Related papers: Theory and modeling of particles with DNA-mediated…
The assembly of colloidal cubic diamond is a challenging process since the shape and interaction parameters and the thermodynamic conditions where this structure is stable are elusive. The simultaneous use of shape-anisotropic particles and…
This mini-review discusses the recent contribution of theoretical and computational physics as well as experimental efforts to the understanding of the behavior of colloidal particles in confined geometries and at liquid crystalline…
The new insights into the atomic structure empower one to develop materials by a bottom-up approach. The study of colloids is profitable in many ways. Considering the research in this field is beneficial. Developing tiny metallic particles…
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…
Cells operate in part by compartmentalizing chemical reactions. For example, recent work has shown that chromatin, the material that contains the cell's genome, can auto-regulate its structure by utilizing reaction products (proteins, RNA)…
Self-Immolative Chemistry is based on the cascade of disassembling reactions triggered by the adequate stimulation and leading to the sequential release of the smaller constituent elements. This review will focus on the possibilities that…
DNA nanocompartment is a typical DNA-based machine whose function is dependent of molecular collective effect. Fundamental properties of the device have been addressed via electrochemical analysis, fluorescent microscopy, and atomic force…
The design of large-scale colloidal quantum dots (QDs) assemblies and the investigation of their interaction with their close environment are of great interest for improving QD-based optoelectronic devices' performances. Understanding the…
This dissertation explores how deep generative models can advance the analysis of challenging biological problems by integrating domain knowledge with deep learning. It focuses on two areas: DNA reaction kinetics and cryogenic electron…
Colloidal particles can self-assemble into various ordered structures in fluid flows that have potential applications in biomedicine, materials synthesis and encryption. These dynamic processes are also of fundamental interest for probing…
We propose a mathematical model of DNA self-assembly using 2D tiles to form 3D nanostructures. This is the first work to combine studies in self-assembly and nanotechnology in 3D, just as Rothemund and Winfree did in the 2D case. Our model…
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with…
Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can…
We investigate general properties of non-deterministic self-assembly with asymmetric interactions, using a computational model and DNA tile assembly experiments. By contrasting symmetric and asymmetric interactions we show that the latter…
Colloidal particles with DNA `legs' that can bind reversibly to receptors on a surface can be made to `walk' if there is a gradient in receptor concentration. We use a combination of theory and Monte Carlo simulations to explore how…
We present a coarse-grained model for evaluation of interactions of globular proteins with nanoparticles. The protein molecules are represented by one bead per aminoacid and the nanoparticle by a homogeneous sphere that interacts with the…
We propose the use of topographic modulation of surfaces to select and localize particles in nematic colloids. By considering convex and concave deformations of one of the confining surfaces we show that the colloid-flat surface repulsion…
The manipulation of geometrically constrained magnetic domain walls (DWs) in nanoscale magnetic strips has attracted much interest recently, with proposals for prospective memory and logic devices. Here we propose to use the high…
In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to…
Periodic arrays of micro- or nano-pillars constitute solid state matrices with excellent properties for DNA size separation. Nanofabrication technologies offer many solutions to tailor the geometry of obstacle arrays, yet most studies have…