Related papers: Topological Catenation-induced Pore Size in 2D Oly…
We construct a micromechanical version of an early model for topologically constrained polymers -- a 2D chain amongst point-like uncrossable obstacles -- which allows us to explicitly elucidate the role of topological forces beyond…
One of the key characteristics of cancer cells is an increased phenotypic plasticity, driven by underlying genetic and epigenetic perturbations. However, at a systems-level it is unclear how these perturbations give rise to the observed…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
Topological photonics provides a robust and flexible platform for controlling light, enabling functionalities such as backscattering-immune edge transport and slow-light propagation. In this work, we design and characterize photonic…
Highly periodic structures are often said to convey the beauty of nature. However, most material properties are strongly influenced by the defects they contain. On the mesoscopic scale, molecular self-assembly exemplifies this interplay;…
This paper presents a synthesis approach in a density-based topology optimization setting to design large deformation compliant mechanisms for inducing desired strains in biological tissues. The modelling is based on geometrical…
Two-dimensional organic porous networks (2DOPNs) have opened new vistas for tailoring the physicochemical characteristics of metallic surfaces. These typically chemically bound nanoporous structures act as periodical quantum wells leading…
In eukaryotic cells, mitochondria form networks that range from highly fused interconnected structures to fragmented populations of individual organelles that undergo transient interactions. These structures can be described as temporal…
The topology of an object describes global properties that are insensitive to local perturbations. Classic examples include string knots and the genus (number of handles) of a surface: no manipulation of a closed string short of cutting it…
The relationship between the regulatory design and the functionality of molecular networks is a key issue in biology. Modules and motifs have been associated to various cellular processes, thereby providing anecdotal evidence for…
How type 2 Topoisomerase (TopoII) proteins relax and simplify the topology of DNA molecules is one of the most intriguing open questions in biophysics. Most of the existing models neglect the dynamics of TopoII which is characteristics for…
The ability to reroute and control flow is vital to the function of venation networks across a wide range of organisms. By modifying individual edges in these networks, either by adjusting edge conductances or creating and destroying edges,…
The formation of neuron networks is a process of fundamental importance for understanding the development of the nervous system and for creating biomimetic devices for tissue engineering and neural repair. The basic process that controls…
We model the transcription factor based regulation network of yeast using a content-based network model that mimicks the recognition of binding motifs on the regulatory regions of the genes. We are thereby able to faithfully reproduce many…
Cells contain elaborate and interconnected networks of protein polymers which make up the cytoskeleton. The cytoskeleton governs the internal positioning and movement of vesicles and organelles, and controls dynamic changes in cell…
Despite their considerable practical and biological applications, the link between molecular properties, assembly conditions and self-organized structure in confined polymer solutions remains elusive. Here, we explore the lyotropic nematic…
Proteins in photosynthetic membranes can organize into patterned arrays that span the membrane's lateral size. Attractions between proteins in different layers of a membrane stack can play a key role in this ordering, as was suggested by…
Proteins are an important class of biomolecules that serve as essential building blocks of the cells. Their three-dimensional structures are responsible for their functions. In this thesis we have investigated the protein structures using a…
We use graph theory simulations and single molecule experiments to investigate percolation properties of kinetoplasts, the topologically linked mitochondrial DNA from trypanosome parasites. The edges of some kinetoplast networks contain a…