Related papers: Modelling DNA Origami Self-Assembly at the Domain …
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
DNA monolayers with inherent chirality play a pivotal role across various domains, including biosensors, DNA chips, and bioelectronics. Nonetheless, conventional DNA chiral monolayers, typically constructed from single-stranded DNA (ssDNA)…
Periodic origami patterns made with repeating unit cells of creases and panels bend and twist in complex ways. In principle, such soft modes of deformation admit a simplified asymptotic description in the limit of a large number of cells.…
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…
Origami-inspired self-deployable structures offer lightweight, compact, and autonomous deployment capabilities, making them highly attractive for aerospace and defence applications, such as solar panels, antennas, and reflector systems.…
Origami morphing, obtained with patches of piecewise smooth isometries separated by straight fold lines, is an exquisite art that has already received considerable attention in the mathematics and mechanics literature. Curved fold lines,…
Membrane morphology and its dynamic adaptation regulate many cellular functions, which are often mediated by membrane proteins. Advances in DNA nanotechnology have enabled the realization of various protein-inspired structures and functions…
We propose a novel computational framework for modeling and simulating origami structures. In this framework, bilinear solid-shell elements are employed to model the origami panels while crease folding is considered through the angle…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
We present a new simulation scheme which allows an efficient sampling of reconfigurable supramolecular structures made of polymeric constructs functionalized by reactive binding sites. The algorithm is based on the configurational bias…
Foundation models in genomics have shown mixed success compared to their counterparts in natural language processing. Yet, the reasons for their limited effectiveness remain poorly understood. In this work, we investigate the role of…
Constitutive modeling lies at the core of mechanics, allowing us to map strains onto stresses for a material in a given mechanical setting. Historically, researchers relied on phenomenological modeling where simple mathematical…
By taking into account base-base stacking interactions we improve the Generalized Model of Polypeptide Chain (GMPC). Based on a one-dimensional Potts-like model with many-particle interactions, the GMPC describes the helix-coil transition…
The possibility of prescribing local interactions between nano- and microscopic components that direct them to assemble in a predictable fashion is a central goal of nanotechnology research. In this article we advance a new paradigm in…
Twisting sheets as a strategy to form functional yarns relies on millennia of human practice in making catguts and fabric wearables, but still lacks overarching principles to guide their intricate architectures. We show that twisted…
The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…
This chapter will provide an overview of how characterizing free-energy landscapes can provide insights into the biophysical properties of DNA, as well as into the behaviour of the DNA assemblies used in the field of DNA nanotechnology. The…
A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and…
Recent experiments have been able to visualise chromosome organization in fast-growing E.coli cells. However, the mechanism underlying the spatio-temporal organization remains poorly understood. We propose that the DNA adopts a specific…
Self-assembly in the laboratory can now yield `information-rich' nanostructures in which each component is of a distinct type and has a defined spatial position. Ensuring the thermodynamic stability of such structures requires…