In the first part of this thesis we study the geometry of folding patterns.

What are the principles of genome folding and dynamics in bacteria?

Science, Leiden Institute of Chemistry (LIC)

In an Advance Online Publication biophysicist John van Noort and others show using magnetic tweezers that DNA is folded in compliant helices of chromatin. This allows enzymes access to the DNA needed for gene expression. Van Noort's research group made the discovery in close partnership with researchers…

The more complex the object, the harder it is to fold up. Space satellites often need many small motors to fold up an instrument, and people have difficulty simply folding up a roadmap. Physicists from Leiden and Amsterdam have now designed a structure that folds itself up in several steps. Publication…

What would be the environmental performance of the Carbon4PUR technology at industrial scale in the future?

Leiden physicist Maarten Kruithof has discovered how our DNA is infallibly able to fold itself and to unfold again. In his dissertation he demonstrates how DNA is folded in a single long, very flexible spiral.

Law researcher Evelien Campfens is calling for a better legal treatment of looted art. ‘For lawyers, ownership is a very absolute concept. There is one legal owner and that is that.’ Campfens is a PhD candidate at the Leiden-Delft-Erasmus Centre for Global Heritage and Development.

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.

Martin van Hecke published an article in Nature, together with physicists from AMOLF and UvA. They have developed a metamaterial that folds itself up, even in multiple steps. Van Hecke appeared in the following media.

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…

Source: Structure , Volume 22, Issue 8, pp. 1120-1139 (2014)

The CIGR brings together a diverse range of unique expertise in genome research rooted in biology, chemistry and physics. Members of the CIGR investigate genome folding and genome transactions. An important aspect is direct as well as long term relevance for medicine. The available expertise extends…

This month, a paper was published in Nanoscale by scientists from Dr. Alireza Mashaghi group at the Systems Biomedicine and Pharmacology Division in collaboration with the group of Dr. Sander Tans from TU Delft/AMOLF. In this paper, the authors studied how nanoscale spatial confinement affects the fold…

The CIGR comprises research groups from the Institute of Biology Leiden (IBL), the Leiden Institute of Chemistry (LIC), the Leiden Academic Centre for Drug Research (LACDR) and the Leiden Institue of Physics (LION).

How can a single origami crease pattern be folded into two precisely defined target shapes? Researchers at AMOLF and Leiden University have created an ‘alphabet’ of 140 origami ‘puzzle pieces’ that allows them to do just that, as described today in Nature Physics. This discovery could help in the construction…

The genetic information of all living organisms is contained in their DNA. Cells modify the degree of DNA compaction by epigenetics, which largely determines what genes are read out and which genes are transcriptionally silent.

The genomic DNA of every organism is organized and compacted in order to fit inside the cell. This is achieved by the joint action of numerous architectural proteins that aid in folding the genome. Genome folding is tightly interconnected with transcription, with genes in certain regions being silenced,…

Mashaghi lab conducts research at the interface of physics, engineering and biomedicine. We develop and use theoretical and experimental approaches to address basic and applied research problems.

Physics and Engineering Approaches to Biomedicine and Pharmacology

The GTGC programme advances interdisciplinary research on how we govern – and could govern – major world-scale changes in contemporary society. These global transformations and governance challenges cover the themes listed here. The distinctions are not rigid, of course, and affiliated researchers often…

The CIGR brings together a diverse range of unique expertise in genome research rooted in biology, chemistry and physics. Members of the CIGR investigate genome folding and genome transactions. An important aspect is direct as well as long term relevance for medicine.

Microneedle-based vaccination has several advantages over vaccination by using conventional hypodermic needles.

This thesis focuses on using liposomes in two different treatment strategies; vaccination (or immunotherapy) and delivery of a small molecule, and in two different disease models; cancer and atherosclerosis.

The thesis describes the use of electron paramagnetic resonance (EPR) spectroscopy, in continuous wave and pulse modes, to address the interaction of α-Synuclein (αS) with membranes and the aggregation of αS.

Inaugural Lecture

Inaugural Lecture

John van Noort

The Centre for Late Antique and Medieval Studies (LAMS) is an academic initiative housed at the Leiden University Institute of Philosophy. It brings together researchers and academics working on one or more aspects of late antiquity and medieval studies, across the fields of philosophy, history, theology,…

BlaC is the β-lactamase of Mycobacterium tuberculosis. We show that it can recover from inhibition by clavulanic acid and that phosphate helps it do so.

In human cells, a meter-long DNA is condensed inside a micrometer-sized cell nucleus. Simultaneously, the genetic code must remain accessible for its replication and transcription to functional proteins.

Throughout all domains of life, from bacteria and archaea to eukaryotes, genomes adopt well-organized three-dimensional structures that can change in space and time to accommodate preferred transcriptional programs for environmental adaptation, the maintenance of cellular identity and differentiation…

A large, 64+ person space with multiple working zones in the Schouwburgstraat building, Den Haag. Tables fold and wheel, and chairs are also on wheels. There are multiple movable whiteboards which allow group working in various sizes. Windows and tables are additional writing surfaces. There is also…

Research at the Macromolecular Biochemistry group is comprised of the following research themes:

The way DNA folds, largely determines which genes are read out. John van Noort and his group have quantified how easily rolled-up DNA parts stack. This costs less energy than previously assumed. Publication in Biophysical Journal.

Relevant publications of the CIGR participants.

Science, Leiden Academic Centre for Drug Research (LACDR)

Promotor: M. Ubbink, Co-Promotor: R. T. Dame

The objective is to develop in vitro antigen degradation assays in order to mimic the fate of the antigen in vivo.

Every week, ISGA organizes the Research Seminar Series discussing works from ISGA staff and externals.

We study the interplay of topology and geometry with chirality for several passive and active systems, employing both analytical and numerical methods.

Promotor: B. vd Water, T. Schmidt, Co-Promotor: E.H.J. Danen

The indane (2,3-dihydro-1H-indene) ring system is an attractive scaffold for biologically active compounds due to the combination of aromatic and aliphatic properties fused together in one rigid system.

This study interrogates contemporary and historical uses of barbarism, arguing that barbarism also has a disruptive, insurgent potential.

The main subject of this thesis is the design and synthesis of paramagnetic molecules for protein studies with NMR and EPR spectroscopy.

The role of grave sets in Corded Ware and Bell Beaker funerary practices

On 21 October 2021, Frederik Behre defended the thesis 'A European Ministry of Finance?'. The doctoral research was supervised by Prof. S.C.G. Van den Bogaert.

On a structural level, the properties featured by a majority of mechanical metamaterials can be ascribed to the finite number of soft internal degrees-of freedom allowing for low-energy deformations.

The writings of Walter Benjamin (1892-1940) are famously and purposely marked by fragmentariness. Paradoxically, a central aim of his work was to connect: all his life he sought to further the integration of scholarship in the humanities which, he believed, had too long suffered from the prevalence…