Related papers: Reactive Molecular Dynamics Simulation on DNA Doub…

Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…

Short, partially complementary, single-stranded (ss)DNA strands can form nanostructures with a wide variety of shapes and mechanical properties. It is well known that semiflexible, linear dsDNA can undergo an isotropic to nematic (IN) phase…

Molecular recognition between two double stranded (ds) DNA with homologous sequences may not seem compatible with the B-DNA structure because the sequence information is hidden when it is used for joining the two strands. Nevertheless, it…

We employ two different atomistic methods to investigate solute-defect interactions in nanosized palladium-hydrogen (Pd-H) systems across multiple time scales. The first method, referred to as Diffusive Molecular Dynamics (DMD), focuses on…

Purpose: To present a closed formalism calculating charged particle radiation damage induced in DNA. The formalism is valid for all types of charged particles and due to its closed nature is suited to provide fast conversion of dose to…

Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…

Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…

We use diagrammatic perturbation theory to construct an effective shell-model operator for the neutrinoless double-beta decay of 82Se. The starting point is the same Bonn-C nucleon-nucleon interaction that is used to generate the…

Base stacking is crucial in nucleic acid stabilization, from DNA duplex hybridization to single-stranded DNA (ssDNA) protein binding. While stacking energies are tiny in ssDNA, they are inextricably mixed with hydrogen bonding in DNA base…

Ion-mediated interaction is critical to the structure and stability of nucleic acids. Recent experiments suggest that the multivalent ion-induced aggregation of double-stranded (ds) RNAs and DNAs may strongly depend on the topological…

While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension…

Here we present the results from two sets of simulations, in two and three spatial dimensions. In two dimensions, the simulations include multifrequency flux-limited diffusion neutrino transport in the "ray-by-ray-plus" approximation,…

We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…

The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…

DNA and RNA are generally regarded as central molecules in molecular biology. Recent advancements in the field of DNA/RNA nanotechnology successfully used DNA/RNA as programmable molecules to construct molecular machines and nanostructures…

Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning. Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called…

We present the first proof-of-concept simulations of detectors using biomaterials to detect particle interactions. The essential idea behind a "DNA detector" involves the attachment of a forest of precisely-sequenced single or…

We investigate the quantum dynamics of the 1D spinless Fermi-Hubbard model with a linear-tilted potential. Surprisingly in a strong resonance regime, we show that the model can be described by the kinetically constrained effective…

We propose a model for the fluctuation dynamics of the local denaturation zones (bubbles) in double-stranded DNA. In our formulation, the DNA strand is model as a one dimensional Rouse chain confined at both the ends. The bubble is formed…

One-dimensional (1D) stellar evolution models are widely used across various astrophysical fields, however they are still dominated by important uncertainties that deeply affect their predictive power. Among those, the merging of…