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Morphological trends in growing colonies of living cells are at the core of physiological and evolutionary processes. Using active gel equations, which include cell division, we show that shape changes during the growth can be regulated by…

The research in topological materials and meta-materials reached maturity and is now gradually entering the phase of practical applications and devices. However, scaling down the experimental demonstrations definitely presents a challenge.…

Accurately modeling multi-class cell topology is crucial in digital pathology, as it provides critical insights into tissue structure and pathology. The synthetic generation of cell topology enables realistic simulations of complex tissue…

Polymers in a melt may be subject to topological constraints, as in the example of unlinked polymer rings. How to do statistical mechanics in the presence of such constraints remains a fundamental open problem. We study the effect of…

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…

Relevant information about the nature of the dynamics of ions in electrolytes can be obtained by studying the nonlinear dependence on an applied electric field. Here we use molecular dynamics (MD) simulations to study the field effects for…

The characterisation of quantum networks is fundamental to understanding how energy and information propagates through complex systems, with applications in control, communication, error mitigation and energy transfer. In this work, we…

Topological data analysis (TDA) uses persistent homology to quantify loops and higher-dimensional holes in data, making it particularly relevant for examining the characteristics of images of cells in the field of cell biology. In the…

Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…

The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…

DNA origami is a powerful method to achieve nanoscale folded structures. Despite rapid improvements in folding and purification methods, DNA origami objects are still often produced in small quantities and studied at single molecule scale.…

There is a long-standing experimental observation that the melting of topologically constrained DNA, such as circular-closed plasmids, is less abrupt than that of linear molecules. This finding points to an intriguing role of topology in…

Nonequilibrium states of quantum materials can exhibit exotic properties and enable unprecedented functionality and applications. These transient states are inherently inhomogeneous, characterized by the formation of topologically protected…

Simulations in which a globular ring polymer with delocalized knots is separated in two interacting loops by a slipping link, or in two non-interacting globuli by a wall with a hole, show how the minimal crossing number of the knots…

Topology provides an essential concept for achieving unchanged (or protected) quantum properties in the presence of perturbations. A challenge facing realistic applications is that the level of protection displayed in real systems is…

The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path…

Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…

Time is the odd dimension out: Unlike space, it follows the arrow of time, forbidding back-reflections and requiring momentum yet not energy conservation. Tailored temporal variations manipulate momentum bands and engineer waves in time. We…

Detecting topological order in cold-atom experiments is an ongoing challenge, the resolution of which offers novel perspectives on topological matter. In material systems, unambiguous signatures of topological order exist for topological…

We explore the interplay of disorder and topological phenomena in honeycomb lattices of atoms coupled by the electromagnetic field. On the one hand, disorder can trigger transitions between distinct topological phases and drive the lattice…