Related papers: Change of Hydration Patterns upon RNA Melting Prob…
Using a combination of dielectric spectroscopy and solid-state deuteron NMR, the hydration water dynamics of connective tissue proteins is studied at sub-ambient temperatures. In this range, the water dynamics follows an Arrhenius law. A…
To comprehend the complexities of the ice-water interface, we perform a study that attempts to correlate the altered dynamics of water to its perturbed structure at, and due to, the interface. The deviation from bulk values of structural…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
Structuring of DNA counterions around the double helix has been studied by the molecular dynamics method. A DNA dodecamer d(CGCGAATTCGCG) in water solution with the alkali metal counterions Na$^{+}$, K$^{+}$, and Cs$^{+}$ has been…
Methanol-water liquid mixtures have been investigated by high-energy synchrotron X-ray and neutron diffraction at low temperatures. We are thus able to report the first complete sets of both X-ray and neutron weighted total scattering…
We investigate the behavior of hydrated sulfonated polysulfones over a range of ion contents through differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FTIR), and molecular dynamics (MD) simulations.…
We describe quantitatively a RNA molecule under the influence of an external force exerted at its two ends as in a typical single-molecule experiment. Our calculation incorporates the interactions between nucleotides by using the…
While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule…
We have performed high-resolution inelastic neutron scattering studies on three samples of hydrogenated tetrahydrofuran-water clathrates, containing either H2 at different para/ortho concentrtion, or HD. By a refined analysis of the data,…
We calculate the spectrum of torsional vibrations of a double-stranded structure that models the double helix of the DNA. We come to the conclusion that within the framework of the model elementary excitations may display an asymmetry as…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
The low-frequency Raman spectra of Na-and Cs-DNA water solutions have been studied to determine the mode of counterion vibrations with respect to phosphate groups of the DNA double helix. The obtained spectra are characterized by the water…
Living cells exhibit a complex organization comprising numerous compartments, among which are RNA- and protein-rich membraneless, liquid-like organelles known as biomolecular condensates. Energy-consuming processes regulate their formation…
The unique structural properties of interfacial water are at the heart of a vast range of important processes in electrochemistry, climate science, and biophysics. At interfaces, water molecules exhibit preferential orientations and an…
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…
Fluids under extreme confinement exhibit unique structures and intermolecular bonding, distinct from their bulk analogs, driving innovative applications at the water-energy nexus. Probing confined water experimentally at the length scale of…
RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by…
We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two…
We report a structural polymorphism of the S-DNA when a canonical B-DNA is stretched under different pulling protocols and provide a fundamental molecular understanding of the DNA stretching mechanism. Extensive all atom molecular dynamics…