Related papers: Nanoscale Structure and Elasticity of Pillared DNA…
Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity.…
Using Molecular Dynamics approach we investigated the structure, dynamics of water confined inside pristine and charged 6,6 carbon nanotubes (CNTs). This study reports the breakdown of 1D water wires and the emergence of triangular faced…
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural…
Channeling of particle beam in straight and bent single-wall nanotubes has been studied in computer simulations. We have found that the nanotubes should be sufficiently narrow in order to steer efficiently the particle beams, with preferred…
This article deals with the multiscale modeling of stress transfer characteristics of nano-reinforced polymer composite reinforced with regularly staggered carbon fibers. The distinctive feature of construction of nano-reinforced composite…
I present a Hamiltonian model and a computational method suitable to evaluate structural and thermodynamic properties of helical molecules embedded in crowded environments which may confine the space available to the base pair fluctuations.…
Plasmonic optical tweezers based on Double Nanohole (DNH) structures are an emerging tool for label-free single-molecule manipulation. However, their current performance is hindered by low signal-to-noise ratios for small proteins,…
The specificity and thermal reversibility of DNA interactions have enabled the self-assembly of crystal structures, self-replicating materials and colloidal molecules. Grafting DNA onto liquid interfaces of emulsions leads to exciting new…
DNA inside the cellular environment works under a confined space. An intense research of the transcription and replication of DNA in the confined state is structurally significant to command the self assembly of DNA in a chamber or channel.…
We present a numerical analysis of a DNA hydrogel that consists of three-valent Y-shaped DNA molecules. The building blocks self-assemble fully reversibly from complementary single-stranded DNA segments. We compare melting curves from both…
While analyzing the persistence length of DNA atomistic simulations Wu et al. [J. Chem. Phys. 142, 125103 (2015)] introduced an empirical formula to account for the observed length-dependence. In particular they found that the persistence…
For single-walled carbon nanotube (SWNT) field effect transistors, vertical scaling of high k dielectrics by atomic layer deposition (ALD) currently stands at ~8nm with subthreshold swing S~70-90 mV/decade at room temperature. ALD on…
Exploring various topological states (TS) and topological phase transitions (TPT) has attracted great attention in condensed matter physics. However, so far, there is rarely a typical material system that can be used as a platform to study…
Determination of sizes and flexibilities of RNA molecules is important in understanding the nature of packing in folded structures and in elucidating interactions between RNA and DNA or proteins. Using the coordinates of the structures of…
Controlling the chirality and yield of carbon nanotubes is essential for their diverse applications from macroscopic composites to nanoelectronics. Floating-catalyst chemical vapor deposition is widely employed as a scalable synthesis…
Concentrated solutions of short blunt-ended DNA duplexes, down to 6 base pairs, are known to order into the nematic liquid crystal phase. This self-assembly is due to the stacking interactions between the duplex terminals that promotes…
Recent advance in nanotechnology has led to rapid advances in nanofluidics, which has been established as a reliable means for a wide variety of applications, including molecular separation, detection, crystallization and biosynthesis.…
Using Langevin Dynamic simulations, we study effects of the shear force on the rupture of a double stranded DNA molecule. The model studied here contains two single diblock copolymers interacting with each other. The elastic constants of…
A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…
Unusually high bending flexibility has been recently reported for DNA on short length scales. We use atomic force microscopy (AFM) in solution to obtain a direct estimate of DNA bending statistics for scales down to one helical turn. It…