Related papers: Comprehensive view of microscopic interactions bet…
DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…
DNA has the potential to realize a controllable liquid-liquid phase separation (LLPS) system, because the design of its base sequences results in programmable interactions. Here, we have developed a novel DNA-based LLPS system which enables…
Bacterial chromosome replication occurs in the absence of a canonical spindle apparatus; yet it reliably produces organised and segregated genomes. While both passive and active mechanisms have been investigated, DNA replication itself is a…
The standard DLVO theory offers a limited description of ionic-surfacted magnetic colloids in near aggregation regimes. Correcting the electrical double layer term for ionic surfactants is not enough to successfully simulate the systems.…
The behavior of long DNA molecules in a cell-sized confined space was investigated. We prepared water-in-oil droplets covered by phospholipids, which mimic the inner space of a cell, following the encapsulation of DNA molecules with…
Molecular ecology uses molecular genetic data to answer traditional ecological questions in biogeography and biodiversity among others. Several ecological principles, such as the niche hypothesis and the competitive exclusions, are based on…
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…
DNNs have gained widespread adoption in feature interaction recommendation models. However, there has been a longstanding debate on their roles. On one hand, some works claim that DNNs possess the ability to implicitly capture high-order…
Harnessing the intrinsic dynamics of physical systems for information processing opens new avenues for computation embodied in matter. Using simulations of a model system, we show that assemblies of DNA tiles capable of self-organizing into…
Controlling laser-induced pattern formation remains a long-standing challenge. A key advance was recognising the pivotal role of intrinsic feedback mechanisms in self-organisation, which enabled self-similar patterns with long-range order…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications…
Coded-illumination can enable quantitative phase microscopy of transparent samples with minimal hardware requirements. Intensity images are captured with different source patterns and a non-linear phase retrieval optimization reconstructs…
DNA is an astonishing material that can be used as a molecular building block to construct periodic arrays and devices with nanoscale accuracy and precision. Here, we present simple bead-spring model of DNA nanostars having three, four and…
We present modeling approaches to explain mechanisms of control of uniformity (narrow distribution) of sizes and shapes in synthesis of nanosize crystals and micron-size colloids. We consider those situations when the nanocrystals are…
We investigate effective interactions between a colloidal particle, immersed in a binary mixture of smaller spheres, and a semipermeable membrane. The colloid is modeled as a big hard sphere and the membrane is represented as an infinitely…
Liquid droplets of biomolecules serve as organizers of the cellular interior and are of interest in biosensing and biomaterials applications. Here, we investigate means to tune the interfacial properties of a model biomolecular liquid…
Engineered electromagnetic fields in plasmonic nanopores enable enhanced optical detection and their use in single molecule sequencing. Here, a plasmonic nanopore prepared in a thick nanoporous film is used to investigate the interaction…
DNA adsorption on solid or liquid surfaces is a topic of broad fundamental and applied interest. Here we study by x-ray reflectivity the adsorption of monodisperse double-stranded DNA molecules a positively-charged surface, obtained through…