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With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, we need a revolutionary sequencing method for the…
Genomes evolve as modules. In prokaryotes (and some eukaryotes), genetic material can be transferred between species and integrated into the genome via homologous or illegitimate recombination. There is little reason to imagine that the…
Biological signaling is imagined as a combination of activation and transport. The former is triggered by local molecular interactions and the latter is the result of molecular diffusion. However, other fundamental physical principles of…
The Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked 2.5 kb-long DNA minicircles found in certain parasites called Trypanosomes. Understanding the self-assembly and replication of this structure are…
Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide…
Protein-Protein Interaction Networks aim to model the interactome, providing a powerful tool for understanding the complex relationships governing cellular processes. These networks have numerous applications, including functional…
Transcription is the first step of gene expression, in which a particular segment of DNA is copied to RNA by the enzyme RNA polymerase (RNAP). Despite many details of the complex interactions between DNA and RNA synthesis disclosed…
We study a protein-DNA target search model with explicit DNA dynamics applicable to in vitro experiments. We show that the DNA dynamics plays a crucial role for the effectiveness of protein "jumps" between sites distant along the DNA…
Two processes can influence the evolution of protein interaction networks: addition and elimination of interactions between proteins, and gene duplications increasing the number of proteins and interactions. The rates of these processes can…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
Capturing the physical organisation and dynamics of genomic regions is one of the major open challenges in biology. The kinetoplast DNA (kDNA) is a topologically complex genome, made by thousands of DNA (mini and maxi) circles interlinked…
A central question in developmental biology is how size and position are determined. The genetic code carries instructions on how to control these properties in order to regulate the pattern and morphology of structures in the developing…
The spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics…
Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
Biological materials are self-assembled with near-atomic precision in living cells, whereas synthetic 3D structures generally lack such precision and controllability. Recently, DNA nanotechnology, especially DNA origami technology, has been…
We calculate the equation of state of DNA under tension for the case that the DNA features loops. Such loops occur transiently during DNA condensation in the presence of multivalent ions or sliding cationic protein linkers. The…
Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for…
Living organisms are the most complex, interesting and significant objects regarding all substructures of the universe. Life science is regarded as a science of the 21st century and one can expect great new discoveries in the near futures.…
The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic…