Related papers: Computational Insight into the Complexation of DNA…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…
Deploying TinyML models on low-cost IoT hardware is very challenging, due to limited device memory capacity. Neural processing unit (NPU) hardware address the memory challenge by using model compression to exploit weight quantization and…
Graphene nanopore based sensor devices are exhibiting the great potential for the detection of DNA. To understand the fundamental aspects of DNA translocating through a graphene nanopore, in this work, molecular dynamics (MD) simulations…
Employing grazing-incidence small-angle X-ray scattering (GISAXS) and X-ray reflectivity (XRR), we demonstrate that films composed of polyethylene glycol (PEG)-grafted silver nanoparticles (AgNP) and gold nanoparticles (AuNP), as well as…
We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average…
Generative models for materials have achieved strong performance on periodic bulk crystals, yet their ability to generalize across scale transitions to finite nanostructures remains largely untested. We introduce Crystal-to-Nanoparticle…
DNA-coated particles are promising as building blocks for functional and finite-sized assemblies because they can be programmed with orthogonal interactions owing to the sequence-specific hybridization of DNA strands. To fully exploit this…
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 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…
The equilibrium statistical properties of DNA denaturation bubbles are examined in detail within the framework of the Peyrard-Bishop-Dauxois model. Bubble formation in homogeneous DNA is found to depend crucially on the presence of…
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One solely relies on base…
The local mechanical properties of DNA are believed to play an important role in their biological functions and DNA-based nanomechanical devices. Using a simple sphere-tip compression system, the local radial mechanical properties of DNA…
Many structures inside the cell such as nucleosomes and protein-mediated DNA loops contain sharply bent double-stranded (ds) DNA. Therefore, the energetics of strong dsDNA bending constitutes an essential part of cellular thermodynamics.…
The control over DNA elongation in nanofluidic devices holds great potential for large-scale genomic analysis. So far, the manipulation of DNA in nanochannels has been mostly carried out with electrophoresis and seldom with hydrodynamics,…
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…
Recent years have seen deep neural networks (DNNs) becoming wider and deeper to achieve better performance in many applications of AI. Such DNNs however require huge amounts of memory to store weights and intermediate results (e.g.,…
The problem of DNA$-$DNA interaction mediated by divalent counterions is studied using a generalized Grand-canonical Monte-Carlo simulation for a system of two salts. The effect of the divalent counterion size on the condensation behavior…
The promise of enhanced performance has motivated the study of one dimensional nanomaterials, especially aligned carbon nanotubes (A-CNTs), for the reinforcement of polymeric materials. While early work has shown that CNTs have remarkable…
The size-dependent electronic, structural, magnetic and vibrational properties of small pure cop- per and silver clusters and their alloys with one and two palladium atoms are studied by using full-potential all-electron density functional…
DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than implied by the widely-used worm-like chain model; many of…