Experimental Biophysics & Optical Manipulation

We investigate the physical properties of both living cells and soft matter using an array of optical and micromanipulation approaches including optical tweezers, thermoplasmonics and micromanipulation.

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. 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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 (jauffred@nbi.ku.dk).

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, bendix@nbi.dk


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:

Colony shape

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

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Information for group members

Group meetings on Mondays at 1PM.

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.

For an update on who presents please check the event calendar on the homepage.

Presentations spring 2021

Date Responsible Content
10.02.21 Alba project presentation
24.02.21 Martin project presentation
10.03.21 Guillermo project presentation
17.03.21 Mads project presentation
14.04.21 Mohammad project presentation
28.04.21 Mireia  project presentation
05.05.21 Natascha project presentation
12.05.21 Helena project presenation
19.05.21 Younes CTRAP presentation
02.06.21 Victoria project presentation

Presentations Fall 2020

Date Responsible Content
09.09.20 Mohammad project presentation
16.09.20 Christoffer project presentation
23.09.20 Martin project presentation
30.09.20 Guillermo project presentation
07.10.20 Mads project presentation
14.10.20 Autumn vacation
21.10.20 Helena project presentation
28.10.20 Mireia project presentation
04.11.20 Mathias Project presentation
11.11.20 Melanie project presenation
18.11.20 Paul project presenation
25.11.20 Natascha project presentation
02.12.20 Safia Project presentation
09.12.20 Signe Mathiasen Project presentation

Spring 2020

Date Responsible Content
05.02.20 Mohammad project presentation
19.02.20 Natascha project presentation
26.02.20 Younes project presentation
11.03.20 Christoffer project presentation
18.03.20 KU-closed KU-closed
25.03.20 KU-closed KU-closed
01.04.20 KU-closed KU-closed
08.04.20 Easter Holiday

All presentations will be 

online until KU opens

online platform

ZOOM

Click here to join

ZOOM LINK

15.04.20 Pavlina project presentation
22.04.20 Joshua project presentation
29.04.20
06.05.20 Helena project presentation
13.05.20 Andreas project presentation
20.05.20 Mads project presentation
27.05.20 Liselotte paper
03.06.20 Poul Martin paper

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.

Setup Noter Login navn
OT1 Dual trap nbitweezer1
OT2 Single trap in Leica SP5 nbitweezer2
OT3 Single trap, low power nbitweezer3
OT4 Leica SP5 (2014), dual trap nbitweezer4
AcCellerator Real-Time Deformability Cytometry nbiaccell@gmail.com
Olympus Light-sheet
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.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Staff

Name Title Job responsibilities Image
Search in Name Search in Title Search in Job responsibilities
Arastoo, Mohammadreza Research Assistant Billede af Arastoo, Mohammadreza
Bendix, Pól Martin Associate Professor Associate Professor, Group Leader Billede af Bendix, Pól Martin
Cordero, Mireia PhD Fellow Billede af Cordero, Mireia
Danielsen, Helena Maria Dávidsdóttir PhD Fellow Billede af Danielsen, Helena Maria Dávidsdóttir
Ebrahimi, Samira Guest Researcher Billede af Ebrahimi, Samira
Farhangibarooji, Younes Academic Staff Billede af Farhangibarooji, Younes
Garcia Vazquez, Alba PhD Fellow Billede af Garcia Vazquez, Alba
Grudtsyna, Valeriia PhD Fellow Billede af Grudtsyna, Valeriia
Jauffred, Liselotte Associate Professor Billede af Jauffred, Liselotte
Leijnse, Natascha Assistant Professor Billede af Leijnse, Natascha
Moreno Pescador, Guillermo Sergio Guest Researcher Billede af Moreno Pescador, Guillermo Sergio
Thusgaard Ruhoff, Victoria PhD Student Billede af Thusgaard Ruhoff, Victoria

Master/undergraduate students

Navn Titel E-mail
Malte Slot Lauridsen  MSc student
mvr902@ku.dk

Hazal Polat

 MSc student

hvg644@adm.ku.dk

Christopher Calvin Spenser Anthony  MSc student

rkt450@alumni.ku.dk

Experimental Biophysics Lab

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.

More about our research facilities >>