RESEARCH TOPICS FOR STUDENTS

Anyone interested in the topics we are investigating is welcome in our lab. We will provide you with the necessary reading and guidance. There are no special prerequisites beyond high-school biology, chemistry, physics and maths, and no outstanding skills are required.

Below is a list of various research topics, grouped into several subjects. Some of them are strongly interdisciplinary, and could qualify for more than one subject, so several keywords are given, hinting at the specific points of interest. A short description is also provided for each of the topics.

Certainly, the options are not restricted to the listed topics only. New ideas are constantly emerging, and perhaps you can come up with one of your own that you feel you could investigate in our lab. So, feel free to contact us with your questions and ideas.

RESEARCH TOPICS  [back to the top]

Numerical modeling

• Calculation of electric field distribution inside tumour tissue
  based on numerical finite element models [find out more]
• Numerical model of electrochemotherapy
  of subcutaneous tumors [find out more]
• Numerical model of electrochemotherapy
  of subcutaneous tumors [find out more]

Hardware and software development

• Automatic counting of survived and fluorescent cells
  from the pictures of fluorescent microscopy [find out more]
• USB 2.0 communication [find out more]
• Setting up Embedded Windows CE operation system
  on Mini-ITX motherboards [find out more]
• Basic user interface for Windows CE
  in .NET environment [find out more]
• Sonoporation of cells [find out more]

Electroporation: mechanisms and applications

• The effect of ionic composition of the medium
  on in vitro electrogene transfer [find out more]
• Algorithm for on-line control of cell electroporation [find out more]
• In vitro electroporation of cells using triangular pulses
  for detection of the electroporation threshold [find out more]
• Voltage breakdown measurements of planar lipid bilayer [find out more]
• Formation of planar lipid bilayers from different lipid molecules [find out more]
• Changes in resistivity of lipid bilayer during breakdown [find out more]
• Nanosecond pulses on lipid bilayers [find out more]
• Nanosecond pulses under the microscope [find out more]
• Electroporation of lipid vesicles [find out more]
• The effect of electroporation on cytoskeleton integrity
  in attached cells [find out more]
• Elimination of bacteria with electroporation treatment
  (high voltage pulses) [find out more]
• Ablation by irreversible electroporation [find out more]
• Manipulation of biological cells using dielectrophoresis [find out more]

Electromyography

• Evaluation of fatigue in skeletal muscles during swimming [find out more]
• Multichannel system for surface electromyography [find out more]
• A miniature surface electromyograph [find out more]
• Electromyogram of uterine corpus and cervix [find out more]

Blood flow and tissue oxygenation

• Changes in properties of microcirculation in tumors after treatment  [find out more]
• User interface for computerised acquisition and processing
  of laser Doppler signals  [find out more]

Electrophysiology of cells

• Cell migration in electric field [find out more]

TASK DESCRIPTIONS

CALCULATION OF ELECTRIC FIELD DISTRIBUTION INSIDE TUMOUR TISSUE BASED ON NUMERICAL FINITE ELEMENT MODELS
Electrochemotherapy is an effective antitumor treatment employing locally applied high electric pulses in combination with chemotherapeutic drugs. Electrochemotherapy is based on electroporation, a phenomenon of increase of membrane permeability due to the cell exposure to the electric field. The efficiency of this therapy strongly depends on electric field distribution within treated tissue i.e. tumor tissue. The aim of this study is to optimize the parameters of electric field strength inside tumor tissues of different geometries (such as spherical, elliptic and finally the realistic tumor geometries) by means of computer simulation. The acquired knowledge will be integrated into the web-application designed for training/learning about electrochemotherapy.
Keywords: numerical modeling; electroporation
Contact persons:
Selma Corovic    Phone +386 1 4768 397
Prof. Damijan Miklavcic    Phone +386 1 4768 456
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NUMERICAL MODEL OF ELECTROCHEMOTHERAPY OF SUBCUTANEOUS TUMORS
When electric pulses are applied to a tissue, its conductivity changes (increases), if the electric field is high enough to cause permeabilization. Consequently, when applying pulses to subcutaneous tumors through skin, an increase in skin conductivity causes high enough electric field to move from highly resistive skin to the underlying tumor. A successful permeabilization of tumor cells and a cytostatic drug uptake is thus achieved.
The aim of the study is to make a numerical model of the tissue permeabilization process during the electrochemotherapy of subcutaneous tumors by means of commercial numerical modeling tool COMSOL Multiphysics based on the finite elements method. The data on tissue conductivities can be found in the literature and derived from experiments. Assess the influence of model parameters changes on the output of the model.
Keywords: numerical modeling; electroporation
Contact persons:
Natasa Pavselj    Phone +386 1 4768 120
Prof. Damijan Miklavcic    Phone +386 1 4768 456
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NUMERICAL MODEL OF A PREGNANT WOMAN EXPOSED TO ELECTROMAGNETIC RADIATION
Electromagnetic radiation induces electric currents in biological tissue. Directive 2004/40/EC of the European Parliament and of the council sets limits on the allowed amplitude of electromagnetic field in our environment, however these reference levels were derived for healthy adults and do not necessarily hold for children or pregnant women. The goal of this study is to build a 3D computer model of a pregnant woman from CT images and one or model models of sources of electromagnetic radiation. The values of induced electric currents in the body of the pregnant woman will then be calculated by a finite element software (COMSOL) and the results compared with the reference levels.
Keywords: non-ionizing electromagnetic radiation, numerical modeling
Contact persons:
Anze Zupanic    Phone +386 1 4768 347
Prof. Damijan Miklavcic    Phone +386 1 4768 456
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AUTOMATIC COUNTING OF SURVIVED AND FLUORESCENT CELLS FROM THE PICTURES OF FLUORESCENT MICROSCOPY
Efficiency of electroporation or transfection of cells is determined by fraction of viable cells, fraction of fluorescent cells and cell fluorescence intensity. Manual counting of viable and fluorescent cells and determination of cell fluorescence intensity from the pictures of fluorescent microscopy is a long-term, demanding and subjective work. Computer algorithm could enable a fast and objective counting of viable and fluorescent cells and determination of cell fluorescence intensity from the pictures of fluorescent microscopy. The aim of present research is to find appropriate algorithms and their practical realization. Find out which algorithm with the smallest error counts out viable and fluorescent cells and determines cell fluorescence intensity. Compare the results with manual counting and determination of cell fluorescence intensity.
Keywords: image processing; algorithms
Contact persons:
Matej Rebersek    Phone +386 1 4768 120
Prof. Damijan Miklavcic    Phone +386 1 4768 456
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USB 2.0 COMMUNICATION
For communication between our devices and user interface we usually use RS-232 communication protocol. Since this protocol is too slow for our requirements and the processor which we used for RS-232 communication is out of production we need to develop a new system with faster communication protocol. The aim of present research is to design and make a system, which will enable communication between the existing devices and user interface with communication protocol USB 2.0.
Keywords: hardware; software
Contact persons:
Matej Rebersek    Phone +386 1 4768 120
Prof. Damijan Miklavcic    Phone +386 1 4768 456
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SETTING UP EMBEDDED WINDOWS CE OPERATION SYSTEM ON MINI-ITX MOTHERBOARDS
Compact motherboard Mini-ITX allows simple programming of user interface, because it is based on worldwide PC technology. The aim of present research is to set up abbreviated version of Windows CE operation system on motherboard Mini-ITX. This will allow further development of user interface by writing the applications in .NET. Create USB 2.0 interface for USB2FPGA system (Cesys) and touch screen. Set up the operation system so that it can not be changed by the user.
Keywords: hardware; software
Contact persons:
Matej Rebersek    Phone +386 1 4768 120
Prof. Damijan Miklavcic    Phone +386 1 4768 456
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BASIC USER INTERFACE FOR WINDOWS CE IN .NET ENVIRONMENT
For further development of user interface we first need to develop basic user interface, which will allow sending and receiving of data over USB 2.0 and will show the data on a touch screen. The aim of present research is to develop user interface in .NET for Windows CE, which sends and receives data from USB2FPGA system (Cesys).
Keywords: software
Contact persons:
Matej Rebersek    Phone +386 1 4768 120
Prof. Damijan Miklavcic    Phone +386 1 4768 456
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SONOPORATION OF CELLS
Exposure of biological cells to ultrasound waves cen result in morphological changes of cellular membrane similar to changes induced by application of external electric field. The method is called sonoporation. Biological cells can be subjected to ultrasound in presence or absence of chemotherapeutic molecules. The purpose of this study is to design an ultrasound applicator for sonoporation of cells along with a suitable application chamber for the cells. The study will also include preliminary measurements needed for assessment of effectiveness of sonoporation.
Keywords: hardware; sonoporation
Contact persons:
Karel Flisar    Phone +386 1 4768 444
Prof. Damijan Miklavcic    Phone +386 1 4768 456
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VOLTAGE BREAKDOWN MEASUREMENTS OF PLANAR LIPID BILAYER
Planar lipid bilayer is a simple model of a cell membrane. Planar lipid bilayer breakdown voltage has an important role in study of electroporation in biomedicine and biotechnology. It has been known that breakdown voltage is dependent on lipid membrane composition, ionic bath solution and amplitude and time of electric field exposure. The aim of the study is to determine breakdown voltage of planar lipid bilayer as a function of duration and the shape of the signal.
Keywords: electroporation; lipid bilayers
Contact persons:
Peter Kramar    Phone +386 1 4768 767
Prof. Damijan Miklavcic    Phone +386 1 4768 456
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FORMATION OF PLANAR LIPID BILAYERS FROM DIFFERENT LIPID MOLECULES
Planar lipid bilayer is a simple model of a cell membrane. Usually it is build of lipid molecules of the same kind. But cell membrane, on the other hand, is composed of many different types of lipid molecules. In this study we are going to find out how the composition of planar lipid bilayer affects its properties.
Keywords: electroporation; lipid bilayers
Contact persons:
Peter Kramar    Phone +386 1 4768 767
Prof. Damijan Miklavcic    Phone +386 1 4768 456
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CHANGES IN RESISTIVITY OF LIPID BILAYERS DURING BREAKDOWN
Planar lipid bilayer as a simple model of cell membrane can be described in mathematical form. Measurement of planar lipid bilayer breakdown voltage reveals that current signal follows the planar lipid bilayer conductance. The aim of the study is to write an algorithm that recognizes typical changes in current signal and describe the parallel changes in planar lipid bilayer membrane as well.
Keywords: electroporation; lipid bilayers
Contact persons:
Peter Kramar    Phone +386 1 4768 767
Prof. Damijan Miklavcic    Phone +386 1 4768 456
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NANOSECOND PULSES ON LIPID BILAYERS
Planar lipid bilayer is a simple model of cell membrane. For better understanding of electroporation we perform experiments also on planar lipid bilayer. The aim of present research is to perform experiments with nanosecond pulses with amplitude of up to 50V on planar lipid bilayer. With results we would complement the knowledge of lipid dynamics in cell membrane during electroporation.
Keywords: electroporation; lipid bilayers
Contact persons:
Matej Rebersek    Phone +386 1 4768 347
Prof. Damijan Miklavcic    Phone +386 1 4768 456
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NANOSECOND PULSES UNDER THE MICROSCOPE
Nanosecond pulses are very promising for electroporation of cell organelles. With observation of dynamics in cells colored with fluorescent dyes right after electroporation we could learn a lot about electroporation with nanosecond pulses. The aim of present research is to develop a system, which will allow us to generate nanosecond pulses with amplitudes up to 1 kV and which can be used for observation of cells under microscope.
Keywords: electroporation; lipid vesicles; hardware
Contact persons:
Matej Rebersek    Phone +386 1 4768 120
Prof. Damijan Miklavcic    Phone +386 1 4768 456
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ELECTROPORATION OF LIPID VESICLES
Lipid vesicle is a simple model of cell membrane. For better understanding of electroporation we perform experiments also on planar lipid vesicles. In frame of German-Slovenian cooperation we received a device, which generates microsecond high voltage electric pulses for observation of electroporation on lipid vesicles. Electroporation can be on this device observed directly over optical sensor or over conductivity meter. The aim of present research is to observe changes in optical absorption and conductivity of lipid vesicles between and after electroporation pulses.
Keywords: electroporation; lipid vesicles; hardware
Contact persons:
Matej Rebersek    Phone +386 1 4768 120
Prof. Damijan Miklavcic    Phone +386 1 4768 456
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THE EFFECT OF ELECTROPORATION ON CYTOSKELETON INTEGRITY IN ATTACHED CELLS
Temporary increase in cell membrane permeability followed by membrane resealing is caused by electroporation. Certain chemicals that affect cytoskeleton integrity at the same time affect the time course of cell membrane resealing. The aim of this work is to observe the changes in cytoskeleton of living cell during elelctroporation and relate the observed changes to the cell membrane resealing.
Keywords: electroporation; cell lab work
Contact persons:
Masa Kanduser    Phone +386 1 4768 767
Prof. Damijan Miklavcic    Phone +386 1 4768 456
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ELIMINATION OF BACTERIA WITH ELECTROPORATION TREATMENT (HIGH VOLTAGE PULSES)
When electroporation pulses exceed critical value they cause irreversible membrane damage and consequently cell death. High voltage electric pulses are therefore used to eliminate bacteria from drinking water and for non-thermal sterilization of liquid foods. The aim of this work is to determine characteristics of bacteria cells that could affect the electroporation efficiency and to determine parameters of electric pulses suitable for elimination of bacteria from drinking water and liquid foods.
Keywords: electroporation; cell lab work
Contact persons:
Masa Kanduser    Phone +386 1 4768 767
Prof. Damijan Miklavcic    Phone +386 1 4768 456
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ABLATION BY IRREVERSIBLE ELECTROPORATION
In medicine, ablation is the removal of a part of biological tissue. Usually it is achieved by radiofrequency waves, laser light or ultrasound. In this study we will quantify the parameters of electric field that assure the removal of the cells.
Keywords: electroporation; theory; cell lab work
Contact person: Assoc. Prof. Alenka Macek-Lebar    Phone +386 1 4768 770
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EVALUATION OF FATIGUE IN SKELETAL MUSCLES DURING SWIMMING
Surface electromyogram (SEMG) signals recorded during dynamic muscle contractions are of nonstationary nature and therefore require a different approach in signal processing than stationary signals. The aim of the study is to find the most appropriate indicators of progressive muscle fatigue during prolonged exercise such as swimming involving periodic submaximal contraction of certain skeletal muscles. A special attention will be paid to frequency analysis of nonstationary signals involving the use of time-frequency methods, such as wavelet transform. The study will be conducted in collaboration with Faculty of Sports in Ljubljana.
Keywords: electromyography of skeletal muscles; signal processing
Contact person: Assoc. Prof. Tomaz Jarm    Phone +386 1 4768 820
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MULTICHANNEL SYSTEM FOR SURFACE ELECTROMYOGRAPHY
Surface electromyogram (SEMG) is a signal recorded on the surface of the skin above skeletal muscles. This signal reflects electrical activity of contracting muscle fibers and therefore contains information about muscle function. SEMG signals can be useful for diagnosis of muscle dysfunction, evaluation of muscle rehabilitation and for assessment of muscle fitness. The aim of the study is to build a multichannel device (at least 8 channels) for computerized measurement and recording of SEMG signals. Special attention will be given to ensuring high quality noise canceling and amplification of the weak SEMG signals.
Keywords: electromyography of skeletal muscles; hardware design
Contact persons:
Assoc. Prof. Tomaz Jarm    Phone +386 1 4768 820
Assoc. Prof. Alenka Macek-Lebar    Phone +386 1 4768 770
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A MINIATURE SURFACE ELECTROMYOGRAPH
The aim of the study is to investigate the possibility for development of a miniaturized and programmable single-channel device for surface electromyography. The device should enable a high degree of portability and autonomy of measurement in a freely moving subject. The device should incorporate a power supply, electrodes, an amplifier with analog filters, and a module for signal acquisition and storing (e.g. using flash memory cards). One of possible solutions may implement wireless signal transfer to a computer in either on-line or off-line mode of operation.
Keywords: electromyography of skeletal muscles; hardware design
Contact person: Assoc. Prof. Tomaz Jarm    Phone +386 1 4768 820
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ELECTROMYOGRAM OF UTERINE CORPUS AND CERVIX
A pre-term labor pathological uterine activity and abnormal labor are main challenges of modern obstetric practice. Electromyographic signals detected non-invasively at the uterine corpus and cervix reflect well the mechanical activity in the uterus. Our aim is to quantify EMG changes that reflects normal or pathological pregnancy.
Keywords: electromyography of smooth muscles; signal processing
Contact persons:
Assoc. Prof. Alenka Macek-Lebar    Phone +386 1 4768 770
Assoc. Prof. Tomaz Jarm    Phone +386 1 4768 820
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CHANGES IN PROPERTIES OF MICROCIRCULATION IN TUMORS AFTER TREATMENT
Tissue microcirculation (blood flow in capillary network) is governed by both systemic and local regulatory mechanisms. Microcirculatory blood flow in tissue can be monitored by means of laser Doppler flowmetry. The goal of the study is to investigate the effects of antitumor treatment on properties of local tumor blood flow and their possible relationship with treatment effectiveness. The study will be performed in cooperation with Institute of Oncology in Ljubljana.
Keywords: microcirculation of tumors; signal processing
Contact person: Assoc. Prof. Tomaz Jarm    Phone +386 1 4768 820
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USER INTERFACE FOR COMPUTERISED ACQUISITION AND PROCESSING OF LASER DOPPLER SIGNALS
The purpose of the study is to build hardware and software parts of a user interface for acquisition and preprocessing of four output signals generated by an existing instrument for laser Doppler flowmetry. The software implemented in Windows environment must enable adjustable on-line acquisition, basic processing, and storage of signals along with an online display of the signals on a screen. The functionality of this program should include setting of sampling frequency, moving averaging and filtering of signals, manual annotation of events during data acquisition, automatic and manual display adjustments, modular upgradeability with additional signal processing functions, and on-line compression and storing of data.
Keywords: microcirculation; hardware; signal processing
Contact person: Assoc. Prof. Tomaz Jarm    Phone +386 1 4768 820
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CELL MIGRATION IN ELECTRIC FIELD
Endogenous electric fields may cause directional migration of a variety of different cells which is important in the process of morphogenesis, formation of tumors and wound healing. How cells sense and transduce electric signals remains largely unknown. We are going to study how cells respond to electric fields of different electric field strength and the reorganization of the actinic cytoskeleton during field-induced migration.
Keywords: cells in electric field; cell lab work
Contact person: Assoc. Prof. Alenka Macek-Lebar    Phone +386 1 4768 770
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