Related papers: C-A test of DNA force fields
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…
Analysis of single-molecule micromanipulation experiments of DNA unzipping process shows some features of the force-distance curve, namely two consequent plateaus in the area of ${\sim}12-14pN$ dependent on nucleotide sequence structure, as…
The structure of DNA double helix is stabilized by metal counterions condensed to a diffuse layer around the macromolecule. The dynamics of counterions in real conditions is governed by the electric fields from DNA and other biological…
A new computational model for Sodium Chloride, the NaCl/{\epsilon}, is proposed. The Force Fields employed here for the description of the NaCl is based on a set of radial particle-particle pair potentials involving Lennard-Jones (LJ) and…
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…
We report the observation of a Twist Grain Boundary (TGB) phase of DNA, a striking motif of three dimensional (3D) equilibrium self-assembly of the DNA tetramer 5'-GTAC-3', a base sequence that is self-complimentary, pairing to form 4-base…
We develop coarse-grained force fields for poly (vinyl alcohol) and poly (acrylic acid) oligomers. In both cases, one monomer is mapped onto a coarse-grained bead. The new force fields are designed to match structural properties such as…
The phase behavior of symmetric diblock copolymers under three-dimensional (3D) soft confinement is investigated using the self-consistent field theory. The soft confinement is realized in binary blends composed AB diblock copolymers and C…
The structure and dynamics of negatively charged nucleic acids strongly correlate with the concentration and charge of the oppositely charged counter-ions. It is well known that the structural collapse of DNA is favored in the presence of…
DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…
The strength of the spin-orbit interaction relevant to transport in a low dimensional structure depends critically on the relative geometrical arrangement of current carrying orbitals. Recent tight-binding orbital models for spin transport…
Recent experiments of translocation of double stranded DNA through nanopores [M. Wanunu \textit{et al.} Nature Nanotech. {\bf 5}, 160 (2010)] reveal that the DNA capture rate can be significantly influenced by a salt gradient across the…
While studying nucleic acids to reveal the weak interactions responsible for their three-dimensional structure and for their interactions with drugs, we also contributed to the field of biomolecular mass spectrometry, both in terms of…
The ionic atmospheres around nucleic acids play important roles in biological function. Large-scale explicit solvent simulations coupled to experimental assays such as anomalous small-angle X-ray scattering (ASAXS) can provide important…
Understanding how lipid bilayers respond to pressure is essential for interpreting the coupling between membrane proteins and their native environments. Here, we use all-atom molecular dynamics to examine the pressure-temperature behavior…
A DFT-based investigation of rhombohedral (ABC)-type graphene stacks in finite static electric fields is presented. Electronic band structures and field-induced charge densities are compared with related literature data as well as with own…
Bacteriophages, phages for short, are viruses of bacteria. The majority of phages contain a double-stranded DNA genome packaged in a capsid at a density of ~500 mg/ml. This high density requires substantial compression of the normal B form…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
We report on our theoretical investigations of the electronic states in a DNA molecule. We have used a two-leg charge ladder model where electron-electron interactions and the electron spin have been taken into account. The energy spectra…
Protein-DNA complexes with loops play a fundamental role in a wide variety of cellular processes, ranging from the regulation of DNA transcription to telomere maintenance. As ubiquitous as they are, their precise in vivo properties and…