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We develop further a statistical model coupling denaturation and chain conformations in DNA (Palmeri J, Manghi M and Destainville N 2007 Phys. Rev. Lett. 99 088103). Our Discrete Helical Wormlike Chain model takes explicitly into account…
Understanding the pressure dependence of the nonlinear behavior of ultrasonically excited phospholipid (PL)-stabilized NBs is important for optimizing US exposure parameters for implementations of contrast enhanced ultrasound, critical to…
Within a simple elastic theory, we study the elongation versus force characteristics of a supercoiled DNA molecule at thermal equilibrium in the regime of small supercoiling. The partition function is mapped to the path integral…
DNA is increasingly employed for bio and nanotechnology thanks to its exquisite versatility and designability. Most of its use is limited to linearised and torsionally relaxed DNA but non-trivial architectures and torsionally constrained --…
We study the effects of covalent functionalization of single wall carbon nanotubes (CNT) on their elastic properties. We consider simple organic molecules -NH, -NH2, -CH2, -CH3, -OH attached to CNTs' surface at various densities. The…
Polymer composites are ubiquitous in biology and industry alike, owing to their emergent desirable mechanical properties not attainable in single-species systems. At the same time, polymer topology has been shown to play a key role in…
Density functional theory calculations have been performed on Indium nanoclusters (Inn, n= 3 to 10) to explore the relative stability among their different isomers and interaction with H2. Geometry optimizations starting from initial…
We here investigated the thermal and mechanical behaviors of three-dimensional beta zeolite-templated carbon nanotube networks (BZCN). These networks are topologically generated by inserting carbon nanotubes (CNTs) into zeolite channels and…
The relaxation of twist in elastic filaments often drives conformational changes. We explore this paradigm using all-atom computations and report the formation of novel supercoiled shapes in individual carbon nanotubes (CNTs). Decreasing…
Graphyne nanotubes (GNTs) are nanostructures obtained from rolled up graphyne sheets, in the same way carbon nanotubes (CNTs) are obtained from graphene ones. Graphynes are 2D carbon-allotropes composed of atoms in sp and sp2 hybridized…
Solid-state nanopore and nanopipette sensors are powerful devices for the detection, quantification and structural analysis of biopolymers such as DNA and proteins, especially in carrier-enhanced resistive-pulse sensing. However, hundreds…
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full…
A new mesoscale mechanical model, describing elastic interactions in carbon nanotubes (CNT) and other nanofilaments, is proposed. Functional form of the developed model is based on enhanced vector model (EVM) that describes basic types of…
Effect of bending anisotropy on a planar DNA loop, using energy minimization and neglecting entropic effects, is studied. We show that the anisotropy results in polygonal shape of the loop and increasing the anisotropy makes the edges…
Nucleic acids physical properties have been investigated by theoretical methods based both on fully atomistic representations and on coarse grained models, e.g. the worm-like-chain, taken from polymer physics. In this article, I present an…
Experimental data of the DNA cyclization (J-factor) at short length scales, as a way to study the elastic behavior of tightly bent DNA, exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of…
To elucidate the possible role of structural waters in stabilizing bent DNA, various conformations of AT-containing decamers, (A5T5)2 and A10:T10, were studied by Monte Carlo simulations. The duplexes were constrained to reproduce the NMR…
Neural network potentials (NNPs) enable large-scale molecular dynamics (MD) simulations of systems containing >10,000 atoms with the accuracy comparable to ab initio methods and play a crucial role in material studies. Although NNPs are…
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…
Carbon nanotube (CNT) fibres are firmly established as a new high-performance fibre, but their tensile mechanical properties remain a relatively small fraction of those of the constituent CNTs. Clear structure-property relations and…