Related papers: Structural stability versus conformational samplin…
Spin-polarized DFT has been used to perform a comprehensive study of the geometric structures and electronic properties for isolated M4X4 nano-clusters between their two stable isomers - a planar rhombus-like 2D structure and a cubane-like…
The aim of the present paper is the study of the entropic elasticity of the dsDNA molecule, having a cristallographic length L of the order of 10 to 30 persistence lengths A, when it is subject to spatial obstructions. We have not tried to…
The electrical properties of DNA molecules are investigated by charge injection and electric force microscopy experiments. Prior to injection, DNA molecules exhibit a weak positively charged state. We probe the electrical behaviour of DNA…
Modeling charge transport in DNA is essential to understand and control the electrical properties and develop DNA-based nanoelectronics. DNA is a fluctuating molecule that exists in a solvent environment, which makes the electron…
We have investigated the stability and conductivity of unsupported, two dimensional infinite gold nanowires using ab-initio density functional theory (DFT). Two dimensional ribbon like nanowires, with 1-5 rows of gold atoms in the…
We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…
Using density functional calculations, we investigate the structural and magnetic properties of ultrathin Gd and Gd-carbide nanowires (NWs) encapsulated in narrow carbon nanotubes (CNTs). The equilibrium geometry of an encapsulated (2…
We study the transport of charge due to polarons in a model of DNA which takes in account its 3D structure and the coupling of the electron wave function with the H--bond distortions and the twist motions of the base pairs. Perturbations of…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
DNA is an attractive medium for digital data storage. When data is stored on DNA, errors occur, which makes error-correcting coding techniques critical for reliable DNA data storage. To reduce the errors, a common technique is to include…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
A theoretical study is presented to quantitatively analyze the transport experiment through individual DNA molecules reported recently by Porath {\it et al.} [Nature {\bf 403}, 635 (2000)]. A variety of valuable quantities are identified by…
In this letter, we study the structure-transport property relationships of small ligand intercalated DNA molecules using a multiscale modelling approach where extensive ab-initio calculations are performed on numerous MD-simulated…
A crucial factor determining charge transport in organic semiconductors is the electronic coupling between the molecular constituents, which is heavily influenced by the relative arrangement of the molecules. This renders quinacridone, with…
Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the…
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…
Crossover motifs are integral components for designing DNA based nanostructures and nanomechanical devices due to their enhanced rigidity compared to the normal B-DNA. Although the structural rigidity of the double helix B-DNA has been…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
The use of deep neural network (DNN) models as surrogates for linear and nonlinear structural dynamical systems is explored. The goal is to develop DNN based surrogates to predict structural response, i.e., displacements and accelerations,…
It had been proposed that overstretching double stranded DNA from the 5-5 ends will produce a new fiber form of dsDNA that is narrower than the S form that has been suggested to result when the dsDNA is overstretched from the 3-3 ends. We…