Related papers: Topological Catenation-induced Pore Size in 2D Oly…
A fundamental task in developmental biology is to identify the mechanisms which drive morphogenesis. In many cases, pattern formation is driven by the positional information determined by both the gradient of maternal factors and hard-wired…
The macroscopic spreading and mixing of solute plumes in saturated porous media is ultimately controlled by processes operating at the pore scale. Whilst the conventional picture of pore-scale mechanical dispersion and molecular diffusion…
Topological insulators are crystalline materials that have revolutionized our ability to control wave transport. They provide us with unidirectional channels that are immune to obstacles, defects or local disorder, and can even survive some…
Understanding the fundamental mechanisms behind plastic instabilities and shear band formation in amorphous media under applied deformation remains a long-standing challenge. Leveraging on the mathematical concept of topology, we revisit…
We study diffusion of information packets on several classes of structured networks. Packets diffuse from a randomly chosen node to a specified destination in the network. As local transport rules we consider random diffusion and an…
Networked structures arise in a wide array of different contexts such as technological and transportation infrastructures, social phenomena, and biological systems. These highly interconnected systems have recently been the focus of a great…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
Soft living tissues like cartilage can be considered as biphasic materials comprised of a fibrous complex biopolymer network and a viscous background liquid. Here, we show by a combination of experiment and theoretical analysis that both…
Geometric graph neural networks (GNNs) that respect E(3) symmetries have achieved strong performance on small molecule modeling, but they face scalability and expressiveness challenges when applied to large biomolecules such as RNA and…
Shear stress is an important physical factor that regulates proliferation, migration and morphogenesis. In particular, the homeostasis of blood vessels is dependent on shear stress. To mimic this process ex vivo, efforts have been made to…
Complex networks are characterized by latent geometries induced by their topology or by the dynamics on the top of them. In the latter case, different network-driven processes induce distinct geometric features that can be captured by…
The function of membrane-embedded proteins such as ion channels depends crucially on their conformation. We demonstrate how conformational changes in asymmetric membrane proteins may be inferred from measurements of their diffusion. Such…
Efforts aimed at large-scale integration of nanoelectronic devices that exploit the superior electronic and mechanical properties of single-walled carbon nanotubes (SWCNTs) remain limited by the difficulties associated with manipulation and…
Manipulation of material properties via precise doping affords enormous tunable phenomena to explore. Recent advance shows that in the atomic and nano scales topological states of dopants play crucial roles in determining their properties.…
An effective model for protein structures is important for the study of protein geometry, which, to a large extent, determine the functions of proteins. There are a number of approaches for modelling; one might focus on the conformation of…
A recurring motif in the organization of biological tissues are networks of long, fibrillar protein strands effectively confined to cylindrical surfaces. Often, the fibers in such curved, quasi-2D geometries adopt a characteristic order:…
Entropic repulsion between DNA ring polymers under confinement is the key mechanism governing the spatial segregation of bacterial chromosomes, although it remains incompletely understood how proteins aid the process of entropic…
Topological properties of native folds are obtained from statistical analysis of 160 low homology proteins covering the four structural classes. This is done analysing one, two and three-vertex joint distribution of quantities related to…
Motivation: Gene regulatory interactions are of fundamental importance to various biological functions and processes. However, only a few previous computational studies have claimed success in revealing genome-wide regulatory landscapes…
Polymer architecture plays critical roles in both bulk rheological properties and microscale macromolecular dynamics in entangled polymer solutions and composites. Ring polymers, in particular, have been the topic of much debate due to the…