Leiden Science Waar wij trots op zijn OUR TALENTS & DISCOVERIES IN 2014
de ontdekkingen van 2012
Faculty of Science Faculteit der Wiskunde & Natuurwetenschappen
Leiden Science, Our Talents and Discoveries in 2014 Editorial team Geert de Snoo, Ron van Veen, Marjolein van Schoonhoven Contributing writers Nienke Beintema, Willy van Strien, Anouck Vrouwe, George van Hal, Arnout Jaspers, Marjoleine van Egeraat, Marjolein van Schoonhoven Photography Pim Rusch, Mark de Haan (photo Marjo de Graauw) Beeldbank Leiden University, Photo archive Faculty of Science English translation Academic Language Centre, Leiden University Design www.balyon.com Printed by De Bink Leiden Contact Faculty of Science, Leiden University Marketing and Communications P.O. Box 9502 2300 RA Leiden The Netherlands firstname.lastname@example.org All rights reserved: Faculty of Science, Leiden University. Privacy and publicity rights apply. Reproduction of (parts of) this publication is only permitted after written permission from the publisher. Enquiries can be sent to: email@example.com
Foreword by the Dean
C.J. Kok Awards and Faculty Award for Education
C.J. Kok Public Award
Awards and Prizes in 2014 Research
C.J. Kok Jury Award
Faculty Award for Education
Awards and Prizes in 2014 Education
Leiden Science for innovation and society
Our Science Community
Facts and Figures
Various special moments in 2014 including the opening of the LCDS, Lego model of E-ELT and the presentation of the book â€˜Chemistry in Conflictâ€™.
Foreword by the Dean
The Faculty of Science: Science for Impact! At the Faculty of Science of Leiden University we aim to excel in both research and education in a broad range of disciplines. In each of our disciplines: mathematics, computer science, astronomy, physics, chemistry, bio-pharmaceutical sciences, biology and environmental sciences, our key criteria in building a strong research and education portfolio are scientific impact, technological innovation and societal relevance. To enhance our impact and visibility the Faculty of Science has organized most of its activities around two large and recognizable profile areas: ‘Fundamentals of science’ and ‘Bioscience: the science base of health’. These areas offer new opportunities for fundamental research across the boundaries of our disciplines and connect with important societal challenges. Our key facilities, such as NeCEN, Lorentz Center, the paramagnetic NMR facility, Cell Observatory, Metabolomics Centre and the new Leiden Centre of Data Science are the platforms were scientists meet, exchange knowledge and share research infrastructure. We are able to attract top talent to Leiden from the Netherlands and abroad. Within our science community 36% of our colleagues is from outside the Netherlands. Again this year the number of students enrolled within our faculty has grown. Today, the total number of students in our faculty is 3000! The number of international students is
20% and the first Massive Online Open Course of the Faculty of Science was launched. This year, more than 110 of our PhD students successfully defended their thesis. Academic teachers, tutors and students are working together intensively in our education programs that are characterized by a strong interrelationship between research and education. We aim to challenge talented students, to inspire and amaze them to become the successful scientists of tomorrow, who will be able to make important contributions to science and technology and to a better global environment and society. The impact and visibility of our science for innovation and society is growing. In many cases fundamental insights obtained from the research in our two domains fundamentals of science and bioscience, the science base of health - are used for improving the quality of life. For example, insights from space technology lead to improved food safety. Moreover, again this year solid contributions were made for enhancing drug development and therapies. The project ‘Vrijplaats’ was set up to enhance knowledge transfer between science and society, and to support and stimulate students to interact with entrepreneurs. We are very proud of the achievements of all our staff, teachers and students who make up our science community in Leiden and have won various distinctions and awards over the past year.
The Board of the Faculty of Science, Geert de Snoo
Han de Winde
Gert Jan van Helden
Facts & Figures Institutes
Leiden Observatory Leiden Institute of Physics Mathematical Institute Leiden Institute of Advanced Computer Science Leiden Institute of Chemistry Leiden Academic Centre for Drug Research Institute of Biology Leiden Institute of Environmental Sciences
Full professors Associate and assistant professors
Post-docs PhD’s (including guest PhD’s)
University research profile areas we participate in Fundamentals of Science Bioscience: the science base of health Translational drug discovery and development
Financial Facts 2014 in K€ Total Turnover
Research funding National funding
Other external (research) funding
€12,215 National funding comprises funding from NWO, KNAW and STW
Astronomy Bio-Pharmaceutical Sciences Biology Computer Science Life Science and Technology * Mathematics Molecular Science and Technology * Physics
Total no. of students Diplomas 2014
Astronomy Bio-Pharmaceutical Sciences Biology Chemistry Computer Science ICT in Business Industrial Ecology * Life Science and Technology Mathematics Media Technology Physics
MSc No.of ofBSc BScstudents; students; No. of MSc No. students; Totaal studenten
64% | 36%
If appropriate with MSc specialisations: Science Based Business, Science ÂCommunication No. of BSc students; and Society andstudenten Education Totaal 1804
63% | 37%
65% | 35%
Number of students enrolled
No.ofofMSc MScstudents; students; No.
Summa Cum Laude
276 44 295 22 1 288 58 5
1194 1804 students700 1194 800
600 500 400 300
64% | 36% 63% | 37% * Joint programme with Delft University of Technology
65% | 35%
200 100 0
Enrollments starting September 2014 (2nd enrollment is February)
Key Facilities NeCEN
The Netherlands Centre for Electron Nanoscopy (NeCEN) offers access to two Titan Krios microscopes, which are advanced cryo-transmission electron microscopes (cryo-TEMs). The Centre is the open access facility for cryo-TEM in the Netherlands. It specializes in using technology for biological research and is a demonstration site for the FEI Company. NeCEN offers research institutes and companies access to advanced cryo-transmission electron microscopes that are specifically designed to explore complex biological structures. All research institutes and companies are welcome to use our equipment. www.necen.nl
The Lorentz Center is an international center that coordinates and hosts workshops in the sciences, based on the philo sophy that science thrives on interaction between creative researchers. Workshops focus on new cooperations and inter actions between scientists from different countries and fields, and with varying seniority. Through a combination of informal talks, working sessions and discussions, participants are able to assess the status of a field and its future, and to cooperate, establish new international contacts, and spot upcoming talent. In 2014 the Center hosted 64 workshops. www.lorentzcenter.nl
Cell Observatory The Cell Observatory houses cutting-edge bio imaging technology and other research facilities, aimed at visualizing the dynamic structures of life, from molecule to cell. The goal of research at the Cell Observatory is to visualize and comprehend the dynamics of the living cell down to molecular level; understanding these fundamental mechanisms of life is essential for progress in tackling disease. The Observatory is also a meeting place and shared facility for scientists from different disciplines. It provides a means for participants to make their facilities available to one another, as well as sharing their knowledge and expertise. cellobservatory.leidenuniv.nl
Paramagnetic NMR Facility
The Paramagnetic NMR Facility in Leiden was established to provide support to researchers who want to apply paramagnetic NMR spectroscopy to biomolecules. Support is offered in the design and synthesis of paramagnetic probes, either for general applications (such as lanthanide tags and spin labels) or for dedicated purposes (such as enzyme substrates modified with a paramagnetic group). Help can also be provided with the attachment of probes to proteins and the acquisition, processing and analysis of data. nmr.lic.leidenuniv.nl/paranmr
The Netherlands Metabolomics Centre (NMC) brings together the vast knowledge and extensive expertise of the Dutch genomics and life sciences community to develop the technologies that will meet the demands of these fields of research. NMC unites researchers from universities, research institutes, university medical centres and industry. Through active community building and cooperation within the field, the NMC liaises between groups develo ping and applying metabolomics technology. The Centre actively promotes the transfer of knowledge and technology in the field of metabolomics through a network of committed partners. www.metabolomicscentre.nl
The Leiden Centre of Data Science The Leiden Centre of Data Science (LCDS) is a network of researchers from different scientific domains within Leiden University with an interest and expertise in data science. The core consists of data science researchers in the Faculty of Science and the Leiden University Medical Center. LCDS focuses on the development of statistical and computational methods for scientific data within the themes ‘Fundamentals of science’ and ‘Life, health and bioscience’. The broad aims are on research, education and to generate knowledge and technology to solve data problems associated with the grand challenges of 21st century. lcds.science.leidenuniv.nl/lcds
Hortus botanicus Leiden The Hortus botanicus, founded in 1590, is the oldest botanical garden in the Netherlands and one of the oldest in the world. The mission of the Hortus is to manage a living plant collection for research and education as well as for public interest and enjoyment. The garden includes many interesting plant collections from different regions, some of which are part of the National Plant Collection. The majority of the collections come from South-East and East Asia. The Hortus also plays an important role in the cultivation and preservation of endangered species. It welcomes more than 100,000 visitors each year; in 2014 there were 127,000 visitors. www.hortusleiden.nl
C.J. KOK AWARDS AND FACULTY AWARD FOR EDUCATION 2014
C.J. Kok Fund
The C.J. Kok fund was formed from the assets of Mr C.J. Kok, biology tutor from The Hague, who was highly committed to the natural sciences. On his death in 1965 he left his entire estate to Leiden University. The C.J. Kok fund was established with this inheritance. In his will Mr Kok determined that annually both the Faculty of Science and the Leiden University Medical Center would be given the opportunity to use the fund’s revenues to award outstanding performance to those demonstrating ‘a pronounced, significant talent for mathematics or solving medical problems’. The will also states that the assessment of performance should be on pure scientific grounds and that no distinction should be made regarding ‘rank, status, race, national character, origin, relationship and so on’.
C.J. Kok Awards
The Faculty of Science grants two C.J. Kok awards annually: the C.J. Kok Public Award, also known as the award for the “Discoverer of the Year” and the C.J. Kok Jury Award, the award for the best PhD thesis from the past year. All institutes within the Faculty are given the opportunity to nominate candidates for both awards.
Education and Research are closely interwoven in our Faculty. Mono-disciplinary education and multi-disci-
plinary cooperation give our students the competences they need to become the scientists of tomorrow. Excellent education is of inestimable value in this respect. Being able to translate research findings successfully into high-quality educational programmes at bachelor’s and master’s level is of great importance to stimulate and enthuse students for science and developing a new generation of successful and motivated (natural) scientists. For this reason, in addition to the C.J. Kok Award, the Faculty also confers an annual Award for Education. Students from the education committees nominate tutors for this award. The jury, comprising the chairpersons of the study associations and the assessor from the Faculty Board, assess each of the nominated lecturers. The students from the education committees advocate their nominee by giving a short presentation to the jury. In many instances, there is just a narrow margin between two or more tutors. In this case, the jury will attend one or more lectures in order to reach a final decision. Both C.J. Kok Awards and the Faculty Award for Education are presented at the Faculty’s annual New Year’s reception.
C.J. KOK PUBLIC AWARD ‘Discoverer of the year 2014’
Simon Portegies Zwart Leiden Observatory
Katy Wolstencroft Leiden Institute of Advanced Computer Science
Marcel Schaaf Institute of Biology Leiden
Alexey Boyarsky Leiden Institute of Physics
Sven Askes Leiden Institute of Chemistry
Ester van der Voet Institute of Environmental Sciences
Charlene Kalle Mathematical Institute
Annelien Zweemer Leiden Academic Centre for Drug Research
SIMON PORTEGIES ZWART Leiden Observatory
The right question Yes, 2014 was a great year. Astronomer Simon Portegies Zwart was happy to win the Dutch national award for high-performance supercomputing. But the nomination for the prestigious Gordon Bell Prize was without doubt the highlight of the year. “The nomination is a prize in itself.” By Anouck Vrouwe
Simon Portegies Zwart received his PhD from
trecht University. In 2005 he became assistant professor U at the University of Amsterdam. In 2009 he was appointed professor of Computational Astrophysics at the Leiden Observatory.
“Science is not about difficult questions,” Simon Portegies Zwart emphasizes. “Asking difficult questions is simple. How did life arise on earth, anyone can ask that. It is much harder to ask questions to which the answers may be within reach if you work hard enough. That is what science is all about.” Portegies Zwart is Professor of Computational Astrophysics at Leiden Observatory. And he loves simple questions. “A couple of years ago, I was curious where the siblings of our sun would be nowadays – the other stars that originated from the same gas cloud as our sun. To my surprise, no one had ever tried to figure that out. So we did.” He is always working on a dozen projects at any given time. Portegies Zwart: “At the beginning of 2014, I promised myself not to write more than ten publications this year. I failed miserably.” It doesn’t seem to bother him too much. The most notable project he is working on is the simulation of the Milky Way on a star-bystar-basis – just another ‘simple to explain, hard to do’ project. “It will tell us more about the formation of our galaxy, for example how the spiral arms evolved.” The brute force of a supercomputer is needed to do the calculations. “Using a supercomputer is not straightforward. A supercomputer works in parallel; it has multiple cores that perform calculations simultaneously. You don’t want cores just hanging out doing nothing, waiting for input from the others.” Portegies Zwart and his colleagues found a way to use American supercomputer Titan up to a level of 90 per cent efficiency, a new record. It resulted in the nomination for the prestigious Gordon Bell Prize for high-performance computing. “We didn’t win, but the nomination was a prize in itself,” Portegies Zwart says. “Time on a supercomputer is scarce. Scientists compete to be allowed to do their calculations. But now, the director of the Swiss supercomputer centre has called to ask if I would be willing to run my simulation on his machine too. He wants to know if we can reach a 90 per cent performance level there as well. Isn’t that great?”
ALEXEY BOYARSKY Leiden Institute of Physics
Discovering a dark matter candidate
Roughly ninety per cent of our Universe is missing, but astronomer Alexy Boyarsky may just have discovered a large chunk of it. A glimmer of light observed from other galaxies could very well be the first real sign of dark matter, a mysterious form of matter that has never been directly observed.
Alexey Boyarsky was
born in Ukraine and did his PhD in Moskou, then still a part of the Soviet Union. After the breakdown of the union, Boyarsky came to Europe and carried out postdoctoral research in Utrecht. After spending time at the Niels Bohr Institute and CERN, he came to Leiden in 2011.
By George van Hal To solve one of the biggest mysteries of our galaxy, Boyarsky and his team were looking at so-called sterile neutrinos. These hypothetical particles have mass and exert gravity, but have no other interactions with matter, making them nearly impossible to detect. Sterile neutrinos are a candidate for the mysterious dark matter hidden in our Universe, which makes up roughly 22 per cent of the ‘missing’ ninety, the rest being so-called dark energy. Astrophysicists had so far only been able to show the presence of dark matter indirectly, by proving that astronomical objects exert more gravity than their visible matter implies. While Boyarsky had been searching for his dark matter candidate since 2005, he was actually betting on the next generation of telescopes to find it. “We were just at the edge of sensitivity we needed to find this signal, and we figured that this was the last thing we needed to do with the current generation of telescopes,” he says. But then he and his team struck gold. They discovered an X-ray signal with the signature they were looking for in both the Perseus galaxy and our close neighbour Andromeda. However, Boyarsky hasatens to add that he can never be certain that he’s actually found sterile neutrinos. “It isn’t possible to confirm whether this is a sterile neutrino, or any other
kind of specific candidate, only whether it is dark matter,” he says. At the same time researchers at Harvard found the same signal in other galaxy clusters. And since then, Boyarsky and colleagues have found the signal in four separate objects, making him more certain that he’s found something, but not what he’s found. “We have too few positive results to claim any certainty. However, all the signals we’ve seen so far have been consistent with each other and the dark matter interpretation. That has never happened before.” Boyarsky hopes to prove that he’s found dark matter by observing the dwarf galaxy Draco, a satellite of our Milky Way. “It’s a very quiet object without a lot of X-ray emissions.” he says, making it easier to pinpoint their dark matter signal, and making the case stronger that what they’re seeing is not something else. “If we see the signal coming from that galaxy, that in my mind would be a very strong, maybe even final, proof.” However, doing that experiment is very expensive. “We need a significant proportion of a year of observational time, which is a lot to allocate to one project,” Boyarsky says. “But I think that now maybe there’s enough motivation to do it.”
CHARLENE KALLE Mathematical Institute
Lining up chaotic numbers Nature is all about dynamical systems: populations of animals and plants change over time, as does the weather. Ergodic theory concerns the evolution of dynamical systems. Charlene Kalle uses tools from ergodic theory to study β-expansions, infinite rows of numbers generated by a simple rule. Yet their structure is related to fractals. By Arnout Jaspers
Charlene Kalle After her PhD in Utrecht and post-docs at the universities of Warwick and Vienna, Charlene Kalle returned to the Netherlands with an NWO-Veni grant to work on ‘Multifractal analysis of Bernoulli convolutions through β-expansions’.
Most numbers have a decimal expansion that never ends and never repeats itself. For instance, the square root of five is 2.23606797749978969........ β-expansions are a more general way of representing a number as an infinite row of digits. Successive digits are produced by applying a transformation over and over again. This process can be visualised as a point bouncing around in a square. Charlene Kalle: “I actually see things moving when I’m thinking about these transformations.” Although Kalle’s research might mainly involve writing down long strings of 0’s and 1’s to check for patterns, she is inspired by thinking about β-expansions at a much more abstract level: “The way I investigate this is quite similar to research on fractals.” In fact, apllying β-expansions can be compared to tiling a plane with fractal tiles. Her research is part of ergodic theory, which tries to understand the long-term behaviour of dynamical systems in general. Compared to that, isn’t it a very modest ambition to understand the digital expansions of numbers? Kalle: “They may look very simple, but their behaviour is rich and chaotic and still not well understood. If we can’t even understand these simple systems, where does that leave us?” In a recent article, she analysed a large class of these systems, to find out which ones were really different. “You want to know if one system might not be the same as another one, but in disguise.” For her, ergodic theory is at a fascinating intersection of proba bility theory, number theory and dynamical systems. Kalle collaborates with computer scientists in France who are interested in representing numbers in this exotic way. β-Expansions have already been applied to improving the conversion of analog signals to digital, a basic operation in electronics. In the future, these mathematical tools might help construct better error-correcting codes or new, robust ways of data compression.
KATY WOLSTENCROFT Leiden Institute of Advanced Computer Science
So new, so dynamic Katy Wolstencroft, Assistant Professor in Bioinformatics, originally wanted to become a clinical biochemist. She changed her plans when she took a job as a research assistant in a bioinformatics laboratory in Manchester. “All the techniques were so new, it was really dynamic. I decided to do my Master’s and PhD in Bioinformatics, and the rest is history.” By Anouck Vrouwe If Wolstencroft explains her work to laymen, she always refers to the Human Genome Project to give people some idea of the massive scale of the datasets she is dealing with. The Human Genome Project sequenced all human genes: 3 billion base pairs of DNA in total. “There are similar datasets for proteins, metabolites, and so on.” In an organism, everything interacts – genes, proteins, other biomolecules, the environment. Looking only at genes or only at proteins clearly isn’t enough to understand complex bio logical processes. “Bioinformatics is not just about building easily accessible databases; it is about finding smart ways to combine knowledge from different fields of biology in such a way that it leads to better understanding,” Wolstencroft stresses. “I am working on yeast, for example. We model the response of the organism to a variety of different environmental factors. Another example would be why drugs have nasty side effects in some people and not in others.” Wolstencroft explains the biggest challenge in data sharing is not a technical, but a social one. “We have to show biologists
Katy Wolstencroft Assistant Professor in Bioinformatics and Computer Science, LIACS, Leiden Postdoc and Research Fellow, School of Computer Science, University of Manchester Visiting Research Fellow in the Molecular Cell Physiology Group, Vrije Universiteit Amsterdam MSc in Bioinformatics, PhD from the Faculty of Life Science, University of Manchester
the added value of collecting and pooling their data. Now, a lot of the data they produce gets lost. And I understand that; it takes time to annotate and curate it. But if everyone shared, we’d end up with such a wealth of information.” Wolstencroft spends a lot of her time developing methods to make data integration and annotation easier. “For example, I work on a data sharing platform for systems biologists”. She is convinced that bioinformatics will raise the field of biology to a whole new level. “We know a lot already, but there is so much more to discover. Combining data allows us to make new inferences, and therefore get the most value from reusing data we have already produced.
SVEN ASKES Leiden Institute of Chemistry
Turning red light into blue The Master’s program in ‘Chemistry and Science Based Business’ at Leiden University prepared Sven Askes for a career in business. But after obtaining his master’s degree, he couldn’t resist the offer of a PhD position in photochemistry. By Willy van Strien “I became interested in photochemistry while I was still in high school,” Sven Askes explains. “So, I’m happy that I’m now working on photodynamic therapy to treat cancer.”
His first publication, in Angewandte Chemie, was reason to nominate him for the title of Researcher of the Year. For more than 20 years, clinicians treating certain types of cancer have experimented with compounds that become toxic after exposure to light. The compounds are packaged in liposomes (lipid vesicles), targeted at tumorous tissue and illuminated. A promising class of light-sensitive compounds are organometallic Ruthenium-complexes. But there is a problem: they are activated by blue light, which doesn’t penetrate into the tissue. Now, Askes’ aim is to ‘upgrade’ red light, that does permeate into tissue, into blue light precisely where that blue light is needed, in the tumour. He chose a comparatively new technique: triplet-triplet annihilation up-conversion, in which two types of molecules cooperate. First, by absorbing red light, a ‘sensitizer molecule’ is excited to a high energy state, called triplet state. While in this state, it may collide with an ‘annihilator molecule’, which then takes up the energy and changes to a triplet state. Finally, when two excited annihilation molecules collide, one of them acquires all the accumulated energy. It then returns to its ground state while emitting blue light. “I used molecules that were known to perform this up-conversion in an organic solvent like toluene,” Askes says. “But in this setting, it has no clinical relevance, so then I looked at whether it might also work when the molecules are incorporated in a double lipid layer, such as in the membrane around liposomes. And to our surprise, it did.” One of the next steps will be to incorporate the molecules in the membrane of liposomes that carry the Ruthenium compounds. Then, in theory, the compounds can be activated by exposing these liposomes to red light. “We’re still a long way from clinical application, but we have provided the first proof of principle.”
ANNELIEN ZWEEMER Leiden Academic Centre for Drug Research
How small molecules affect receptors The CCR2 receptor is a transmembrane protein that plays an important role in many immunerelated diseases. Annelien Zweemer studied how small molecules can alter the functioning of this receptor, thus paving the way for pharmaceutical interventions. She made an important discovery: some molecules affect the receptor from the inside of the cell. By Nienke Beintema
Receptors are some of the most vital ‘switches’ in living organisms. They transmit signals from a cell’s environment to its inside, triggering a chain of intracellular reactions. However, they also play a role in diseases such as rheumatoid arthritis, multiple sclerosis, and cardiovascular disease. Modulating a receptor called CCR2 – the objective of Annelien Zweemer’s research – could help to combat these diseases. In these diseases, CCR2 receptors – particular proteins within the membranes of blood cells – react to an overload of inflammatory proteins, called chemokines. “These chemokines bind to the CCR2 receptor on the outside of the cell,” says Zweemer, “which somehow changes the receptor’s structure. This, in turn, starts the signalling reactions on the inside of the cell and ultimately contributes to disease progression.” “We know”, she continues, “that certain small, synthetic molecules may hamper this process. They bind to the receptor on the outside, which prevents receptor activation by the chemokine – either by competition, or by changing the structure of the chemokine’s binding site.
Annelien Zweemer a Leiden biopharmaceutical sciences graduate, conducted PhD research at the Leiden Academic Centre for Drug Research (LACDR), winning several prizes. She is currently a postdoc at MIT in Cambridge (US). This is very interesting from a pharmaceutical point of view,” according to Zweemer. “The challenge is to find out how this modulation works, which molecules are best suited for the job, and, ultimately, how they can combat disease in patients.” “This final step”, she emphasizes, “has not been successful for any CCR2 small molecule inhibitor so far.” Zweemer addressed one of the basic questions in this field of research: how – and where – small synthetic molecules bind to the CCR2 receptor. Using radiolabeling techniques and computer modelling, she discovered that different molecules bind at different sites, with some of them actually traveling into the cell and binding to the receptor on the inside. “ The discovery of this intracellular binding site allows the design of novel CCR2 small-molecule inhibitors,” says Zweemer. “Moreover, given the structural similarity of CCR2 and many other receptors, these findings could well benefit drug discovery for a wide variety of targets and diseases.”
MARCEL SCHAAF Institute of Biology Leiden
The restless behaviour of transcription factors
One of the best-known steroid hormones is the stress hormone His interests have focused on steroid hormones, cortisol. It is secreted by the adrenal cortex when we are under which he studies from the molecular to the physistress and it prepares the body for action, for instance by reguological level. This year, he was senior author of lating metabolism and suppressing immunity. “All cell types two papers (Journal of Cell Science; PLoS One) that respond to cortisol,” Schaaf explains. “The physiological consedescribe the surprising mobility of steroid hormone quences are amazing.” When delivered to a cell, cortisol binds to a receptor that then receptors in cell nuclei, where they regulate DNA enters the nucleus and functions as a transcription factor: it transcription. binds to DNA and enables the transcription of genes into RNA. By Willy van Strien
After a degree in Medical Biology in Utrecht, a PhD in Leiden and a wandering existence as a postdoc, Marcel Schaaf (1968) was employed at Leiden University in 2004.
Schaaf: “There are no fewer than 10,000 places on the DNA where this receptor hormone complex can bind. We wanted to know how it finds those places.” His group was able to show how the transcription factor behaves in living cells by combining a range of advanced microscopy imaging techniques. Surprisingly, the transcription factor appeared to be very mobile within the nucleus. At any point in time, roughly half of the receptor-cortisol complexes are diffusing freely. The rest are bound to DNA, but for a short period of time. Complexes either stay at a location for only half a second, or they leave after a few seconds. Schaaf: “While a piece of DNA is being transcribed, a transcription factor is always in place. However, it isn’t the same complex continuously. Instead, many transcription factors come and go. It is a very dynamic picture.” He thinks that the transcription factors continuously probe the DNA by briefly binding at aspecific sites. When they hit one of the 10,000 binding places, they stay a bit longer and enhance the transcription process. But after a short while, they dissociate to make way for another transcription factor. “This means that cells are able to constantly regulate the transcription process.” Other steroid hormone receptors behave similarly, for instance the receptor for the sex hormone testosterone, Schaaf and colleagues discovered. In the coming years, they aim to shed more light on this dynamic behaviour.
ESTER VAN DER VOET Institute of Environmental Sciences
Teaching thousands online about a circular economy Metals are becoming increasingly scarce. This presents a major challenge for economies worldwide. Ester van der Voet initiated a Massive Open Online Course (MOOC) addressing the need and options for a circular economy for metals. The course, which brings in international experts and their most recent research, is a huge success. By Nienke Beintema Metals are one of the fundamentals of modern society. From household uses to mass applications in construction and communication technology; our world cannot function without metals. Yet, as demand is rapidly growing, supply has problems keeping up with demand. There is an urgent need for people with the knowledge and skills to address this challenge. Ester van der Voet therefore initiated a Massive Open Online Course (MOOC) on reusing and recycling metals: Wheels of Metals. The course is a joint undertaking by Leiden University and the UN Environment Programme (UNEP). “It has attracted around 6000 students from 150 countries around the world,” says Van der Voet, “which we think is fantastic.” Beside Van der Voet herself, the MOOC’s instructors include several of the world’s leading experts on circular economies. Through their papers and lectures, which are recorded on video, they teach students the latest insights on the issue of metal scarcity and ways to address it.
Ester van der Voet has been working at the Institute of Environmental Sciences since 1984, specializing in industrial ecology. She is now an associate professor and serves on UNEP’s International Resource Panel. “Currently the rate of metal reuse is low, sometimes even less than one per cent worldwide,” comments Van der Voet. “Obviously this has to change. Primary production is becoming increasingly difficult and energy-intensive. We need to find efficient ways to recover metals from waste and reuse them.” This is not just a technical problem, as Van der Voet points out. There is also a range of bureaucratic and legal obstacles to be overcome. “Legislation currently prevents effective recycling, especially in countries like the Netherlands,” she says. “Technically, metals can be recovered after use. And the more scarce metals become, the more economically viable this will be.” Wheels of Metals is one of Leiden’s six current MOOCs. “I think this is a very valuable teaching,” according to Van der Voet. “It is a concrete and accessible tool to address a pressing global issue, and it is also an excellent way for the university to present itself to the outside world.”
Awards and Prizes in 2014 research Prizes and Honours
Prof. Ewine van Dishoeck received the Gothenburg Lise Meitner Award Prof. Simon Portegies Zwart and PhD students Tjarda Boekholt and Guilherme Gonçalves Ferrari received the Wim Nieuwpoort prize of SURFSara/NWO Matteo Brogi MSc and Dr. Jayne Birkby received Hubble and Sagan Fellowships Prof. Tim de Zeeuw received an honorary doctorate from the University of Padua (Italy) Alumnus Dr. Karin Öberg, NWO postdoc at Harvard University was awarded the Packard Fellowship Leiden Institute of Physics Prof. Dirk Bouwmester received the Spinoza award Björn de Rijk MSc was winner of the posterprize at SIAM Conference on Nonlinear Waves and Mathematical Institute Coherent Structures Prof. Roeland Merks was winner of the Leiden round of the IgNobel 24/7 battle Julián Facundo Martínez received the Francisco Aranda Ordaz Award for his PhD Research in Probability Leiden Institute for Prof. Jaap van den Herik received the Humies Award Advanced Computer Science Prof. Thomas Bäck received the 2015 Evolutionary Computation Pioneer Award Prof. Grzegorz Rozenberg received an honorary doctorate from the Åbo Akademi University in Turku (Finland) Leiden Observatory
Leiden Academic Centre for Drug Research
Leiden Institute of Biology
Leiden Observatory Leiden Institute of Chemistry Leiden Academic Centre for Drug Research
Prof. Ron de Kloet was awarded the Golden Kraepelin Medal Dr. Elke Krekels received both the best Thesis Award as the TOP Publication Award of the Dutch Society of Clinical Pharmacology & Biopharmacy Prof. Meindert Danhof received a Royal decoration "Knight in the Order of the Lion of the Netherlands" Dr. Marjo de Graauw was elected as inaugural member of the Leiden Teachers’ Academy Prof. Ben Lugtenberg received the Arima Award Prof. Peter Klinkhamer and collegues received the ‘Prix “Innovation Procédé’ for their online Exctract Library Prof. Han van Konijnenburg-van Cittert received a Royal Decoration "Officer in the Order of Orange-Nassau"
Cum laude PhD
Dr. Matteo Brogi for his thesis 'Atmospheres of Hot Alien Worlds' Dr. Sasha Hoogendoorn for her thesis 'A chemical biology approach for targeting of ligand-Drug conjugates' Dr. Lianne Willems for her thesis 'Direct and two-step activity-based Prof.iling of proteases and glycosidases' Dr. Koen van der Maaden for his thesis 'Microneedle-mediated vaccine delivery.'
Dirk Bouwmeester received the prestigious Spinoza prize in 2014, the highest Dutch award in science. He is Professor of Physics at Leiden University and is also a professor at the University of California in Santa Barbara. His research has lead to breakthroughs in physics on several occasions. Bouwmeester’s current research includes artificial atoms in semiconductors, with possible applications in quantum informatics, and silver nanoclusters with optical properties inserted in DNA, which have possible medical applications. Photo credits: NWO, Ivar Pel
Universe Awareness (UNAWE) received a Creative Industries Grant from NWO Dr. Pedro Russo and collegues reveived a grant form the International Astronomical Union for Cosmic Light Awareness Dr. Pedro Russo and his team reveived the Science Education Award from Scientix, the European network for Science communication Prof. George Miley, Dr. Pedro Russo and Dr. Jarle Brinchmann received 2 million euros from the EU for EU Space Awareness (EUSPACE-AWE) Leiden Observatory is part of a consortium receiving 12 M€ for the development of the Square Kilometre Array Leiden Institute for Prof. Thomas Bäck and Prof. Stephan Manegold (LIACS and CWI) and collegues received a 1 M€ Advanced Computer Science Technology area grant from NWO Prof. Hermen Overkleeft, Prof. Hans Aerts and Prof. Huib Ovaa reveived a 2 M€ TOP-PUNT Leiden Institute of grant from NWO Chemistry Dr. Mario van der Stelt en Dr. Alexander Kros received a Technology area grant from NWO Prof. Gilles van Wezel en Prof. Michael Richardson received a 1.4 M€ Technology area grant from NWO Dr. Remus Dame received a 1.3 million US dollar HFSP Grant Leiden Academic Centre for Spin off MIMETAS, Dr. Paul Vulto and colleagues received the MipTec 2014 innovation prize Drug Research for OrganoPlate™ Institute of Biology Leiden Spin off InOvo, Wouter Bruins and Will Stutterheim received a 200 K€ funding from Leiden University and amongst others the Dutch Ministry of Economic Affairs and the Dutch association for the protection of animals Leiden Observatory
Leiden Observatory Leiden Institute of Physics
Prof. Jelle Kaastra was appointed Professor of High Energy Astrofysics Prof. Ewine van Dishoeck was installed as member of the Leopoldina National Akademie der Wissenschaften Dr. Martin van Exter was appointed as director of education Prof. Arnold Tukker was appointed as scientific director
Leiden Institute for Prof. Stefan Manegold was appointed Professor of Data Management Advanced Computer Science Prof. Jaap van den Herik was appointed Professor of Law and Computer Science Prof. Aske Plaat was appointed Professor of Data Science
Prof. Huub Röttgering and Prof. Joost Kok received a NWO grant in the programme: ‘Big Bang, Big Data: Innovating ICT as a Driver for Astronomy’ for their proposal ‘The Computer Science challenge of calibrating the ionosphere over the SKA sky’. Leiden University also participates in a consortium that has been awarded 12M€ for the design of the Square Kilometre Array (SKA). The SKA will be the world’s largest and most powerful radio telescope. Photo: artist’s impression Source: www.jodrellbank.manchester.ac.uk
Leiden Institute of Chemistry Leiden Academic Centre for Drug Research Leiden Institute of Biology
Prof. Hans Aerts was appointed Professor of Medical Biochemistry
Institute of Environmental Sciences
Prof. Peter van Bodegom was appointed Professor of Environmental Biology
Prof. Ewine van Dishoeck received an NWO medium grant Prof. Harold Linnartz received an NWO medium grant Prof. Koen Kuijken, Dr. Elena Rossi and Dr. Ivo Labbé received a TOP NWO grant Prof. Huub Röttgering and Prof. Joost Kok (LIACS) received a grant from NWO-EW and DOME for their proposal ‘The Computer Science challenge of calibrating the ionosphere over the SKA sky’ Dr. Martina Huber received an ECHO award from NWO Dr. Louk Rademaker received a Rubicon award from NWO Prof. Carlo Beenakker received a grant from FOM Prof. Ana Achúcarro received a programme grant from FOM
Leiden Institute of Physics
Mathematical Institute Leiden Institute for Advanced Computer Science Leiden Institute of Chemistry
Leiden Institute of Biology
Prof. Miranda van Eck was appointed Professor of Cardio Vascular & Metabolomic Therapeutics Prof. Jos Raaijmakers was appointed Professor of Microbial Interactions and Diversity Prof. Herman Spaink was appointed as scientific director
Dr. Robin de Jong received a TOP NWO grant Dr. ir. Fons Verbeek together with Prof. Herman Spaink (IBL) received an NWO medium grant Dr. Mario van der Stelt received an ECHO award from NWO Dr. Roxanne Kieltyka received an ECHO award from NWO Dr. Dennis Hetterscheid received an ECHO award from NWO Dr. Ludo Juurlink received a KIEM grant from NWO Prof. Marcellus Ubbink received a KIEM grant from NWO Prof. Jan Pieter Abrahams received a valorization grant from STW and a Technology Area (TA) grant from NWO Dr. Dennis Hetterscheid and Dr. Sander van Kasteren received an ERC starting grant from the EU Dr. Athrur Ram received a KIEM grant from NWO Prof. Herman Spaink together with Dr. Fons Verbeek (LIACS) reveived an NWO medium grant Dr. Kirsten Leiss and Prof. Peter Klinkhamer received a 0.9 M€ grant from STW Prof. Gilles van Wezel and Prof. Jos Raaijmakers and collegues reveived a 3 M€ grant from STW
NWO Talent Scheme Grants Leiden Observatory Leiden Institute of Chemistry
Mathematical Institute Leiden Institute of Chemistry Institute of Environmental Sciences Leiden Institute of Physics
Veni Dr. John Tobin received a VENI grant for his proposal'Revealing the origin of solar systems: research on the formation of protoplanetary discs and binary stars' Dr. Wangyang Fu received a VENI grant for his proposal 'Graphene as biological sensor' Dr. Federico Calle-Vallejo received a VENI grant for his proposal 'Towards a general methodology for catalyst design' Dr. Fabrizio Chiodo received a VENI grant for his proposal 'Vaccins against worm infections' Vidi Dr. Lenny Taelman received a VIDI grant for his proposal 'Cohomological methods for function field arithmetic' Dr. Grégory Schneider received a VIDI grant for his proposal 'Reading through proteins with graphene' Dr. Martina Vijver received a VIDI grant for her proposal 'The added risk of size' Vici Dr. John van Noort received a VICI grant for his proposal 'Chromatin dynamics in single genes.'
C.J. Kok Awards and faculty award for education
Leiden Institute of Physics Prof. Tjerk Oosterkamp was elected as teacher of the year 2013 Leiden Institute for Dr. Wouter Duivesteijn reveived the C.J. Kok Jury Award for 'The best thesis of the year 2013' Advanced Computer Science Leiden Academic Centre for Dr. Gerard van Westen received the C.J. Kok Public Award for the 'Discoverer of the year 2013' Drug Research
Gerard van Westen awarded ‘Discoverer of the year 2013’
Wouter Duivesteijn awarded for ‘Best Thesis of the year 2013’
Tjerk Oosterkamp awarded ‘Teacher of the year 2013’
C.J. KOK JURY AWARD ‘PhD Thesis of the year 2014’ Jury criteria for the best thesis of the year
What makes a thesis a winning one? The jury makes her selection firstly based on the thesis itself and the corresponding recommendation, which is usually written by the (co) promotor or the scientific director. Main criteria for assessment are: • The scientific quality such as innovative content for it’s field of research, other disciplines and science in general. • Are the results of direct relevance for society? • Is the thesis easy accessible and clearly written? Career prospects after being promoted are also considered in the jury’s assessment if this information is available. Members of the 2014 jury are: Professor Marcellus Ubbink (chair) Professor Carel ten Cate Professor Aart van der Vaart Professor Miranda van Eck Professor Paul van der Werf
Winner C.J. Kok Jury Award 2013
In 2013 the jury has rewarded the ‘C.J. Kok Jury Award’ to Wouter Duivesteijn for his thesis ‘Exceptional model mining’. The jury report stated her decision as follows: “Wouter’s thesis provides, in very detail, a number of practical, new and widely applicable methods to tackle problems and questions within complex datasets. These methods are apposite for the type of relation that is the subject of research: correlation, regression or even more complex connections between large sets of data. Each method is illustrated with examples from the fields of Biology, Economics, Drug research and so on. Very valuable is a statistical analyses method to avoid promiscuous characteristics. The dissertation is easy to ready and can be used directly by anyone who needs to study datasets and therefore has the potential of having major impact.“ All theses of the Faculty of Science can be found in the Leiden Repository via https://openaccess.leidenuniv.nl
C.J. KOK JURY AWARD Nominees best PhD Thesis of 2014
Atmoshperes of hot alien worlds
On the geometry of fracture and frustration
Matteo Brogi Leiden Observatory Keywords: Exoplanets, Atmospheres, Spectroscopy, Transits
Vinzenz Koning Leiden Institute of Physics Keywords: Nematic liquid crystals, Defects, Cracks, Chirality, Elasticity
This thesis presents observations of exoplanets orbiting very close to their parent star, with a particular focus on a novel technique for characterizing their atmospheres. This is based on the use of high-resolution spectroscopy from the ground. The first detection of the atmosphere of a non-transiting planet is presented, together with the determination of its mass and orbital inclination. Moreover, it is shown that high-dispersion spectroscopy is very effective in recognizing molecular species, measuring their relative abundances, and determining whether temperature increases or decreases with altitude in the observed planetary atmospheres. The method also led to the measurement of the rotational period of a transiting exoplanet, which was found to be tidally locked, in line with theoretical predictions. Finally, the evidence for the disintegration of a small, rocky planet candidate in the Kepler database is presented. This result was obtained by fitting the light curve of the object with a model of a trailing tail of dust.
Geometric frustration occurs when local order cannot propagate through space. A common example is the surface of a soccer ball, which cannot be tiled with hexaganons only. Geometric frustration can also be present in materials. In fact, geometry can act as an instrument to design the mechanical, optical of physical properties of fluids and solids. The first two parts of this thesis discuss frustrated liquid crystals confined to droplets of various shapes and sizes. The droplet shape determines the orientation of the liquid crystal molecules and in turn its response to light. In the final part we study the fracture mechanics of curved elastic plates. By tuning the curvature of the plate, the critical length at which the crack starts growing can be controlled. Finally, we find that the path the crack takes depends on the curvature.
C.J. KOK JURY AWARD Nominees best PhD Thesis of 2014 The parabolic Anderson model and long-range percolation.
Algorithms for Analyzing and Mining Real-World Graphs
This thesis has two parts. The first part deals with the parabolic Anderson model, which is a stochastic differential equation. It models the evolution of a field of particles performing independent simple random walks with binary branching. The focus of this work is on the exponential growth rate of the solution, where several basic properties are derived. The second part deals with two long-range percolation models. The occupied set of the first model is obtained by taking the union of a collection of independent Brownian motion running up to time t whose initial positions are distributed according to a Poisson Point process. Basic properties such as the existence of a percolation phase transition and the uniqueness of the unbounded cluster are proven. The second model is the model of random interlacements. It is shown that the vacant set of random interlacement is transient for almost all values of the supercritical phase as the dimension tends to infinity.
This thesis is about algorithms for analyÂ zing large real-world graphs (or networks). Examples include (online) social networks, webgraphs, information networks, biological networks and scientific cooperation and citation networks. Although these graphs differ in terms of what kind of information the objects and relationships represent, it turns out that the structure of each these networks is surprisingly similar. For computer scientists, there is an obviousÂ challenge to design efficient algorithms that allow large graphs to be processed and analyzed in a practical setting, facing the challenges of processing millions of nodes and billions of edges. Specifically, there is an opportunity to exploit the non-random structure of real-world graphs to efficiently compute or approximate various properties and measures that would be too hard to compute using traditional graph algorithms. Examples include computation of node-tonode distances and extreme distance measures such as the exact diameter and radius of a graph.
Dirk Erhard Mathematical Institute Keywords: Parabolic Anderson equation, Percolation, Quenched Lyapunov exponent, Brownian motion
Frank Takes Leiden Institute of Advanced Computer Science Keywords: Graphs, Networks, Shortest path, Diameter, Radius, Eccentricity, Social networks, Information networks
Direct and two-step activitybased profiling of proteases and glycosidases Lianne Willems Leiden Institute of Chemistry Keywords: Activity-based profiling, Irreversible inhibitors, Proteases, Glycosidases, Fluorescent probes, Tetrazine ligation
Activity-based protein profiling provides a powerful approach for the monitoring of active enzyme populations in complex biological samples by making use of activity-based probes (ABPs), chemical probes that are designed to bind specifically to the active site of an enzyme (family). The research described in this thesis concerns two main topics. First, new techniques are developed for the two-step labeling of enzymatic activity, a strategy that involves the targeting of enzymes with an ABP followed by introduction of the desired reporter entity via a bioorthogonal ligation reaction. In these approaches, both regular and inverse-electron-demand Diels-Alder ligations are applied. The latter of these proved superior in terms of efficiency and selectivity and enables the labeling of enzymatic activity in living cells. Furthermore, two tandem ligation strategies are presented that allow the simultaneous monitoring of multiple biomolecules in a single experiment. The second topic involves the synthesis and biological evaluation of novel activity-based probes for two classes of glycosidases, the retaining α- and β-galactosidases. A fluorescently labeled α-galactopyranose-configured aziridine is demonstrated to enable the labeling of endogenous levels of human retaining α-galactosidase activity in cell extracts. Finally, a number of epoxide-based β-galactopyranose-configured probes is synthesized that target the human retaining β-galactosidase galactocerebrosidase.
Towards a system-based pharmacology approach to predict developmental changes in real drug clearance in children
Roosmarijn de Cock Leiden Academic Centre for Drug Research Keywords: Renal function, Antibiotics, Glomerular filtration, Developmental changes, Pharmacokinetics, Neonates Renal clearance is responsible for the elimination of a large number of water-soluble drugs and metabolites and is therefore of large importance when characterizing the pharmacokinetics of drugs. Renal clearance includes glomerular filtration, tubular secretion and reabsorption and each of these processes is subject to different developmental changes. To estimate the renal clearance of drugs in children, a thorough understanding of these developmental changes in the different sub processes contributing to renal function is needed. Therefore the aim of the research described in this thesis was to characterize the developmental changes in renal function over the entire pediatric age range. To this end, a system-based pharmacology approach was applied implicating that within the models for the different subprocesses contributing to renal function a distinction was made between system-specific and drug-specific properties. The transition to a more system-based pharmacology approach and the combination of different strategies (extrapolation to other drugs, adult data or non-clinical data) will result in an approach focusing on the underlying system instead of focusing on the drugs and may facilitate development of pharmacokinetic models and evidence-based dosing regimens in the pediatric population.
C.J. KOK JURY AWARD Nominees best PhD Thesis of 2014 Surviving embryogenesis Chris Jacobs Institute of Biology Leiden Keywords: Insect egg, Serosa, Survival, Diversity Insects are the most diverse group of animals on earth. They inhabit nearly all terrestrial habitats. One of the factors underlying this success is the ability of insect eggs to survive in adverse conditions. For a long time the ability to survive these adverse conditions has been attributed to maternal investment in the form of a protective eggshell. In this thesis, It is shown that contrary to common belief, insect eggs are far from helpless. The insect egg itself develops a cellular layer around the egg called the serosa. This serosa protects the developing embryo from dehydration which enables it to survive in dry habitats. The serosa furthermore protects against infection, mounting an impressive immune response upon the entry of bacteria in the egg. The data presented in this thesis show the importance of the serosa in the survival of the insect egg. It is proposed that this multifunctional serosa contributed to the great success of insects.
Impact assessment modelling of matter-less stressors in the context of Life Cycle Assessment Stefano Cucurachi Institute of Environmental Sciences Keywords: Life cycle assessment, Life cycle impact assessment, Matter-less stressors, Noise pollution, Light pollution, Electromagnetic pollution In the last three decades, the Life Cycle Assessment (LCA) framework has grown to establish itself as the leading tool for the assessment of the environmental impacts of product systems. LCA studies are now conducted globally both in and outside the academia and are also used as a basis for policy making. Now that the science behind existing and established impact assessment models is more solid, LCA modellers may work on deepening and broadening LCA, and on tackling the issues that make the framework incomplete or uncertain. This work of thesis deals with the complete modelling of stressors that are not related to the standard extraction/emission pattern, thus that do not relate to the extraction of a certain quantity of matter or to the emission of matter to the environment. These stressors may be defined here as matter-less. The thesis analyses the development of impact assessment models for the case of sound emissions determining noise impacts, radio-frequency electromagnetic emissions leading to electromagnetic pollution, and light emissions determining ecological light pollution. Through the study of these matter-less stressors the computational structure and other methodological topics of the LCA framework are put to the test.
FACULTY AWARD FOR EDUCATION 2014
In 2014 eight of our teaching staff members were nominated by our students for the Faculty Award for Education. They were nominated for a variety of reasons but all nominees are praised for their commitment and enthusiasm. The chairs of the study associations and the assessor from the Faculty Board have the final decision on who will be granted the award. The assessor presents the award at the Faculty’s New Year’s reception.
Dr. Matthew Kenworthy Leiden Observatory
Dr. Vincenzo Vitelli Leiden Institute of Physics
The astronomy teaching commit tee nominated lecturer Matthew Kenworthy on behalf of the students for the 2013-2014 Teaching Prize. He teaches Modern Astronomical Research in the bachelor’s phase and Detection of Light in the master’s phase. Kenworthy is described by his students as a pleasant and enthusiastic lecturer. He uses humour in his lectures and is able to explain topics clearly, making them easy for students to understand. This shows his understanding of students’ needs. All in all, Kenworthy is a first-class teacher who truly deserves the Teaching Prize.
Vincenzo Vitelli is a theoretical physicist whose research focuses primarily on soft condensed matter. He is also well known among students for teaching the master’s course on Statistical Physics, and starting from April he will also be teaching the second-year course on Relativistic Electrodynamics. Vincenzo is appreciated for his enthusiastic style of lecturing and his ability to get his message across to his audience. He draws on his own experiences and shares with his students his fascination for the subject. He has a keen ability to motivate his students. His style of lecturing is informal and he is not afraid to throw in a joke once in a while. He has the ability to make the whole class participate, which is no mean feat! Through detailed explanations and encouraging students to ask questions as well as stimulating them by asking questions himself, he makes the content understandable for everybody. The homework assignments, to be handed in every two weeks, are challenging and are designed to help the students understand all the details of the material.
Dr. Owen Biesel Mathematical Institute Owen has designed a Calculus course for a wider audience than just mathematicians and taught the course at Leiden University College the Hague (LUC). He also designed the Commutative Algebra course. During his lectures he uses a card system with which students can indicate whether the pace of the lecture matches their own speed of learning. Students can choose from: A) could be speeded up, B) too rapid, C) I need more background information and D) I can’t follow this lecture any more. He regularly asks his students for feedback during his lectures, by getting them to hold up their cards so he can respond to their needs. Contact sessions are divided into two parts, focusing either on understanding the material or noting down the solution. Owen always starts with the basics, and keeps the students’ attention with a balanced curve of difficulty. Material remains understandable for all students, while the more mathematically minded are still challenged. Owen’s passion for maths is plain to see. He is interested in people, easy to approach and accessible outside the lectures.
Dr. Walter Kosters Leiden Institute of Advanced Computer Science
Prof. Jan Pieter Abrahams Leiden Institute of Chemistry (Life Science & Technology)
Dr. Kosters has been a popular teacher for quite some time, also in other science departments such as mathematics and physics. Not surprisingly this is his second nomination in a row for the annual Teaching Award. Many students know him from the Programming Methods course he teaches in year one, the ‘Artificial Intelligence’ course in year two and supervising Bachelor and Master projects. All students are generally very pleased with his approach. Walter is very committed to his students and very accessible to them. With his enthusiastic, story-telling teaching methods he is able to make students enthusiastic about partici pating in his lectures. The assignments he sets are relevant and he always looks for “out-of-the-box” solutions for his assignments. Walter is also involved in a raft of other activities, including various open days and information days and the first-year diploma graduation. Currently he is the director of bachelor education at LIACS.
Prof. Abrahams is an inspiring teacher who attaches great importance to working in an interdisciplinary environment. This year, he set up a new interdisciplinary course ‘Cyttron II’ for all master students at our Faculty. For this course prof. Abrahams has put a lot of effort into inviting speakers from several universities and companies and made sure there was an original examination. Everyone had to meet one of the speakers to discuss the subject in order to write a research proposal and a corresponding poster. The posters where shown during the Cyttron symposium at Naturalis. Prof. Abrahams also teaches the master course “Analysis of the 3D structure of proteins by diffraction and imaging methods” (PSDI). During this course complex techniques are explained very clear with a lot of examples. Students have the opportunity to do a research project with his research group and during such a project, he makes you feel very welcome. He is really open to the ideas of students. It is easy to ask him something, which is sometimes different from other professors!
Prof. Lies Bouwman Leiden Institute of Chemistry Lies Bouwman has been nominated for the BSc course on ‘Chemistry and the Application of Overgangs metals’ and the MSc courses on ’Organic Metallic Chemistry’, ‘Homogeneous Catalysis’ and ‘Physical Methods in Inorganic Chemistry’. Lies Bouwman teaches in a very vivid way and her lectures are highly structured. This year she added a way to indicate the priority on her slides, which make it much easier for students for study for their exams. She also includes specific lectures which she calls intermezzo’s to give an overview of the application of the research on Metals in Catalysis, Biomimetics and Inorganic Materials.
Dr. Marjo de Graauw Leiden Academic Centre for Drug Research With her fresh approach to teaching, Marjo is continually looking for ways of improving our programmes. The mentorate system, that has undergone major changes over the past two years, is a good example. One change is the special training now given to student mentors, which means they are better prepared for their first-year classes, and are able to improve their supervision. First year students were confronted with their future as scientists early during the course on “case effects”. Which taught the students to work together. And they came into contact with their potential future in the medical industry. For Marjo, the idea of ‘motivation’ is really important. Even though the group of Bio-pharmaceutical students is increasing, she always finds new ideas to keep them motivated. She is always ready for a good discussion and is always keen to find out what will work and what won’t. Students say: “The whole Faculty can learn a lot from Marjo’s inventive method of teaching.”
Dr. Dennis Claessen Institute of Biology Leiden Dennis starting working at Leiden University in 2010. At his lab, which his students call the ‘Dennis Lab’, it’s always busy. PhD candidates, students on an internship and students from the BSc and MSc programmes are actively involved with the research as part of their degree programmes. As a tutor Dennis is closely involved with his students, and is known for his sharp mind and the continual smile. He teaches several courses on microbiology and others that focus on biotechnology, including ‘Exploitation of Natural Products’, ‘Molecular Microbiology’ and ‘Microbial Evolution & Ecology , ‘Microbial & Plant Biotechnology’ and the Minor ‘Fundamentals of Molecular Biotechnology’. Apart from firm supervision of his students, Dennis also focuses on improving research and teaching methods using the most up to date technology and software. Dennis is known for his active use of social media in his teaching and in his research. He regularly posts interes ting items about developments in his research area, as well as sharing personal news from time to time, particularly about his children.
Awards and Prizes in 2014 Education Physics Mathematics Computer Science
MSc students Henk Snijders and Misha Klein, each have won a Casimir PhD position Stéphanie van der Pas received the MSc Thesis Prize 2014 from Leiden University MSc students Media Technology Lisa Rombout and Arjen Suijker together with PhD student Robin de Lange won the Hack the Brain hackathon MSc student Tom Groentjes and PhD student Bas van Stein won the originality prize in the Hackaton contest organised by the Dutch Ministry of Foreign affairs for their anti identity fraud App Team Syntax Error with MSc students Bas Nieuwenhuizen, Mathijs van de Nes and Niels ten Dijke won the Benelux Algorithm Programming Contest (BAPC) Wendy Gunther MSc student ICT in Business graduated 'summa cum laude' Amaya Verschuur and Maarten Stam, BSc students Molecular Science & Technology received a Topsector Chemistry scholarship Anthe Janssen graduated ‘summa cum laude’ and received the Unilever Research Prize Thijmen Breeschoten received the annual award for being the best BSc-student in 2013 from the 'Professor Dr. K. Bakker Foundation' Wouter Bruins received the Mr. K.J. Cath Prize for being an exemplary student entrepreneur Marie-Anne Frenken was chosen as Leiden University sportswoman of the year 2014 MSc students Lizah van der Aart and Blair Berger received an NWO Topsector scholarship in the Chemistry Student Competition Jelle Rademaker received a prize for his article in Environmental Science & Technology Anica Regett received the Stans Prize for her MSc thesis
Other Biology students Anne van der Meij and Marielle van Kooten and Life Science & Technology student Tomek Diederen were in the team (with colleagues from Delft and Hogeschool Rotterdam) won the golden medal in the iGEM competition at MIT The Almanak 2014 from student association ‘De Leidsche Flesch’ was elected by Mare as best almanak of Leiden University Jasper Bouman (Mathematics), Dennis van der Zwaan (Computer science), Nashwan Sabti (Physics), Amber Barendrecht (Life Science and Technology), Lois van Druten (Molecular Science and Technology) and Indy du Fosse (Molecular Science and Technology) received a Jong Talent Support Prize from the Royal Dutch Society for Science (Koninklijke Hollandsche Maatschappij der Wetenschappen).
Various moments in 2014 including the presentation of student projects at the Industrial Ecology Alumni Event, group pictures of the Summer Schools, graduation ceremony â€˜P-in-1â€™ and the Physics Ladies Day.
LEIDEN SCIENCE FOR INNOVATION AND SOCIETY Scientific research is vital for society. By carrying out fundamental research and providing excellent education, universities become a breeding ground for innovation and entrepreneurship. These activities are needed to address the challenges society is facing today. The Faculty of Science greatly values the societal impact of scientific knowledge, and we are proud to present the highlights of impact activities at our faculty over the course of the past year. Apart from commercializing an invention through a spin-off company or patent, there are many ways to make an impact. These highlights show a broad spectrum of knowledge transfer to society, for example by making knowledge and expertise available for small and medium enterprises, by applying academic methods to issues such as food safety and waste, and by disseminating academic insights to general audiences. In the interests of science for society we encourage our students and researchers to address societal challenges and open up further research and innovation activities
Inspire children by the beauty of our Universe George Miley
To help primary school teachers introduce young children to the beauty and secrets of our Universe, Professor Miley and Methodelink are working together to produce an innovative video for training purposes. This will be followed by a further four videos. Methodelink is a creative organization in the field of education that focuses on producing videos for primary schools The project has been funded with a KIEM prize and is closely related to the Universe Awareness program of which Miley is the founding father. Leiden Institute of Biology
The development of a sustainable polystyrene foam replacer with mycelium and organic fibers Arthur Ram
Conventional foam is made from fossil fuels. Bonding – or gluing - organic fibers to each other with the aid of solid networks of fungal threads creates a strong and lightweight material. Further research is needed to find the optimum combination of fiber sources, fungal species and growing conditions in order to make the material suitable for applications in the packaging industry. To this end microbiologist Arthur Ram together with ‘Generation of Change VOF’ received a KIEM prize in 2014 from the Dutch Organisation for Scientific Research (NWO) to conduct research on these fibers .
Leiden Institute of Chemistry
Viewing the 3D structure of biomolecules Jan Pieter Abrahams
Professor Jan Pieter Abrahams will be carrying out research on the 3D structure of biomolecules, aiming to gain a better understanding of certain difficult to treat diseases. The STW Technology Foundation has awarded him a grant of € 25,000 to carry out this research. Abrahams wants to examine the 3D structures of biological molecules, many of which can be determined using crystallography. However, this method
is not universally effective. Abrahams will therefore be investigating whether electron microscopy can help determine the 3D structure of those molecules for which crystallography is not an option. Electron microscopes can focus so precisely that even the most minute details such as the atoms in a virus become visible. This is the first step towards gaining a better understanding of diseases such as tuberculosis, malaria and cancer.
Institute of Biology Leiden
“Pulp Fraction”: Tackling the orange waste mountain MSc students Lizah van der Aart and Blair Berger Around 70 million tons of oranges are grown worldwide every year. It is estimated that during the production of orange juice up to 20 million tons of waste are produced, mainly from the peel, pulp, seeds, orange leaves and fruits that do not meet quality standards. The orange residue consists of soluble sugars, cellulose, hemicelluloses, pectin, flavonoids and essential oils, which can be used to create a number of interesting products. Our students proposed a new method - using solvents identified by Dr. Young Choi from the IBL and a so-called Upper
Fluid Extraction (SFE) method at the TU Delft, in which flavonoids can be kept intact. Different flavonoids could provide a natural nutraceutical product from a currently underused raw material stream. The word nutraceutical is a combination of nutrition and pharmaceutical, and refers to a food or foods that provide health and medical benefits, including the prevention and treatment of disease. The students convinced NWO of the high potential of their method and received a scholarship of € 27,000 to implement their project.
Leiden Institute of Advanced Computer Science
Algorithms and Data Science for industry Thomas Bäck
Professor Thomas Bäck was the winner of the prestigious 2015 IEEE CIS Evolutionary Computation Pioneer Award. This award was in recognition of his pioneering research conducted in the early nineties on developing a unifying algorithmic and theoretical framework for genetic algorithms, evolution strategies, and evolutionary programming. This framework made it possible, for the first time, to systematically compare algorithms and their components. The generic algorithm was called the “evolutionary algorithm”, which later evolved into “evolutionary computation” as a name for this field of research. Evolutionary algorithms are used today for optimizing a vast range of products and processes, ranging from automotive development to logistics and supply chain applications. Thomas Bäck has contributed to their understanding in multiple projects, such as a project for Tata Steel and BMW to improve the production process of cars. In October, together with several partners, he received a grant from the Netherlands Organisation for Scientific Research within the data science program ‘Challenging big data’. This new funding will enable LIACS to engage in a four-year project aimed at developing a new system for controlling and optimizing industrial production processes.
One method of transferring technology and knowledge from Leiden University to society is by setting up new companies, bridg ing the gap between science and society. This year, a new project, ‘Vrijplaats’, was set up to support and stimulate students to do exactly that. Students from Leiden University who have the ambition of starting an innovative company, are welcome to join the project and meet fellow student entrepreneurs in an informal and relaxed atmosphere. ‘Vrijplaats’ organizes talks by successful entrepreneurs, and startup experts and provides new entrepreneurs with experienced mentors. It aims to provide support to entrepreneurial students from the Leiden University community and in turn stimulates the creation of companies that put knowledge into practice. The project originated in the Science Faculty, and is now taking in more and more students from all faculties and disciplines. Vrij plaats is expected to move into a building across from Leiden Central Station at the start of 2015. Entrepreneurial students from all disciplines are invited to join this hub of entrepreneurship and create exciting new companies.
Leiden Academic Center for Drug Research
Cooperation with Treeway on ALS therapy development Piet Hein van der Graaf
Treeway and LACDR have joined forces to form a cooperation that focuses on optimizing clinical trial designs and data analysis for ALS (Amyotrophic Lateral Sclerosis) through the use of population disease progression models. Both obtain a better understanding of the disease by developing ALS physiology-based disease models and to test the effect of interventions in the different pathways identified. Inez de Greef, CEO of Treeway: “By applying pharmacometric modeling and clinical trial simulations we can streamline our clinical development programs for new treatments for ALS. In addition, the physiology-based model will provide direction
for our discovery efforts.” Professor Piet Hein van der Graaf, Director of LACDR and head of the Department of Pharmacology at Leiden University, believes the cooperation with Treeway signals an important trend in drug discovery and development. “Rare and neglected diseases have been ignored by large pharmaceutical companies due to the limited return on high-risk R&D investment,” Therefore, cooperations like this between academics and small entrepreneurial biotech companies will be of vital importance in bringing new medicines to patients in areas of high, unmet medical need like ALS.”
Leiden Institute of Physics
Food safety and astronomy? Marco Beijersbergen
‘Scanning’ food for quality and freshness during the production proces. That’s possible using space technology! Spin-off company Condi Food has won the Hermen Wijfels Innovation Prize for 2014 in the ‘Food & Agri’ category. “Food safety will be an important theme for the coming decades,’ was the jury’s comment. Technology is already being used to determine the freshness of fish at Schmidt Zeevis. By scanning the fish we can measure how old it is, within a margin of 6 hours. According to
Marco Beijersbergen, Extraordinary Professor at the Leiden Institute of Physics and co-owner of Condifood: “At the moment quality control of food is done by random checks. With our techniques, you can check all the products. It avoids wastage of food and is a lot more secure.” Beijersbergen already knows what Condifood is going to do with the prize money: ‘We are working on bacteria detection with our camera systems. We can now speed up the development process.”
37 Leiden Academic Centre for Drug Research
€ 4.1 million investment for ‘organ-on-a-chip’ technology Paul Vulto Investments by the ‘Zeeuws Investerings Fonds’ (ZIF) and the ‘Participatiemaatschapij Oost Nederland’ (PPM Oost) will make it possible for the spin-off company MIMETAS to become the leader in the field of organ-on-achip technology. MIMETAS is developing this technology for drug screening in 3D tissues. Its unique microfluidic platform enables testing of compounds at high throughput on miniaturized organ models. These models show better predictivity compared to laboratory animals and conventional cell culture models. The MIMETAS OrganoPlate™ platform supports 3D cell culture under continuous perfusion, with membrane free co-culture and control of boundary and gradient formation, mimicking the important aspects of tissues and organs. MIMETAS develops and validates customized disease, toxicology and transport tissue models.
Institute of Environmental Sciences
Improved online pesticide atlas Specific pesticides are used for particular types of land usage in different areas of the world. The online atlas has been providing information on pesticides in surface water in the Netherlands for over ten years. The website shows researchers and policymakers where pesticides are being measured in surface water, where and when the prescribed norms are not being met and what the most important problem substances are.
New features have now been added that make the site more effective for use in regional and national environmental policies. One way this is being achieved is by making a link between land usage and pesticides. Other features provide information about concentrations of pesticides in surface water in relation to land usage, instances of non-compliance and the number of substances involved in non-compliance for the different
water quality standards. The pesticide atlas was developed in cooperation with Royal Haskoning DHV at the request of the Ministry of Infrastructure and the Environment.
Building for the future After the festive launch of the construction of our new Science Campus in 2013, the building activities have progressed rapidly over the past year. The outline from the first phase of construction is making its appearance felt in the surroundings of the existing Science buildings, next door to the University Sport complex. Just one year of building activities lies ahead; the first phase of the Science Campus is expected to be ready by the end of 2015. With a total floor area of 100,000 square meters for all project phases, the new campus will offer a high-tech environment to achieve our research and education goals at international level. Sixteen islands are planned in the low vibration area (in Dutch, the ‘meethal’) of the construction site. These heavy concrete islands (each weighing 30,000 kg) are dilated from the environment and will be placed on steel or air springs on the foundation floor that measures 65 x 20 x 1 meters. About a hundred enormous concrete mixer trucks drove back and forth over the past months to deliver the material for constructing this floor. The expected vibration curve will be one of the best in the Netherlands. The design of the new housing is based on grouping related activities together, meaning that, wherever
possible, all chemical-related activities are located into the same area. The same applies to biochemical activities, heavy equipment, low vibration, imaging, nano microscopy, etc. This will create a more efficient working environment for our staff and students, that will be equipped with high level areas challenging and facilitating interdisciplinary cooperation. The central axis that runs through the complex from front to back will serve as a meeting place, enabling staff and students to connect.
Some interesting facts about the first phase of construction: • About 45,000 m2 of floor area, including a car parking facility underneath the complex, systems and storage in the basement • 12,200 m2 land surface • Buildings about 9,100 m2 • 1 2% of the new building will house offices, 38% laboratories, 24% laboratory-d space and room for other users, 4% meeting rooms and storage and 22% will comprise building-related areas
Progress and activities relating to the building of the new Science Campus can be followed via our website (Dutch) which also provides a live stream connection from the construction site and a virtual model of the complex. You can also follow the Science Campus via Facebook and Twitter. www.science.leidenuniv.nl/index.php/betacampusfwn @BetaCampusFWN Beta Campus FWN
• Sustainability: the new Science Campus will be one of the first buildings in the Netherlands with laboratories that are certified by the Dutch Green Building Council Breeam • Ready by the end of 2015 • The first phase will end with a six-month period of extensive furnishing and removals. Staff and students will be able to occupy the new buildings from mid-2016.
Our science community Staff members
24 | 11
Staff members Faculty of Science* Total
1910 1283 67% 627 33% Male
* End 2014, including guest lecturers and honorary staff members.
839 | 387
24 | 8 12 | 4
43 | 25
20 | 10 8 | 5 10 | 12
41 | 26
73 | 38
12 | 10
18 | 7
Dutch vs other nationalities Dutch
1226 64% 684 36%
Our science community Students
1580 | 821
17 | 12
Students Faculty of Science
2998 1917 64% 1081 36% Male
25 | 11
24 | 22 16 | 6
11 | 5 5|5
11 | 5 9|2
20 | 10
36 | 19
20 | 17
20 | 38
8 | 12
Dutch vs other nationalities Dutch
2401 80% 597 20%
Faculty of Science P.O. Box 9502 2300 RA Leiden 071 527 69 90 science.leidenuniv.nl
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