For the first time, astronomers have detected the presence of complex organic molecules, the building blocks of life, in a protoplanetary disc surrounding a young star. The discovery reaffirms that the conditions that spawned the Earth and Sun are not unique in the Universe. The results are published…

A single tiny molecule that can destroy flu, corona, HIV and Zika viruses? Yes, it really does exist. Biophysicist Niek van Hilten, who will receive his doctorate on 14 September, contributed to this discovery.

Despite being the object of intense study, embryonic development has been difficult to model due to a number of reasons. First, complex tissues can be comprised of many cell types, of which we probably only know a subset.

The deeper understanding of an organism's pathology is important for developing treatments. Over centuries of systematic research, clinical researchers have demonstrated that the more information they acquire about the cellular properties and their organisation in the tissue, the better they can understand…

Biophysicist Rolf Harkes has developed a microscope to optically localize individual molecules in living cells. It improves monitoring of diseases like cancer and Parkinson’s at the cellular level. Defende PhD thesis on t13 January 2016.

Can the venom of snakes, scorpions and other animals be sources of new antibiotics?

This thesis consists of two main parts. The first part (Chapters 2 and 3) deals with a class of Markov process called Quasi-Skipfree (QSF) processes.

Michel Orrit has received an NWO-TTW Open Technology Programme grant. He will use it to image single molecules without the need for fluorescence.

Detecting molecules with temperature instead of chemical reactions: that’s what scientists from the Leiden Institute of Physics want to do. They are developing a sensor that utilizes special nanoparticles to keep track of certain molecules. In this way, they can for example see how well new drugs do…

The Joan van der Waals colloquium is an ongoing bi-weekly lecture series.

This Thesis shows discoveries in non-linear astrochemical kinetics as well as a deeper analysis of dark clouds chemistry.

Is it possible to diagnose diseases using molecular switches? The new international consortium LogicLab will address this question. Leiden chemist Sylvestre Bonnet and Leiden pharmacologist Thomas Hankemeier are involved in the project. LogicLab will run for four years and will receive over 3.5 million…

Single-celled organisms have stiffer DNA than multicellular lifeforms like humans and rice. Theoretical physicists managed to simulate the folding in full genomes for the first time to reach this conclusion. Publication in Biophysical Journal on February 7.

Leiden physicists have developed a way to address how accurately a superconducting single photon detector (SSPD) can be characterized by detector tomography. SSPDs are not fully understood, and tomography is a key element to determine how these devices detect light. A better understanding of these detectors…

Nucleoid associated proteins maintain the architecture of the bacterial chromosome and regulate gene expression, hinting that their role as transcription factors may involve local three-dimensional chromosome re-modelling.

In this thesis, we describe the potential of cell mechanical phenotyping for immune cell characterization, diagnosis, drug testing, as well as treatment of disease.

Molecules are extremely hard to see in visible light, especially without using fluorescence. Leiden physicists have now made their optical technique sensitive enough to image the molecules of their interest in all sizes. Publication in Nanoletters.

The surface and the edges of graphene are expected to provide higher sensitivity and specificity in detecting and characterizing single molecules. However fundamental physical limits exist in reaching an ultimate precision in detecting the dynamics of chemical and biological systems. The research in…

An accurate description of reactive scattering of molecules on metal surfaces often requires the modeling of energy transfer between the molecule and the surface phonons. Although ab initio molecular dynamics (AIMD) can describe this energy transfer, AIMD is at present untractable for reactions with…

Freshwater is an important resource, but at a great risk of species decline due to habitat loss, pollution and over-exploitation, and invasive alien species.

Planets are formed in disks of gas and dust around young stars.

This thesis investigates how cell shape and collective behavior influence the dynamics and structure of biological tissues, which are crucial for understanding processes like embryonic development, tissue regeneration, and metastasis.

A team of scientists, including Leiden Astronomer Alice Booth, has discovered silicon monosulfide molecules in the dust disk around a young star. Such molecules indicate planet formation. The team made the discovery using the ALMA telescopes. This method provides an alternative when direct observation…

Leiden chemists, together with colleagues at the University of York (UK) and Technion (Israel) have discovered a small, sugar-like molecule that maintains the integrity of tissue around a tumour during cancer. This molecule prevents tumour cells from spreading from the primary cancer site to colonise…

The E2CB programme has been launched to bring CO2 emissions to zero by 2050. The goal: to produce all raw materials for the chemical industry from sustainable sources. Professor of Electrochemistry Marc Koper is involved in the project.

The way genes are folded determines their activity in our body. Leiden biophysicists are now the first to unravel this structure molecule-by-molecule. Publication on December 1st in Nature’s Scientific Reports.

Visualising cell proteins without invasive techniques is possible with the help of fluorescence. During a lecture of the Natuurwetenschappelijk Gezelschap Leiden on 18 January, winner of the Spinoza Prize 2017 and founder of the field of single molecule optics Michel Orrit explained how this works.

Alexander Kros studies supramolecular systems in a biological environment. The unifying theme between the projects in my lab is specific molecular recognition, i.e. the intermolecular interaction between complementary molecules with high affinity and selectivity. Studying, imitating and dissecting processes…

The research presented in this thesis makes use of small molecules (as H2 , D2 and O2 ) on well-defined single crystal surfaces (flat Pt(111), flat Cu(211) and curved Pt(111)) to elucidate the role of surface structure and degrees of freedom in the reactant in specific surface reactions.

Exactly a century ago, astronomers observed the first two diffuse interstellar bands (DIBs) in space. A DIB manifests itself as a colour of light that is missing in the radiation from stars behind an interstellar cloud. Although about 500 DIBs are yet discovered, they remained inexplicable until recently.…

Researchers from the THEOR CHEM group at Leiden University strive to set new benchmarks in the accuracy of the prediction of interaction energies between molecules and metal surfaces.

Michel Orrit was awarded the Physica prize 2016 for his groundbreaking work on single molecule spectroscopy.

The standard approach to build a quantum computer with Majoranas as building blocks is to convert them into qubits. However, a promising application of quantum computing—quantum chemistry—would require these qubits to be converted again into so-called fermions. Physicists from Leiden and Delft suggest…

It's pretty hard to spot a single 5 nanometer particle. Leiden physicists pulled it off by turning a 120 nm gold rod into a detector.

The long-held desire - to link structure directly to function and to explain molecular mechanisms based on basic chemical or physical principles - is finally coming closer, satisfying not only our scientific curiosity but also offering new solutions to the many challenges in the field of health, energy…

On September 12, Michel Orrit received his Spinoza prize in the Royal Theatre in The Hague from OCW Secretary of State Sander Dekker. With the award comes a budget of 2.5 million euro, to be spent freely on scientific research, and the coveted Spinoza statue. Orrit shared the honor with Eveline Crone…

Research projects for students of the University of Leiden and other Dutch Universities are often available at the MacBio group. The research lines are also described in the Research section. For details of specific projects contact the supervisor (Ubbink, Dame, Boyle, Jeuken or Wentink).

Key publications of the Medical Systems Biophysics and Bioengineeringgroup (Mashaghi Lab)

Stars like the sun are born in large molecular clouds existing from gas and dust. During the formation process, the chemical composition of the material can be altered drastically by the changing physical conditions.

Promotor: T. Schmidt

Before researchers can develop targeted drugs, they need to know exactly how a disease works. Biochemist Bert Beerkens created molecules that allow them to find out. He used caffeine as the basis for new molecules that enable research into certain receptor proteins on cells.

The Royal Netherlands Academy of Arts and Sciences (KNAW) selects prominent researchers as members based on their scientific achievements. On September 17th, the KNAW will install 21 new members, including Leiden physicist Michel Orrit.

The team of Alireza Mashaghi at the Leiden Academic Centre for Drug Research has found a way to determine and classify the shape of proteins. Their new theory defines the topology of proteins as a simple and precise barcode that allows the identification of all types of folds. ‘This barcode enables…

During embryonic growth, cells proliferate, differentiate, and collectively migrate to form different tissues at the right position and time in the body.

A dense region of a gaseous and dusty cloud collapses to form a protostar surrounded by a disk and an envelope. This thesis uses both observations and models to study physical and chemical conditions of these protostellar systems which are likely where planets start to form.

Leiden biophysicists have found a new possible way to attack cancer cells. They have located ‘sinkholes’ on the cells where receptor proteins disappear from the surface. If a drug could push these proteins towards those areas, it would kill the cancer cell.