Open Calls for PhD


AIM - PhD Open callsINL is proud to be part of the Advance Integrated Microsystems PhD Program, in which we are partner with INESC-MN, INESC-ID, Instituto de Tecnologia Química e Biológica, Institute for Biotechnology and Bioengineering, and Research Institute for Medicines and Pharmaceutical Sciences.

The AIM PhD program has a focus on Advanced Integrated Microsystems and aims to offer advanced training that includes: micro and nanofabrication of devices and systems; sensing and actuating; application to physical, biotechnological, pharmaceutical, and biomedical challenges. Microsystem technologies are a deeply interdisciplinary subject, and advanced training at the doctoral level will be challenging and rewarding producing graduates with a broad scientific vision, who are knowledgeable in a wide variety of scientific disciplines, from basic sciences such as biology and quantum mechanics, to electrical, mechanical, and biotech engineering applications.

The doctoral degrees are awarded by the Universidade de Lisboa and the Universidade Nova de Lisboa. The research will take place in the laboratories of the team institutions in Lisbon and Braga in Portugal, with stays in Portuguese and international associate partner laboratories in academia and in industry.

2018 Calls

The AIM Call 2018 will offer 9 PhD Fellowships. Applications can be made through this link between February 1 and March 31 2018.

Further information about the application procedure, including details regarding the registration of the academic degrees obtained outside Portugal can be found here. Please make sure that your read this page and the official text of the calls.

Open Calls for Collaborative Research Projects with INL

Project 2: Advanced Microfabrication and NMR Electronic Instrumentation Development


With advances in microelectronics technology, magnetic resonance (MR) community sees´the emergence of portable and compact MR spectrometer (i.e., pulse programmer,transreceiver, and digital signal processing) on a highly integrated circuit platform (e.g., field programmable gate array, ASIC, integrated coils and field probes) targeting applications such as geological studies, disease diagnosis/monitoring, and precision agriculture at point-of-use setting.


INL and INESC (ID/MN) is seeking PhD students to work on a project aiming at designing and developing an integrated (chip scale), scalable, low power, low field (0.1T) Nuclear Magnetic Resonance (NMR) spectrometer.

Proponents: Peng Weng Kung (INL); Leonel Sousa (INESC ID); Susana Freitas (INESC MN)

Research Group: Precision Medicine Engineering

More Information: Project 2: Advanced Microfabrication and NMR Electronic Instrumentation Development

Project 8: Sample Processing device to integrate a Magnetoresistive Platform for the Stroke Patients stratification


Ischemic stroke is a leading cause of death and disability in developed countries. Thrombolytic therapy with recombinant tissue plasminogen activator (rtPA) remains the only pharmacological treatment effective in acute ischemic stroke. However, rtPA is tightly restricted in its therapeutic window (< 4.5 hours from stroke onset) and is linked to severe side effects – a severe hemorrhagic transformation (HT). Around a quarter of patients with ischemic stroke arrive at the hospital within the first three hours, but only 25% of these patients finally receive thrombolytic therapy. Researchers have found some biomarkers related to severe HT with high relevance for stroke patient’s stratification. Adding this information to a point-of-care (POC) diagnostic/prognostic tool will facilitate patient classification enabling a more efficient therapy. As we are dealing with a medical emergency, time is a critical point for stroke diagnosis. Therefore, an accurate and fast device is vital to define the most appropriate treatment. A sample preparation device will benefit the detection system to decrease the time of the measurement. In this case, the blood sample will be processed from the beginning on-chip, avoiding the variability caused by the operator, and the time-consuming steps related to the sample pre-treatment (e.g. centrifugation steps).


The main motivation of this project is not merely restricted to the detection of all panel of biomarkers by using a magnetoresistive (MR) biochip platform but also related to the sample processing. The present project proposes to develop a simple and autonomous microfluidic device capable to process a patient sample without requiring any pre-treatment (e.g. Plasma separation by using centrifugation or other standard techniques) together with the components necessary for the measurement (e.g. Magnetic Nanoparticles). The validation of the device will be validated by using patient samples related to different disease states and cross-validated with a standard technique.

Proponents: Paulo Freitas and Elisabete Fernandes (INL); Susana Cardoso (INESC MN)

Research Group: Nanodevices

More Information: Project 8: Sample Processing device to integrate a Magnetoresistive Platform for the Stroke Patients stratification

Project 11: Septicemia detection using graphene transistors integrated in a microfluidic platform


Septic shock – one of the most deadly diseases nowadays – is a medical emergency caused by a severe blood infection. The key to improve survival rate is to detect and control the source of infection at an early stage. Clinical symptoms, such as fever, arterial hypotension and thrombocytopenia, are variable and unspecific. Consequently, the need for finding specific septicemia blood biomarkers is increased, and the idea of making a diagnostic and prognostic tool (e.g. point-of-care) based on that information has gained interest. C-reactive protein (CRP), procalcitonin (ProCT), various cytokines, and cell surface markers are examples of biomarkers studied to detect early stages of sepsis. However, the difficulty remains in the inexistence of assays with sensitivity and specificity for those biomarkers, and in the need to detect a panel of biomarkers to identify septicemia. Multiplex assays are thus required to determine personalized treatment and decrease the mortality. Graphene low-dimensionality, high carrier mobility and chemical stability, allow for the design of extremely sensitive biosensors. Target specificity is achieved by immobilization of biomarker specific probes on the graphene surface. Transducing is provided by the change of resistance of a graphene channel defined between two metal contacts, capacitively coupled to the liquid electrolyte that floods the channel. Changes in the dielectric environment of the graphene will produce, through the mechanism of local gating, modifications in the conductivity of the channel. These will appear as changes in voltage or current in an external circuit built around the graphene transistor. Integration of these sensors in a multiplexed microfluidic platform, will allow to signal a panel of biomarkers in human blood for septicemia diagnosis.


1) Fabrication and functionalization of the graphene biosensor;

2) Test of the graphene immuno-sensor in the microfluidic system in model systems using spiked samples;

3) Benchmarking the graphene immuno-sensor against technologies based on optical detection;

4) Test of the graphene immuno-sensor in the microfluidic system using clinical samples.

Proponents: Elizabete Fernandes and Pedro Alpuim (INL); João Pedro Conde (INESC MN)

Research Group: Nanodevices and 2D Materials and Devices

More Information: Project 11: Septicemia detection using graphene transistors integrated in a microfluidic platform

Project 12: Thin-film silicon nanoelectromechanical systems (NEMS) for sensing


The Thin-Film MEMS and BioMEMS group at INESC MN has developed a low-temperature, large-area process for the fabrication of thin-film silicon-based MEMS resonators that allows these resonators to be implemented on glass and flexible polymeric substrates, as well as integrated with CMOS in a backend process. MEMS resonators can be used as mass sensors with high sensitivities. These sensors have a wide range of potential applications. The mass sensitivity scales with the resonator frequency. To increase the frequency, either a stiffer resonator is engineered (but this creates hurdles in the actuation and sensing of the resonator motion) or a smaller resonator is microfabricated. This project aims at exploring the nanofabrication, characterization, and application of thin-film silicon NEMS.


The first part of the project will consist on the development of the nanofabrication process to achieve thin-film silicon nano-ressonators. This will involve the use of e-beam lithography to reach submicron lateral dimensions and fine tuning of the etching processes of electrodes, sacrificial layer, and structural layers. The emphasis will be on flexural resonators (bridges, cantilevers, and membranes). The second part of the project will consist in simulating and experimentally characterizing the electromechanical properties of the nano-resonators. Both optical and electronic detection of the resonator motion will be used. The electromechanical properties (such as resonant frequency, quality factor, motional resistance, and frequency and phase noise) will be assessed to evaluate the possibility of integrating the MEMS as the frequency-setting element in an oscillator. The third part of this project is to use the nano-ressonator as the mass sensor in a sensing system and benchmark its performance in terms of sensitivity against a similar, micron-sized resonator. This performance will be modeled in terms of the electromechanical properties of the nano-resonator.

Proponents: João Gaspar (INL); João Pedro Conde (INESC MN)

Research Group: Microfabrication and Exploratory Nanotechnology

More Information: Project 12: Thin-film silicon nanoelectromechanical systems (NEMS) for sensing

Project 15: Biosensor integrated cell culture systems for monitoring biological responses


Tumours are highly heterogeneous and show different sensitivity to available treatment options. Their microenvironment, including intercellular crosstalk, has been shown to be crucial for cancer progression and dissemination. Thus, a better understanding of the interactions established between tumour, host cells and secondary organs is required to identify new potential anti-cancer targets. Current co-culture assays do not mimic very closely the physiological environment as they are done under static conditions and do not allow for the identification of soluble factors produced by a specific cell population as co-cultured cells share the culture media. The use of dynamic systems with integrated biosensors would greatly contribute to unravel cellular interactions in situ and throughout time, while recapitulating more closely in vivo dynamic microenvironments.


This project focuses on the use of innovative dynamic co-culture systems to study cellular crosstalk either through soluble factors and/or direct cell-cell interactions, overall important for the development of new innovative therapeutic approaches. The devices consist of two interconnected chambers where different cell types are cultured under flow and the influence of “donor” cells (well 1) over recipient cells (well 2) is evaluated. Two approaches for integration of biosensors will be taken: (i) in the first, a label-free sensor will be developed and used to quantify the amount of specific soluble factors released by recipient cells to the cell culture media; (ii) in the second, an optical/fluorescent or magnetic sensor will be integrated in a microfluidic channel located in the interface of the two wells, to measure the levels of relevant mediators being produced by donor cells. In this case, the mediators will be previously labeled. The biosensors will be optimized for their sensitivity in cell culture medium and after detailed characterization, the presence of relevant soluble biomarkers will be studied.

Proponents: Marta Oliveira e Paulo Freitas (INL); João Pedro Conde (INESC MN)

Research Group: Diagnostic Tools and Methods and Nanodevices

More Information: Project 15: Biosensor integrated cell culture systems for monitoring biological responses

Project 16: Integrated optical spectroscopy device for fruit growth monitoring


The growing demand for non-invasive and cost-effective chemical sensing strategies for monitoring biological and environmental processes is leading to a quest for new optical-based analytical strategies based on miniaturized optical devices. One of the main potential application fields is the monitoring fruit growth, where the technological and organoleptic properties of the products are closely related with biochemical processes that could be indirectly monitored using diffuse reflectance and/or fluorescence.


The main goal of this project is to provide a fully integrated, miniaturized, stand-alone device capable of performing optical spectroscopy at specific wavelength ranges. The project will require the integration in a single package/device of solid state light sources, photodetectors, optical interference filters and analog/digital circuitry.

Proponents: Paulo Freitas and João Piteira (INL); Susana Freitas (INESC MN)

Research Group: Nanodevices and System Engineering

More Information: Project 16: Integrated optical spectroscopy device for fruit growth monitoring

Project 18: Development of a point-of-care device for fast detection of pathogens involved in hospital- acquired infection


Hospital-acquired infections are considered one of the leading causes of death worldwide. Moreover, according to the Centers of Disease Control and Prevention (CDC), more than 70% of the bacteria now causing hospital-acquired infections are resistant to at least one of the drugs most commonly used to treat them. Among pathogens causing nosocomial infections, methicillin resistant Staphylococcus aureus (MRSA), vancomycin resistant enterococci (VRS) and carbapenem resistant Acinetobacter baumannii (CRAB) have become predominantly reported. The problematic of hospital-acquired infections and antibiotic resistance is due, in part, to the inability to rapidly detect, identify and thus, to treat patients within the early stages of infections. Point-of-care (POC) devices are a promising technology for pathogen detection enabling an increased response speed, sensitivity and portability. In these devices, biochips are combined to electronic and microfluidic platforms enabling a multiplex detection signal acquisition and processing. Magnetoresistive (MR) sensors have promising characteristics as sensing devices, as they are highly sensitive and allow a discrete quantification of magnetic entities which, when related to the number of molecular recognition events, results in a quantitative analytical mode. In a standard biochip-based bioassay, the specificity of the biorecognition elements is the most important aspect of biosensor development for pathogen detection to enhance detection of true positives while minimizing the probability of false positives and negatives. Bacteriophages (or phages) are viruses that infect bacteria. They specifically recognize and bind to bacteria, and are capable to discriminate between live and dead cells and recognize viable but non-cultivable bacteria (VBNC) bacteria. Moreover, they are cost-effective, robust, thermally and chemically stable and easy to conjugate with other motifs such as biomolecules or nanoparticles offering potential as probes for specific biosensing. Moreover, some of their proteins such as the receptor binding proteins (RBPs) and the cell wall binding domains (CBDs) of phage endolysins are responsible for the phage host recognition and thus are promising molecules to be used as biorecognition elements per se on biosensing platforms.


This project aims at developing a fast, sensitive and accurate multiplexed POC device to be used in hospitals for the detection of pathogens responsible for problematic nosocomial infections, namely methicillin resistant Staphylococcus aureus (MRSA), vancomycin resistant enterococci (VRS) and carbapenem resistant Acinetobacter baumannii (CRAB). To achieve this goal, the POC will integrate a sample preparation module and a magnetoresistive platform so that biological samples can be directly loaded and analysed. For the detection and quantification of the target bacteria, magnetoresistive (MR) sensors integrated along with microfluidics and associated with magnetic particles as reporter systems will be used. The
specificity of the assay will rely on the use of bacteriophages or derives thereof as sensing elements. Additionally, the POC will incorporate an optical system based on gold nanoparticles, enabling the identification of antibiotic resistance genes on the targeted bacteria. Overall, it is envisaged that the developed POC will allow patient’s samples to be screened specifically for nosocomial pathogens and their antibiotic resistance, with sample-in-answer-out results in few hours.

Proponents: Carla Carvalho (INL); Susana Freitas (INESC MN)

Research Group: Nanodevices

More Information: Project 18: Development of a point-of-care device for fast detection of pathogens involved in hospital- acquired infection

Project 19: Advanced microsystems to study intracellular pattern formation


Most living systems, ranging from animal flocks, self-motile microorganisms to the cytoskeleton rely on self-organization processes to perform their own specific function. Inside the cell, order and pattern formation may be transient and localized as many reactions within a cell occur in specialized locations, where the basic tenets of biochemical kinetics may break down. Developing microsystems to observe and control localization, geometric and temporal regulation of complex artificial biochemical networks as well as of living cells will allow us to elucidate principles of active pattern formation.


The major goal is to obtain a sound physical unders tanding of cellular self-organization, by successively increasing the complexity of the experimental system in a bottom up approach. Some of the goals are:

1) to implement a recent super resolution microscopy technique based on near field interactions to investigate the role of geometry (by PDMS microfluidics) and spatial localization (by surface functionalization) of components in a reconstituted cellular system;

2) to develop further the technique for 3D imaging in order to monitor cellular force sensing and signaling in live cell studies of;

3) to design and develop advanced microsystems to combine geometry, spatial location and volume to mimic cellular structures to elucidate the complex interplay of signal transduction and active pattern formation.

Proponents: Jana Nieder (INL); Alvaro H. Crevenna (ITQB-NOVA)

Research Group: Ultrafast Bio- and Nanophotonics

More Information: Project 19: Advanced microsystems to study intracellular pattern formation

Project 20: Biomimetic micro-patterned surfaces for 3D complete human skin growing for bioassays


The production of nanoscale patterned surfaces for tissue-engineering applications is an emerging area of research that provides new tools towards exploring interaction between cells during development. Micro- and nano-structured surfaces offer a wide range of alternatives to affect cells, from adhesion to differentiation or induction of response, providing alternatives for the biological studies in cell growing tissues and evaluation of pharmacological therapies. The possibility of integrating vascularization structures in the 3D skin is an advantage to perform a closer approach of the real interaction of the delivery of nutrients to the basal cells at the dermis, resembling the natural organization of the skin tissue. Such microfluidic structures can be fabricated by including dedicated tailored nanostructures onto the support of tissue culture. Such fabricated structures can be used for growing 3D skin, perfusion of culture media, studies of delivery of therapeutic drugs or even feeding with human plasma of ill patients, towards induction of disease phenotypes. An ultrafast femtosecond Laser shall be used for the 3D fabrication of the scaffolds via a two photon polymerization (TPP) process of a biocompatible polymer. Evaluation of tissue formation, its morphology and cell bioenergetics as well as drug delivery shall additionally be studied with deep tissue nonlinear multiphoton microscopy, and fluorescence lifetime imaging techniques.


The support for growing skin has an important effect in the developed tissue, and the interaction of the microstructures and chemical groups present onto the surface in contact with the cells is determinant of the biological development. Treatment of biocompatible surfaces with ultrafast femtosecond laser shall be used for the 3D fabrication of biocompatible scaffolds that mimic biological components, for cell seeding. Those structures will be used to grow skin in vitro and to allow studies of physiology effect of drugs, delivery and migration of compounds as well as optimization of the 3D skin mimicking, integrating vascularization or other cell structure through stem cell insertion and differentiation. Evaluation of the biological phenomena will be performed in a non-destructive way, in real time by with deep tissue multiphoton microscopy.

Proponents: Jana Nieder (INL); Abel G. Oliva (ITQB-NOVA)

Research Group: Ultrafast Bio- and Nanophotonics

More Information: Project 20: Biomimetic micro-patterned surfaces for 3D complete human skin growing for bioassays