?

In general our group researches novel materials for solar cells, photodetectors, thermoelectrics, light emitting diodes & neuromorphic microelectronics applications. The materials we work on have in common that they are solution processable. This property holds the promise of cheap production methods with a low energy demand.

What can students expect to do when doing a project in your group?

Perform experiments with state of the art equipment in our laboratories and/or cleanroom. Work on hot research topics in opto-electronics and materials physics.

What would be topics of interest for students in which they can do a project?

• Metal halide perovskites (optical properties, solar cells and light emitting diodes)
• Colloidal semiconducting quantum dots (solar cells and photodetectors)
• Polymer-wrapped single walled carbon nanotubes (Neuromorphic electronics)
• Organic semiconductors (solar cells, thermoelectrics)
• Device modelling

What courses are related to your research field?

Nanophysics, Solid state physics, Preparations of Nanomaterials & Devices, (NS003: Fundamental and functional properties - for top masters), Device Physics.

What can students learn when doing a project in your research group?

How to operate equipment used in the manufacturing steps and testing of semiconducting materials (used for solar cells, photodetectors, transistors, etc) How to work in a small research team (supervised by a PhD student or Postdoc) How to solve technical and conceptual problems

Contact information

Maria Loi: m.a.loi@rug.nl

Optical Spectroscopy of Functional Nanosystems

What is the topic of your research group?

The research in our group focuses on optical spectroscopy and microscopy on organic functional materials that are relevant for nanophotonics and molecular (opto-)electronics applications. Such materials are for instance conjugated polymers and oligomers, small molecules, as well as supramolecular nanostructures based on those molecules. In general, we are interested in the optical and electronic properties of these materials. Specifically, we want to understand how energy flows through such systems, how light propagates within nanostructures, and how we can actively control and manipulate energy flow and / or light propagation. As experimental methods we employ a broad range of (time-resolved) optical spectroscopy and microscopy techniques down to the single-molecule (single-object) level. If required, we combine experiments with numerical modelling.

What can students expect to do when doing a project in your group?

The main task is to perform optical spectroscopy and microscopy experiments using home-built, state-of-the-art equipment. Others tasks are writing code to improve the experiments (e.g. allowing for faster data acquisition) and to optimise data analysis (e.g. fitting optical spectra). Depending on the specific interest, we also offer opportunities to perform numerical modelling of our experiments.

What would be topics of interest for students in which they can do a project?

On our group‘s website (see link below) we have a continuously updated section with potential student projects. Examples are time-resolved optical spectroscopy on single supramolecular nanostructures to resolve the dynamics of excitation energy, in-situ spectroscopy of the formation and disassembly of nanostructures using heating-stages, and Fourier-spectroscopy of nanostructures combining experiment and numerical simulations.

What courses are related to your research field?

Quantum mechanics, structure of matter, nanophysics and nanotechnology, physics of lasers

What can students learn when doing a project in your research group?

• Teamwork
• Operating state-of-the-art equipment for optical spectroscopy and microscopy
• Writing code for controlling experiments and for data analysis
• Numerical simulations

Contact information

Richard Hildner: r.m.hildner@rug.nl
Webpage

Molecular Biophysics

What is the topic of your research group?

Research in the "Molecular Biophysics" group revolves around the understanding of the fundamental design principles of life. We solve intriguing research questions that necessitate the application of advanced biophysical approaches. A selection of our techniques includes atomic force microscopy, fluorescence (confocal, FLIM, FCS, TIRF, smFRET) and super-resolution (PALM, STORM & STED) microscopy, single-molecule detection, all in combination with classical molecular biology techniques and biochemistry. The research interests of the groups covers various aspects of life, including: viral stability and entry, membrane transport and vesicle structure, mechanisms of DNA replication and other molecular machines, method development, spectroscopy of fluorescent dyes and structural biology approaches.

What can students expect to do when doing a project in your group?

Perform experiments with advanced biophysical techniques such as (High speed-)AFM, STED super-resolution microscopy and Optical Tweezers. Depending on the interests and capacities of the students, the project can also involve code writing to optimise experimental and data analysis approaches. We have a lively, interactive group where the group members help each other a lot and also socially interact frequently, both in the lab as well as outside the lab. This stimulating, collaborative environment is very important for successful projects and is highly stimulated by the group leaders. All in all you will be able to perform state-of-the-art biophysics research in a stimulating and productive environment.

What would be topics of interest for students in which they can do a project?

• Protein-DNA interaction dynamics
• Real-time virus self-assembly
• Live cell super-resolution imaging
• Mechanics of artificial and naturel nanoparticles
• Vesicle and liposome structure and dynamics

What courses are related to your research field?

Medical Physics and Biophysics, Nanophysics, Molecular Biophysics, Modelling Life, Biophysical imaging & Manipulation techniques, Characterisation of Nanomaterials

What can students learn when doing a project in your research group?

To operate state-of-the-art microscopy equipment. To address and solve challenging problems in physics. To perform team work in an academic research environment. To gain experience in programming and scripting skills.

Contact information

Wouter Roos: w.h.roos@rug.nl
Webpage

Environmental Physics | Dee Group

Please note that there is no predefined research question or project proposal. Thesis topics will be explored and developed together with the students under supervision.

Research Group: Cosmogenic Isotopes and Environmental Research

What is the topic of your research group?

Cosmogenic isotope production (especially carbon-14) and the history of solar activity (Grand Solar Minima; extreme solar storms). I also work on 14C dating (of volcanic eruptions and other environmental and climate related events) and more recently d18O records in tree rings for dating and climatic reconstruction. I also work on determining the rates of carbon sequestration by peatlands (particularly in the Netherlands).

What can students expect to do when doing a project in your group?

They will doubtless obtain environmental samples such as tree rings of known age or a core of peat material. They usually spend about 2 weeks in a wet-chemistry laboratory preparing samples for analysis. Then they get back a lot of data that they have to analyse and interpret.

What could be topics of interest for students in which they can do a project?

Solar activity over time. Solar storms. The impact of past volcanic events on the climate. The rate of natural carbon storage by peatlands.

What courses are related to your research field?

Introduction to Environmental Science. Climate Systems and Atmosphere.

What can students learn when doing a project in your research group?

How the Earth naturally encodes records of the climate and solar activity. How to prepare samples for isotope analysis. Accelerator mass spectrometry.

Contact: Michael Dee m.w.dee@rug.nl

Computational Quantum Materials | Sławińska Group

Research Group: Computational Quantum Materials

What is the topic of your research group?

My research group works on computational quantum materials, with a particular focus on spintronics, spin-orbit coupling phenomena, topological materials, low-dimensional systems, and unconventional magnetic materials such as altermagnets. We use first-principles electronic structure methods to understand how the symmetry and electronic properties of materials determine their functionalities relevant for future electronic and spintronic technologies.

What can students expect to do when doing a project in your group?

Students working in the group can expect a combination of computational work, data analysis and literature research. Depending on the project, students may learn how to perform electronic structure calculations, analyze band structures and spin textures, or study charge-to-spin conversion and related phenomena. Projects are typically adapted to the student’s background and interests.

What could be topics of interest for students in which they can do a project?

Possible thesis topics include spin-orbit phenomena in low-symmetry materials, spin textures and charge-to-spin conversion, topological phases in two-dimensional systems, altermagnetism, chiral materials, and computational design of materials for spintronics. Both more fundamental and more application-oriented projects are possible.

What courses are related to your research field?

Relevant courses include Quantum Mechanics, Solid State Physics, Computational Physics, Computational Methods, and courses related to condensed matter theory and materials physics.

What can students learn when doing a project in your research group?

Students can gain experience in computational materials science, scientific programming, electronic structure theory, and modern condensed matter physics, as well as develop independent research and scientific communication skills.

Suitable students:

The topics are mainly intended for MSc students, although selected projects may also be suitable for motivated BSc students. Bachelor students topics are always closely related to ongoing project of a daily supervisor (PhD student or postdoc)

Contact: Jagoda Sławińska jagoda.slawinska@rug.nl

Solid-state NMR | Van der Wel Group

Research Group: Solid-state NMR (ZIAM)

PI: Patrick van der Wel

What is the topic of your research group?

Our group specializes in nuclear magnetic resonance (NMR) spectroscopy applied to solid or semi-sold samples. We use ssNMR to determine atomic-level structure and dynamics in diverse types of (nano)materials, with an emphasis on biological topics. For instance, a big part of our work is on studies of aggregated proteins that are relevant to diseases, including Huntington’s disease, where we use ssNMR to determine the structure of the nanometer sized aggregates. We apply ssNMR methods also to polysaccharides, nanoparticles, hydrogels, as well as protein—lipid complexes, where we are often interested in studying surface characteristics.

What can students expect to do when doing a project in your group?

We have diverse types of projects for BSc and MSc students, which vary over time. One theme is to get involved in the design and modeling of NMR pulse sequences, which we use to probe unique atomic level details when it comes to structure and dynamics. Alternatively, a more biophysical project can contribute to our studies of protein aggregates or other biomolecules. So, there can be a combination of computational and experimental work.

What could be topics of interest for students in which they can do a project?

New NMR methods for probing structures (dihedral angles), or dynamics/surface features, via numerical simulations. Protein aggregation in disease: aggregation mechanisms, inhibitors, structural analysis. Polysaccharide hydrogels: solvent-matrix interactions, NMR analysis. Materials science: collaborative projects on nanomaterials.

What courses are related to your research field?

Within Physics: molecular biophysics, quantum experiments. (NB. There is limited coverage of NMR spectroscopy in physics BSc). Outside physics: Spectroscopy, Imaging (for LS&T); Surface Characterization (BME BSc).

What can students learn when doing a project in your research group?

Principles and applications of advanced ssNMR; biophysics of protein aggregation; numerical simulations of (NMR) spectroscopy experiments; advanced data analysis; structural analysis of materials and biological samples; physical chemistry/biochemistry (wet lab) work.

Contact: Patrick van der Wel p.ca.van.der.wel@rug.nl

Website: https://www.vanderwellab.org

Atomic and Molecular Physics | Willmann Group (MEPA)

Thesis Project: Precision Measurements in Atomic and Molecular Physics and the Connection to the Standard Model of Particle Physics

Atoms, molecules and photons are quantum sensors which can be used to determine parameters of the Standard Model of Particle Physics. We are designing, building, executing and analyzing experiments which exploit these fundamental quantum sensors. This work requires a combination of a good understanding of physics on an experimental or theoretical level and the ambition to build an unique experiment. We work in collaboration of a number of people from junior to senor level.

What can students expect to do when doing a project in your group?

You will be integrated in a group and will work together with them. The work can be experimental, conceptual in design of experiments, doing measurements and analysis, providing a solid theoretical framework of the experiments and formulating conclusions.

What would be topics of interest for students in which they can do a project?

The topics for Bachelor research will be matched to the needs of the current activities, which provides for a good integration in an group. Master research topics will provide more freedom in the selection and are best discussed with me. Please contact me by email.

What courses are related to your research field?

A solid physics education. No specific courses are required.

What can students learn when doing a project in your research group?

You will learn the discussion of physics topics, technical skills required for building experiments, operation of advanced equipment, and the description of the work in scientific language.

Contact: Lorenz Willmann l.willmann@rug.nl

Website: MEPA – Research

Mechanical, Acoustic, and Elastic Metamaterials | Metamechanics

Research Group: Mechanical, Acoustic, and Elastic Metamaterials

What is the topic of your research group?

Two-fold: (1) we study fundamental relations between material and its structure, with the goal of manipulating the mechanical, acoustic, and dynamic properties of materials in predefined ways; (2) we develop metamaterials with specific physical behavior for robotics, medicine, fluid-flow control, and underwater applications.

What can students expect to do when doing a project in your group?

Engineering the structure of metamaterials using numerical simulations and experimental tests, and additive manufacturing (FDM, SLA, FFF) of prototypes, hands-on activities with mechanical, acoustic, and dynamic characterization setups (universal testing machine, impedance tube, water tank, laser Doppler vibrometer, digital image correlation, robotic-arm manipulation, etc.)

What could be topics of interest for students in which they can do a project?

• Smart implants and stents;
• Shape-adaptive, self-recovering metamaterials;
• Metamaterials enabling frequency shift;
• Temperature-controlled metamaterials;
• Metamaterials for fluid flow control;
• Metamaterials for underwater applications;
• Acoustic metamaterials for sound manipulation.

What courses are related to your research field?

Composites and Metamaterials

What can students learn when doing a project in your research group?

Designing and manufacturing metamaterials; Additive Manufacturing techniques; Finite-element simulations; hands-on experience in mechanical characterization of materials and structures; developing test setups and setting up lab-scale experiments.

Contact: Anastasiia Krushynska (a.o.krushynska@rug.nl)

Website: www.metamechanics.net