Related papers: Substrate-assisted 2D DNA lattices and algorithmic…
The Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked 2.5 kb-long DNA minicircles found in certain parasites called Trypanosomes. Understanding the self-assembly and replication of this structure are…
The optimal design of DNA origami systems that assemble rapidly and robustly is hampered by the lack of a model for self-assembly that is sufficiently detailed yet computationally tractable. Here, we propose a model for DNA origami that…
Spatial transcriptomics (ST) is a promising technique that characterizes the spatial gene profiling patterns within the tissue context. Comprehensive ST analysis depends on consecutive slices for 3D spatial insights, whereas the missing…
This study presents innovative nested-isotropic lattices for additive manufacturing, drawing inspiration from bio-architectures found in cortical bone osteons, golden spirals, and fractals. These lattices provide tunable anisotropy by…
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
The process of self-assembly is guided by the minimization of free energy, which limits the symmetries available for assembly and ultimately the usefulness of devices fabricated in this fashion. Here, we demonstrate experimentally for the…
A single-step, single-material 4D printing method is developed for programmable structures featuring spatially patterned strain trapping for one-way actuation. This approach enables fabrication on desktop fused filament fabrication 3D…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
Renaturation of complementary single strands of DNA is one of the important processes that requires better understanding in the view of molecular biology and biological physics. Here we develop a stochastic dynamical model on the DNA…
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…
We use Monte Carlo simulations and free-energy techniques to show that binary solutions of penta- and hexavalent two-dimensional patchy particles can form thermodynamically stable quasicrystals even at very narrow patch widths, provided…
The spatial and dynamical structure of star-forming regions can help provide insights on stellar formation patterns. The amount of data from current and upcoming surveys calls for robust and objective procedures to detect structure, so the…
In contrast to the sequence dependent elasticity of the DNA strand, which is revealed as nonlocal and nonlinear, the geometric constraints derived by differential geometry have not been fully elaborated in DNA strand dynamics, even though…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
Folding nanopatterned flat sheets into complex 3D structures enables the fabrication of meta-biomaterials that combine a rationally designed 3D architecture (e.g., to tune mechanical and mass transport properties) with nanoscale surface…
Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the…
In this work, we present an automated platform for trapping and stretching individual micro- and nanoscale objects in solution using electrokinetic forces. The platform can trap objects at the stagnation point of a planar elongational…
The problem addressed here can be concisely formulated as follows: given a stable surface orientation with a known reconstruction and given a direction in the plane of this surface, find the atomic structure of the steps oriented along that…