Related papers: Computational Insight into the Complexation of DNA…
We present a comprehensive theoretical and experimental study of the solution phase properties of DNA-based family of nanoparticles - dendrimer-like DNA molecules (DL-DNA). These charged DNA dendrimers are novel macromolecular aggregates,…
Advances in deep neural network (DNN) based molecular property prediction have recently led to the development of models of remarkable accuracy and generalization ability, with graph convolution neural networks (GCNNs) reporting…
Polymeric single-chain nanoparticles (SCNPs) are soft nano-objects synthesized by purely intramolecular cross-linking of single polymer chains. By means of computer simulations, we investigate the conformational properties of SCNPs as a…
Protonation of DNA basepairs is a reversible phenomenon which can be controlled by tuning the pH of the system. Under mild acidic conditions, the hydrogen bonding pattern of the DNA basepairs undergoes a change. We study the effect of…
The curvature stress of DNA packed inside a phage is balanced against its electrostatic self-interaction. The DNA density is supposed nonuniform and as a result the Donnan effect is also inhomogeneous. The coarse-grained DNA density is a…
Ultra-nanocrystalline diamond is a polycrystalline material, having crystalline diamond grains of sizes in the nanometer regime. We study the structure and mechanical properties of this material as a function of the average grain size,…
Growing and studying large Coulomb crystals, composed of tens to hundreds of thousands of ions, in linear quadrupole ion traps presents new challenges for trap implementation. We consider several trap designs, first comparing the total…
The accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. Examples…
The macroscopic curvature induced in double helical B-DNA by regularly repeated adenine tracts (A-tracts) is a long known, but still unexplained phenomenon. This effect plays a key role in DNA studies because it is unique in the amount and…
A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers…
In analogy with classic rigidity problems of networks and frames, the elastic properties of hydrogels made of DNA nanostars (DNAns) are expected to strongly depend on the precise geometry of their building blocks. However, it is currently…
The interaction between metal atoms and nucleobases has been a topic of high interest due to the wide scientific and technological implications. Combining density functional theory simulations with a literature overview, we achieved an…
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…
Application-specific integrated circuit (ASIC) implementations for Deep Neural Networks (DNNs) have been adopted in many systems because of their higher classification speed. However, although they may be characterized by better accuracy,…
The paper deals with the two-state (opening-closing of base pairs) model used to describe the fluctuation dynamics of a single bubble formation. We present an exact solution for the discrete and finite size version of the model that…
We unzip DNA molecules using optical tweezers and determine the sizes of the cooperatively unzipping and zipping regions separating consecutive metastable intermediates along the unzipping pathway. Sizes are found to be distributed…
The recent trend in deep neural networks (DNNs) research is to make the networks more compact. The motivation behind designing compact DNNs is to improve energy efficiency since by virtue of having lower memory footprint, compact DNNs have…
Solid-state nanopores are promising tools for single molecule detection of both DNA and proteins. In this study, we investigate the patterns of ionic current blockades as DNA translocates into or out of the geometric confinement of such…
This study presents the results of atomistic structural characterisation of 3.7 nm diameter gold nanoparticles (NP) coated with polymer polyethylene glycol (PEG)-based ligands of different lengths (containing $2-14$ monomers) and solvated…
We study the size fluctuations of a local denaturation zone in a DNA molecule in the presence of proteins that selectively bind to single-stranded DNA, based on a (2+1)-dimensional master equation. By tuning the physical parameters we can…