Related papers: Computational Insight into the Complexation of DNA…
We present a study on the role of defects on the stability of short DNA molecules. We consider short DNA molecules (16 base pairs) and investigate the thermal as well as mechanical denaturation of these molecules in the presence of defects…
Recent breakthroughs by deep neural networks (DNNs) in natural language processing (NLP) and computer vision have been driven by a scale-up of models and data rather than the discovery of novel computing paradigms. Here, we investigate if…
DNA toroids are compact torus-shaped bundles formed by one or multiple DNA molecules being condensed from the solution due to various condensing agents. It has been shown that the DNA toroidal bundles are twisted. However, the global…
A theory is presented of DNA hairpins enclosed in a nanochannel. A hairpin becomes constrained as it approaches the wall of a channel which leads to an entropic force causing the hairpin to tighten. The free energy of the hairpin computed…
DNA deformations play crucial roles in many biological processes and material applications. During DNA deformation, DNA structural parameters often exhibit non-trivial and counterintuitive couplings, such as the twist-stretch and…
This study explores the stabilization mechanisms of concentrated emulsions with tunable morphology using amphiphilic polymer-grafted nanoparticles (PGNPs). We employ coarse-grained molecular simulations to investigate concentrated…
Homologous gene shuffling between DNA promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous…
Antibody-drug conjugates (ADCs) have emerged as a promising class of targeted cancer therapeutics, but the design and optimization of their cytotoxic payloads remain challenging. This study introduces DumplingGNN, a novel hybrid Graph…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
Ionic transports in nanopores hold the key to unlocking the full potential of bi-continuous nanoporous (NP) metals as advanced electrodes in electrochemical devices. The precise control of the uniform NP metal structures also provides us a…
DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…
Computational drug discovery provides an efficient tool helping large scale lead molecules screening. One of the major tasks of lead discovery is identifying molecules with promising binding affinities towards a target, a protein in…
Due to their large coherent scattering cross section, diamond nanoparticles (DNPs) are considered as a promising candidate material for a new neutron reflector. For investigation of scattering cross sections of packed samples, we have…
The dependence of DNA assemblies conductance on relative humidity is investigated theoretically. Following earlier suggestions, we consider the ionic conductivity through the layers of water adsorbed by DNA molecules. The increase in…
Functionalized metal nanoparticles (NPs) have been proposed as promising radiosensitizing agents for more efficient radiotherapy treatment using photons and ion beams. Radiosensitizing properties of NPs may depend on many different…
The stability of DNA molecule during the encapsulation process is a topic of intense research. We study the thermal stability of the double-stranded DNA molecule of different lengths in a confined space. Using a statistical model we…
A DNA-protein complex modelled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in…
The macroscopic curvature of double helical DNA induced by regularly repeated adenine tracts is well-known but still puzzling. Its physical origin remains controversial even though it is perhaps the best-documented sequence modulation of…
In the demanding biosensing environment, improving selection efficiency strategies has become an issue of great significance. DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, are representative of the…
Dynamic nuclear polarization (DNP) of molecules in a solution at room temperature has potential to revolutionize nuclear magnetic resonance spectroscopy and imaging. The prevalent methods for achieving DNP in solutions are typically most…