Structural Biophysics and Soft Matter

Funding Partners

CoNeXT

CoNeXT is a University of Copenhagen interfaculty collaborative project to develop and use the full potential of the new neutron and X-ray research infrastructures close to Copenhagen University. The project is supported for the period 2013-2016 through the UCPH2016 programme of Excellence. The CoNeXT acronym stands for Copenhagen University Neutron and X-ray Techniques.

The CoNeXT project was initiated because of the neutron and X-ray synchrotron research infrastructures presently available, or under development, in Lund, Sweden and Hamburg, Germany: ESS, MAX IV, Petra III and the European XFEL. The aim of the project is to ensure that UCPH will be ready to harness the full potential of these new neutron and X-ray sources and act as a portal for Danish and North European Industries to use these unique research fascilities.

For further information, please see the UCPH CoNeXT website.

Synergy

SYNERGY is a project funded by the Novo Nordisk Foundation Interdisciplinary Synergy Programme with the aim to explore the synergistic protein-membrane co-structural interplay as a new avenue for treatment of disease. It establishes a unique experimental platform with a highly interdisciplinary focus on structure, function and dynamics, in vitro and in a cellular context, investigating a virtually unexplored area of macro-molecular relationships between selected membrane proteins and the lipid bilayer.

The challenges of the SYNERGY endeavor require competences in pharmaceutical sciences, structural biology, lipid membrane physics, biophysics, biochemistry, spectroscopy, cell and cancer biology and signaling. The core group, consisting of Profs. Birthe B. Kragelund (main applicant), Lise Arleth, Stine F. Pedersen and Assoc. Prof. Bente Vestergaard, jointly cover these, and bring together three departments at UCPH.

The Arleth Group will contribute to the SYNERGY Programme with knowledge of SAXS and SANS, and structural investigation of Tissue Factor, and the associated complex through the use of in-house-developed nanodisc technology.

For further information, please see the UCPH SYNERGY website.

Brainstruc

BRAINSTRUC is a Lundbeck Foundation initiative that aims to understand the molecular basis of selected brain functions and diseases. The initiative unites five strong research groups from five different fields and two universities (UCPH and Århus University). The consortium is focusing on two distinct goals: To develop new, and improve existing, methods for structural biology data collection and interpretation. Secondly, to investigate structural aspects of select biomolecular systems which are central to neuronal signaling, inflammation, and disease.

The initiative is tailored to exploit the unique possibilities surfacing with the construction of the European Spallation Source (ESS) and MAX-IV in Lund and XFEL in Hamburg.

The Arleth group will focus on the development of new experimental strategies for obtaining time-resolved structural data on the dynamics of proteins, and improving methods for data analysis for deconvoluting data from an ensemble of structural states.

For further information, please see the UCPH BRAINSTRUC website.

Software Development

Software for analysis and modelling of small-angle scattering data of biological molecules and dispersions of nanocrystals has been developed in the group. All programs are open source, and the links to major programs can be found below.

Most programs can be found at our github repository:
https://github.com/Niels-Bohr-Institute-XNS-StructBiophys

If you use the software in your work, please cite the relevant publications.

• WillItFit - An analysis tool for refining structural models from small-angle scattering data.
• BayesFit - An analysis tool using a Bayesian method to analyze the structure of macromolecules from small-angle scattering data.
• CaPP - A tool that can calculate the pair distance distribution function (PDDF) p(r) from a given PDB structure and add dummy water molecules (hydration layer).
• XNDiff - A software to analyze small-angle X-ray and neutron scattering patterns of nanocrystal dispersions.

Small-angle X-ray and neutron scattering can be used for studying structures in many industrial materials. If you think that it might be relevant for your company, feel free to contact us for an informal discussion or a test experiment. Our mission is to use these powerful small-angle scattering techniques to solve the real problems that companies encounter.

We have worked together with a variety of companies in a wide range of industries since 2013 through two different projects:

NXUS was a pilot project promoting industrial use of X-rays and neutrons through collaborations with university scientists. It gave the opportunity for members of industry to have their samples investigated using advanced X-ray and neutron scattering techniques.

Following the success of the NXUS project, it was continued in the framework of the LINX project which was launched in 2016.

Below, we provide some information about previous projects that we have performed.

Industry Case Studies (LINX)

Novo Nordisk
SAXS Analysis of Protein-Based drugs
Project Summary

Alvotec
Verifying the similarity of monoclonal antibodies
Project Summary

Biomodics
Interpenetrating polymer networks for drug delivery
Project Summary

Rockwool
Biobased binders for stone wool
Project Summary

Einar Willumsen
Stabilizing emulsions for beverages
Project Summary

Grundfos
Liquid crystalline polymers for protecting sensitive equipment
Project Summary

Biomodics
Micrometer structure of interpenetrating polymer networks
Project Summary

TetraPak
X-ray scattering from thin polymer layers
Project Summary

Industry Case Studies (NXUS)

Aquaporin
Revolutionizing water purification through biotechnology
Project Summary

Arla
Revealing the consequences of processing milk
Project Summary

Du Pont
Adding value and stability to fermented milk drinks
Project Summary

Ferring Pharmaceuticals
Controlling the stability of pharmaceuticals
Project Summary

Gubra
Revealing peptide structure-function relationship
Project Summary

Haldor Topsøe
Speeding up catalysis
Project Summary

Novo Nordisk
Improving the stability of protein based medicine
Project Summary

Novozymes
New angles on understanding the use of enzymes
Project Summary

PPG
Watching paint dry
Project Summary

Rigshospitalet
Stopping microorganism invasions
Project Summary

Symphogen
On the road to effectively treating cancer
Project Summary

Former group members listed alphabetically

Martin Nors Pedersen

Post-doctoral researcher

Martin obtained his PhD in 2015 from the Department of Drug Design and Pharmacology at University of Copenhagen. The main focus of the PhD was investigating transiently formed oligomeric species of alpha-synuclein either on or off pathway to the fibrillar species well known from Parkinson’s disease. After finishing his PhD, he went on to work as a beamline postdoc at the European Synchrotron Radiation Facility (ESRF). At ESRF he gained valuable experience with both pump-probe and stopped-flow techniques for time-resolved experiments with X-rays.

Martin’s main interest is developing methods, both experimentally and in data analysis, to investigate the underlying nature of protein-protein and protein-ligand interactions. Time-resolved experiments (pump-probe, stopped-flow and continuous-flow) are key in this pursuit, and one of his main foci in the group is to make use of microfluidic chips for time-resolved experiments. Martin’s work is funded by the BRAINSTRUC project.
Contact: martinnors (at) nbi.ku.dk
ORCID: 0000-0001-6975-5071

Martin Schmiele

Post-doctoral researcher

Martin finished his diploma thesis in physics at the Friedrich-Schiller-University in Jena in 2009 in the at that time emerging field of transformation optics. During his PhD in Tobias Unruh's work group at the FRM-II / Technical University of Munich (2009-11), and later on at Friedrich-Alexander-University Erlangen-Nuremberg (2011-15), he studied structures in lipid soft-matter dispersions by small-angle X-ray and neutron scattering, wide-angle X-ray scattering, differential scanning calorimetry and dynamic light scattering. He used the same techniques to assist other researchers in their studies on liquid crystals, polymers and porous materials. Now he is working as a postdoc on the LINX project to analyze nanostructures with small-angle scattering in products from various Danish companies.
Contact: martin.schmiele (at) nbi.ku.dk
ORCID: 0000-0001-6973-3155

Andreas Haahr Larsen

Post-doctoral researcher

Andreas obtained his PhD in physics at the Niels Bohr Institute, University of Copenhagen (2016). Andreas' PhD was part of the CoNeXT project, where he was mainly working with small-angle X-ray and neutron (SAS) experiments at large-scale facilities - from design to data analysis. His main interest lies in development of analytical tools for obtaining structural information on biomolecules with SAS and complementary techniques, molecular dynamics simulations in particular.
Contact: andreas.larsen (at) nbi.ku.dk
ORCID: 0000-0002-2230-2654

Søren Roi Midtgaard

Post-doctoral researcher

Søren Roi Midtgaard is a post doctoral researcher at the Niels Bohr Institute at University of Copenhagen, Denmark. After undergraduate studies in nanoscience at University of Aarhus, Denmark Søren moved to Copenhagen to perform doctoral studies at the department of Chemistry where he was awarded the PhD degree in 2013.
Søren’s main interest lies in the structural understanding of biological processes, which after initial projects centered around NMR and crystallography has led to heavy use of small-angle scattering. As especially small-angle neutron scattering (SANS) is currently under rapid development, a desire to exploit these possibilities to the fullest has led to involvement in numerous industrial and scientific collaborations.
Contact: soromi (at) nbi.ku.dk
ORCID: 0000-0001-6694-0626

Martin Cramer Pedersen

Post-doctoral researcher

Coming from a background in theoretical physics and applied mathematics, Martin's research focuses on the theory and application of scattering methods; in particular in the context of structural biology as well as colloid and polymer science. He received his Ph.D. in 2014 from the Niels Bohr Institute and spent the following two years at the Department of Applied Mathematics at the Australian National University. His interests comprise high-performance computing, Bayesian statistics, and the structure and function of various biophysical systems as well as differential geometry and topology and the mathematical and technical aspects of scattering - in particular solution-based small-angle scattering. Martin's work is funded by the Synergy- and the BRAINSTRUC-projects.
Contact: mcpe (at) nbi.ku.dk
ORCID: 0000-0002-8982-7615

Nicholas Skar-Gislinge

Post-doctoral researcher

Nicholas is a post-doctoral researcher within the LINX and NXUS projects. He has a PhD in biophysics from the Niels Bohr institute from 2014, where he investigated the use of nanodiscs as a tool for low resolution structural studies of membrane proteins. From 2013 to 2015 he was awarded a novo STAR fellowship at department of formulation and biophysics at Novo Nordisk A/S and physical chemistry at Lund University. In 2015, he was a post-doctoral researcher at physical chemistry at Lund University.
Nicholas academic interests revolves around studying protein interactions using scattering methods, and applying scattering methods to the challenges found in industry.
Contact: nicholas.skar-gislinge (at) nbi.ku.dk
ORCID: 0000-0003-0549-8074

Viktor L. Holm

Former MSc student

Viktor L. Holm is a recent master student from the group. Viktors has a BSc in nanoscience (2015) and a MSc in Biophysics (2017) from the Niels Bohr Institute at University of Copenhagen.
Viktors research profile is in solution small-angle scattering techniques, simulation and modelling of proteins based and scattering data, and biochemical techniques for protein sample preparation.
Contact: jrk732 (at) alumni.ku.dk

Unsolicited applications:

Are more than welcome!
Do not hesitate to contact us if you are a student and interested in:

• any of our current research projects
• the research methods we specialize in
• both of the above

We can almost certainly define a Bachelors or Masters project that fits your interest. See Group members page for contact information.

Available projects:

• Industry research projects (Student / BSc / MSc projects)
• Studying the structure of proteins and protein complexes by solution small-angle X-ray scattering (MSc project)
• Investigation of interpenetrating polymer networks for drug delivery under mechanical deformation by Small-Angle X-ray Scattering (MSc project)
• Parallel computing for a faster analysis of small-angle scattering patterns of macromolecules in dispersion (MSc project)

Erik Stieper Brok, Research Coordinator
Phone: +45 353-37590
E-mail: e.brok@nbi.ku.dk

Niels Bohr Institute
University of Copenhagen
Universitetsparken 5, 3.309
2100 København Ø
Denmark

Office location

H.C. Ørsted Institute, Building 3 (D), Room 309 (3rd floor)

Map (clickable)