Experimental Biophysics & Optical Manipulation
We employ methods from physical chemistry, nanoscience and advanced imaging to investigate biological specimens ranging in size from molecular scales to macroscopic embryos and cancer spheroids.
We are a group of enthusiastic and creative scientists interested in understanding physical properties of biological systems at the single molecule to whole cell level.
The group has a strong interdisciplinary profile with a number of close collaborators in biology, nanoscience, medicine, chemistry and theory (see staff section for more details).
We have dual optical trapping platform combined with a confocal microscope which allows cutting edge experiments to be performed. Also, we have super resolution microscopy based on the STORM method. For imaging larger specimens, like embryos, we have light sheet microscopy which facilitates fast and low photo-toxicity imaging. Microscopic physical properties of cells are quantified using an optical trap as a force sensor/actuator whereas whole cell properties can be explored using the cell deformation cytometry.
Additionally, we have an extensive expertise in working with model membrane systems and also isolated plasma membrane systems containing the membrane proteins from the cell.
We are located at the Niels Bohr Institute at the University of Copenhagen
Living cells have interesting mechanical properties and behave like active materials. Investigation of these is done by advanced optical microscopy combined with optical manipulation. Due to the immense complexity of living cells we also study the biophysics of reconstituted model systems which are simple systems containing only a few cellular components. Major areas of research include the biophysical properties of the cell surface and viscoelastic properties of the cellular cytoplasm. Development of advanced optical techniques, like optical trapping and nanoscale thermoplasmonics, allows us to perform state-of-the art experiments to answer scientific questions in biophysics.
Tumor elimination We investigate biophysical properties of a number of biological systems ranging from single stem cells to invasive cancer cells. The cells are investigated as single cells, but also in their natural complex environment where they can grow and interact freely in three dimensions. The core aspect of our research deals with how the physics of the cell affects or controls diverse biological functions. The main research areas include mechanical investigations of the cell surface, these include the cell membrane, and associated membrane proteins, as well as viscoelastic properties of the cell interior.
The biological complexity inherent in most living systems makes it difficult to examine the function of single components in a biological system. Therefore, we invest significant efforts into the development of minimal model systems which allow us to investigate single proteins in cell-like systems that contain only few biological components. Moreover, we also develop and test cellular model systems like 'organoids' to understand how tumors grow and develop.
The building of advanced equipment has been an integral part of the research group and has provided the platform for a number of state-of-the-art experiments which have been conducted to address fundamental scientific questions in both nanoscience and biophysics.
BIOPHYSICS OF THE CELL SURFACE
In this group of Projects our aim is to understand how cells dynamically organize their cell surface and perform all the functions associated with the surface of the cell. Examples include remodeling of the plasma membrane, cell - cell interactions, lateral redistribution of proteins in the membrane and membrane repair. We study these physical phenomena like filopodia dynamics, cell surface repair by annexins, membrane curvature sensing by proteins, lipid order in plasma membranes and resulting protein segregation into distinct lipid phases. To explore these phenomena we use confocal imaging, super resolution (STORM), optical trapping, plasmonic heating and membrane manipulation tools.
Specific questions include:
What kind of dynamics do filopodia exhibit?
The cell surface contains mechanically active antennae-like structures called filopodia. Our lab has contributed significantly to the understanding of the biophysical properties of these structures. We have found that they have the ability to rotate, pull and form helical buckles – all at the same time. These properties have been measured quantitatively using optical trapping in conjunction with 3D confocal imaging (Lejinse et al. PNAS, 2015).
Funding: Villum Foundation (2012-2015)
How do cells cope with plasma membrane ruptures?
Currently, we are exploring the mechanism of plasma membrane repair in living cells. Cells are punctured using thermoplasmonics which allows nanoscopic holes to be formed in the cell membrane. Several annexins are involved in the cell repair and we are doing parallel imaging and puncturing to reveal the mechanism of the cell surface repair machinery. In parallel we study the biophysical properties (curvature affinity and mechanical effects of protein binding) of the same proteins in models systems like GUVs and plasma membrane vesicles.
Collaborators: Robert Daniels (FDA), Jesper Nylandsted (Kræftens Bekæmpelse), Adam Cohen Simonsen (SDU), Himanshu Khandelia (SDU)
Funding: Novonordisk synergy grant (2019-2022).
How do proteins affect membrane mechanics?
Proteins which sense and generate membrane curvature are often found to mechanically stiffen membranes. We have studied the mechanical effects of proteins bound within nanotubes (Ramesh et al. Sci. Rep., 2013 & Barooji et al. Sci. Rep., 2016). The mechanical effect is typically correlated with the ability of the protein to oligomerize.
Do proteins sense lipid order and membrane curvature?
Both peripheral and integral proteins are found to sense the lipid ordering in plasma membranes. Influenza virus protein Neuraminidase was found to sort exclusively into lipid disordered domains in isolated plasma membranes (Moreno et al. ACS Nano, 2019).
Membrane curvature also constitutes another mechanism of lateral organization of proteins. We have shown that F-BAR (Ramesh et al. Sci. Rep., 2013), I-BAR (Barooji et al. Sci. Rep., 2016), Annexin V (Moreno et al. ACS Nano, 2019) and GPCR (Rosholm et al. Nat. Chem. Biol., 2017) effectively sense membrane curvatures and the sensing correlates with the molecular shape of the protein.
Collaborators: Robert Daniels (FDA), Jesper Nylandsted (Kræftens Bekæmpelse), Dimitrios Stamou (Nanoscience Center, KU), Szabolcs Semsey (SNIRP BIOME)
Funding: Villum Foundation (2012-2015) and Sapere Aude DFF (2015-2019).
Can the plasma membrane of living cell be isolated with all its content intact?
During recent years we have focused on development of a method for isolation of the plasma membrane from living cells. This method is highly attractive since it allows us to investigate the plasma membrane proteins in their natural membrane environment, and in absence of the cellular skeleton and other organelles. The isolated membrane forms a spherical vesicle containing the proteins from the mother cell and also internal cytosolic proteins. Importantly, these proteins preserve their correct orientation in the membrane which is in striking contrast to reconstitution of proteins in membranes. This work was published in ACS Nano in 2019 (Moreno et al.) where we showed the feasibility of using these vesicles for optical manipulations and for studying lipid phase behaviors.
Collaborators: Robert Daniels (Food and Drug Administration, USA), Jesper Nylandsted (Kræftens Bekæmpelse), Szabolcs Semsey (SNIRP BIOME).Funding: DFF Sapere Aude (2015-2019) and Nonordisk synergy grant (2019-2022).
Development of optical tools for manipulation of the cell surface
Optical trapping of nanostructures
Our group has a long history of quantitative characterization of the optical trapping of nanostructures and micro particles. Trapping potentials and heating effects have been extensively characterized and published in numerous high impact journals (Chemical Reviews, ACS Nano, Nano Letters, Nanoscale, Scientific Reports).
Thermoplasmonics for manipulation of membranes and cells
The ability of nanostructures to heat upon irradiation using biologically harmless near infrared light, has opened up an array of new possibilities to manipulate soft matter and living cells. We exploit the local heating generated in optically trapped nanostructures for nanopuncturing of cells, local melting of membranes (Andersen et al. Soft Matter, 2014) and fusion of membranes (Rørvig-Lund et al. Nano Lett., 2015) and cells (Bahadori et al. Nano Res., 2017 & Bahadori et al., ROPP, 2018) to mention a few examples, see also (Jauffred et al. Chem. Rev., 2019).
Optical extraction of nanotubes from plasma membrane vesicles
High membrane curvatures are generated by optical extraction of nanotubes from cells and vesicles. This has allowed us to investigate the membrane curvature affinity of G-protein coupled receptor (Rosholm et al. Nat. Chem. Biol., 2017), BAR domain proteins (Ramesh et al. Sci. Rep., 2013, Barooji et al. Sci. Rep., 2016), several annexins and the virus protein Neuraminidase (Moreno et al. ACS Nano, 2019).
The membrane nanotubes also allow investigation of protein and lipid mobility by combing the optical trapping with fluorescence recovery after photobleaching (FRAP) experiments.
Collaborators: Robert Daniels (FDA), Jesper Nylandsted (Kræftens Bekæmpelse), Dimitrios Stamou (Nanosceince Center, KU)
Stem cell decision making
Stem cells are un-differentiated cells with the potential to differentiate into any specialized cell of an organism.
There does not yet exist a complete understanding of how biological, chemical and physical factors act in concerto to determine the destiny of a stem cell. The novel StemPhys center joins forces of stem cell biologists from DanStem and theoretical and experimental physics from the Niels Bohr Institute with the goal of significantly progressing our quantitative understanding of stem cell commitment.
StemPhys combines unique stem cell lines with expertise in modelling, bio-imaging, and mechanical manipulation of living matter. One goal is to control the differentiation of stem cells and produce long-living functional cells.
Our research on pancreatic progenitors, with the capacity to generate beta cells producing insulin, could produce new prospects for stem-cell based treatment of diabetes, and our work on liver progenitors could enhance drug development by providing hepatocytes for drug screening. Long-term goals include the development of methods to possibly reverse differentiation of stem cells.
StemPhys is a Danish National Research Foundation Center of Excellence (2015-2021).
Irradiated metallic nanoparticles absorb part of the incoming laser light and the absorbed energy will be released in the surroundings as heat. In LANTERN we utilize this effect to develop a novel nanoparticle based cancer therapy.
Such plasmonic nanoparticles are extremely efficient light-to-heat converters and if a metallic nanoparticle is resonant, or close to resonant with the incoming light, the temperature elevation can easily reach hundreds of degrees Celsius.
Within the project we both develop a laser activated assay for targeted drug delivery and a laser activated photo-thermal treatment of cancer, both of these strategies being based on nanoparticles and being usable in concerto. The effects of the therapy are evaluated by PET imaging. The project is a collaboration between physicists at the NBI and molecular imaging and cancer experts at Panum / Rigshospitalet.
Supported by a Synergy Grant from the Novo Nordisk Foundation (2015-2018).
Force mapping during cancer cell division and invasion
The cells of living tissues are constantly exposed to forces, they experience tension, compression, pressure and shear stress. Also, cells can themselves grow and divide, change shape and actively move, hence exerting forces on their microenvironment.
In this project, we focus on the mechanics of cancer cell invasion, both in terms of how cancer cells differ from non-cancerous cells, and the mechanical interaction between cancer cells and their microenvironment. Cancer cells are deadly once they cross the endothelial barrier of the blood stream, invade into local and distant tissue, and proliferate in vital organs.
Thus, we will focus on mapping the mechanical forces and dynamics associated with these processes to better understand the mechanisms and uncover potential avenues of inhibition. This project is a collaboration between physicists from NBI and cancer cell biologists from BRIC, KU.
Supported by a Research Project 2 Grant from the Danish Research Councils (2015-2018).
Vi har mange forskellige projekter for Kandidat studerende og også lejlighedsvis projekter for bachelor studerende. For yderligere info kontakt Poul M. Bendix (Bendix@nbi.ku.dk) eller Liselotte Jauffred (firstname.lastname@example.org).
Cellular repair system investigated by laser based nano-surgery
When cells migrate in the body they often experience membrane ruptures which results in excessive calcium flowing into the cell. This can be lethal unless the membrane is sealed within milliseconds. Cells have a built-in surface repair kit which is activated by calcium influx and hence can allow the cell to self-heal within seconds after injury. Cancer cells are extremely efficient in repairing their surface since they have an increased expression of various annexin proteins which are thought to be the major proteins involved in the membrane repair.
The project will involve testing the membrane repair system in cells by using thermoplasmonics to inflict a nanoscopic hole in the membrane. This will be done by irradiating a plasmonic gold nanostructure placed on the surface of the cell. Confocal microscopy and super-resolution microscopy will be used to monitor the recruitment of various annexins which are labeled with fluorescent proteins. The overall aims are to i) investigate whether invasive cancer cells are more efficient in dealing with thermoplasmonic ruptures than non-invasive cells ii) investigate the role of several different annexins in the repair process including other proteins like ESCRT and actin.
The project is a collaboration with Kræftens Bekæmpelse samt Syddansk Universitet.
Contact: Poul Martin Bendix, email@example.com
Patterning in large bacterial communities
In nature, bacteria actively search for a surface to form larger communities, i.e., biofilm, with extended cooperativity and defense. We know that sectors with low genetic diversity form within the colony, even among cells of similar fitness. This self-organization of microbial cell communities is the result of genetic drift in complex interplay with evolution, competition, and cooperation.
We offer various projects to explore pattern formation by growing bacteria both in vivo and in silico. We believe the close interplay between theory and experiments will provide a more complete understanding of cooperation and competition among cells in larger communities. We aim to point out general features of growth pattern, which can be generalized in wider class of systems. In the long term, we may draw parallels to mammalian cell systems, where patterning is crucial for example in embryonic development.
Possible subprojects include:
The relation between the individual cell shape and the colony shape
This project combines theory and experiments depending on your interests. Experimentally, the project can include bacterial cell culture, colony growth, and advanced fluorescence microscopy. Theoretically, we plan to first simulate an individual cell-based model where the particles grow, divide, and interact through mechanical force. Depending on the development of the project, simplified lattice models or partial differential equation-based models can also be used.
Supervisors: Liselotte Jauffred & Namiko Mitarai
Joshua Brickmann, Danstem, University of Copenhagen
Jesper Nylandsted, Kræftensbekæmpelse
Elke Ober, Danstem, University of Copenhagen
Janine Erler, Biotech & Research Innovation Center (BRIC) University of Copenhagen
Robert Daniels, Dood and Drug Administration, the States
Karen Martinez, University of Copenhagen
Adam Cohen Simonsen, University of Southern Denmark
Himanshu Khandelia, University of Southern Denmark
Weria Pezeshkian, University of Groningen
Christine Selhuber-Unkel, Institute for Materials Science, Kiel University
Petra Hamerlik, Brain Tumor Biology, Danish Cancer Society Research Center
Kirstine Berg Sørensen, Biophysics, Danish Technical University
Ralf Metzler, Technical University of Munich
Karina K. Sand, Molecular Geobiology Group, University of Copenhagen
Henrik Siegumfeldt, Microbology and Fermentation, Department of Food Science, University of Copenhagen
StemPhys: Danish National Research Foundation Center for Stem Cell Decision Making 60.000.000 Dkr granted by Danish National Research Foundation, 2015-2021. PI: Joshua Brickmann, Danstem. Click HERE to see the homepage of StemPhys.
A multidisciplinary platform for revealing mechanisms of annexin-mediated plasma membrane repair 3.748.705 Dkr granted by The Novo Nordisk Foundation. 2019-2022. Co-applicant: Poul M. Bendix, NBI (PI Jesper Nylandsted, Kræftens Bekæmpelse).
Coupling Celluar Shapes Sapere Aude Grant from Danish Research Councils 7.000.000DKK, 2015-2019. PI: Poul M. Bendix, NBI.
- Lundbeck PhD fellowship (2017-2020), PI Poul M. Bendix
Coming to the Experimental Biophysics with an external grant
The Experimental Biophysics supports researchers' applications to international and Danish public and private funding agencies.
If you come to the group with your own funding, you will become a full member of the team with office space, access to IT and admin support, laboratories, and you are expected to contribute to the scientific and social life in the group.
Examples of agencies funding research in biophysics in Denmark:
Independent Research Fund Denmark | Natural Sciences (FNU) and Medical Sciences (FSS) - public; postdocs, phd's, research groups, mobility
European Research Council (ERC) - international; research groups
European Commission Horizon 2020 - international; postdocs, mobility
Novo Nordisk Foundation - private; postdocs, research groups, mobility
- Lundbeck Foundation - private; postdocs, phd's, research groups, mobility
.. and several others. You may also consider applying for funding from private or national agencies in your home country, and name the Optical Tweezers Group at the Niels Bohr Institute as your host institution.
Contact Group Leader, Assoc. Prof. Poul Martin Bendix, if you are considering applying for external funding.
Please contact us:
- at least 8 weeks in advance of the application deadline in the case of individual post doc stipends and smaller projects (i.e., 1-3 years, under DKK 3M);
- at least 3 months in advance of the application deadline in the case of larger projects.
The group's faculty will review your request to apply. The Niels Bohr Institute may be able to offer some co-funding in the case of larger projects/grants. A needs assessment for equipment may also be conducted, to ensure that the Institute can adequately house your project and the expected personnel associated with it.
If approved, we can provide considerable support for the application process, for example including budget development, text about the host institution, review of application's science case, and contact with the funding agency if needed. The Faculty of Science Research Funding Office at the University of Copenhagen also provides support for applications.
An application budget is developed online using the University's application tool and must be approved by the group leader and the Niels Bohr Institute at least one month before the application deadline. The budget process also facilitates the conversation about possible co-financing from the Institute or Center, laboratory set-up if needed, and any HR issues that need to be addressed.
Information for group members
Group meetings on Wednesdays at 9.00 AM online.
Group meetings are paused July and August as well as throughout January. Participation in the group meetings is mandatory and all scientists interested are also welcome. All questions regarding the group meetings should be addressed to Liselotte Jauffred.
For lab reservations see bottom of the page.
Many group meetings are followed by presentation at 9.15 AM online.
Members of the group will take turns presenting the progression of their projects.
Presentations spring 2021
Presentations Fall 2020
|09.12.20||Signe Mathiasen||Project presentation|
All presentations will be
online until KU opens
Click here to join
Booking of laboratories
We have 3 setups with optical tweezers where two of them are combined with a confocal microscope (Leica SP5). Google Kalender is used for bookings. Password: Ask Poul Martin.
|OT2||Single trap in Leica SP5||nbitweezer2|
|OT3||Single trap, low power||nbitweezer3|
|OT4||Leica SP5 (2014), dual trap||nbitweezer4|
|AcCellerator||Real-Time Deformability Cytometryfirstname.lastname@example.org|
|Olympus||No trap, confocal||otgroupolympus|
|Cell Lab||Flow Hood, incubators||Booking schedule on lab door|
During weekdays reservation slots run from before or after 2 PM. A maximum of 2 active timeslots per week and 4 per 2 weeks is allowed within normal working hours. Please only book two weeks in advance. The setups can be freely used during evenings and weekends.
Internal documents and wiki
The group has a wikipage for experimental protocols and manuals for the different lab equipment.
Contact Poul Martin for username and password.
Poul Martin Bendix,Group leader
Tel: +45 35325251 or +45 61602454
Blegdamsvej 17, DK- 2100 Copenhagen
Ann-Katrine Vransø West, Postdoc & StemPhys Research Coordinator
E-mail (Coordinator): stemphys-coordinator @ nbi.ku.dk
Tel: +45 93509177
News on Biokomplexity and Biophysics
|Search in Name||Search in Title||Search in Job responsibilities|
|Arastoo, Mohammadreza||Research Assistant|
|Bendix, Pól Martin||Associate Professor||Associate Professor, Group Leader|
|Danielsen, Helena Maria Dávidsdóttir||PhD Fellow|
|Farhangibarooji, Younes||Academic Staff|
|Gerganova, Veneta||External Postdoc|
|Jauffred, Liselotte||Associate Professor|
|Leijnse, Natascha||Assistant Professor|
|Moreno Pescador, Guillermo Sergio||Guest Researcher|
|von Borries, Mads Kasper||PhD Fellow|
|Victoria Thusgaard Ruhoff||MSc student||+45 20300765|
|Alba Garzía Vásquez||MSc email@example.com|
|Paul Rammer||Molecular Biologistfirstname.lastname@example.org|
|Anne Sofie Busk Heitmann||PhD email@example.com|
Experimental Biophysics Lab
We have a number of research facilities which we would also like to use for Research collaboration internationally, Industrial collaboration and Student projects.