Related papers: A DNA-encoded recipe to direct multi-stage colloid…
One of the frontiers of nanotechnology is advancing beyond the periodic self-assembly of materials. Icosahedral quasicrystals, aperiodic in all directions, represent one of the most challenging targets that have yet to be experimentally…
We construct a theoretical model for the dynamics of a microscale colloidal particle, modeled as an interval, moving horizontally on a DNA-coated surface, modelled as a line coated with springs that can stick to the interval. Averaging over…
The design and implementation of regulation motifs ensuring robust perfect adaptation are challenging problems in synthetic biology. Indeed, the design of high-yield robust metabolic pathways producing, for instance, drug precursors and…
Complex nonequilibrium self-assembly enables the formation of materials with specific patterns and functions from the bottom up. How to directionally control the assembly to form the target configuration is a challenge. Here, we propose a…
Self-assembly, the process by which interacting components form well-defined and often intricate structures, is typically thought of as a spontaneous process arising from equilibrium dynamics. When a system is driven by external…
The goal of inverse self-assembly is to design inter-particle interactions capable of assembling the units into a desired target structure. The effective assembly of complex structures often requires the use of multiple components, each new…
Protein aggregation is of great importance in biology, e.g., in amyloid fibrillation. The aggregation processes that occur at the cellular scale must be highly stochastic in nature because of the statistical number fluctuations that arise…
Selective configuration control of plasmonic nanostructures using either top-down or bottom-up approaches has remained challenging in the field of active plasmonics. We demonstrate the realization of DNA-assembled reconfigurable plasmonic…
Non-equilibrium assembly, driven by fluxes controllable by continuous external energy inputs, enables dynamic and reconfigurable structures. Such controlled 3D assembly is desired for the design of adaptive materials that exploit…
We formulate statistical-mechanical inverse methods in order to determine optimized interparticle interactions that spontaneously produce target many-particle configurations. Motivated by advances that give experimentalists greater and…
Understanding the three-dimensional (3D) structure and stability of DNA is fundamental for its biological function and the design of novel drugs. In this study, we introduce an improved coarse-grained (CG) model, incorporating a more…
The self-assembly of functionalized (patchy) particles with directional interactions into target structures is still a challenge, despite the significant experimental advances on their synthesis. The self-assembly pathways are typically…
Multiple dissipative self-assembly protocols designed to create novel structures or to reduce kinetic traps have recently emerged. Specifically, temporal oscillations of particle interactions have been shown effective at both aims, but…
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…
DNA nanotechnology allows for the realization of complex nanoarchitectures in which the spatial arrangements of different constituents and most functions can be enabled by DNA. When optically active components are integrated in such…
Anisotropy at the level of the inter-particle interaction provides the particles with specific instructions for the self-assembly of target structures. The ability to synthesize non-spherical colloids, together with the possibility of…
Cells deploy robust mechanisms to repair DNA damage, safeguarding genomic stability and cellular health, but the physical principles underlying these processes remain incompletely understood. Experiments show \emph{in vitro} that upon a DNA…
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…
Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…
We simulate the assembly of DNA copolymers from two types of short duplexes (short double strands with a single-stranded overhang at each end), as described by the oxDNA model. We find that the statistics of chain lengths can be well…