相关论文: Simulation and Experimental Verification of DNA Da…
Chemical purity of RNA samples is critical for high-precision studies of RNA folding and catalytic behavior, but such purity may be compromised by photodamage accrued during ultraviolet (UV) visualization of gel-purified samples. Here, we…
We construct a theoretical model for the dynamics of a microscale colloidal particle, modeled as an interval, moving horizontally on a DNA-coated surface, modelled as a line coated with springs that can stick to the interval. Averaging over…
DNA-coated colloids are a popular model system for self-assembly through tunable interactions. The DNA-encoded linkages between particles theoretically allow for very high specificity, but generally no directionality or long-range…
We have performed single molecule stretching experiments and dynamic light scattering (DLS) in order to characterize the interaction between the DNA molecule and the fluorescent stain GelRed. The results from single molecule stretching show…
We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…
In this second part of a series we attempt to construct an empirical model that can mimick all experimental observations made regarding the role of an alternative interleaved scan pattern in STEM imaging on the beam damage in a specific…
We demonstrate the potential of X-ray free-electron lasers (XFEL) to advancethe understanding of complex plasma dynamics by allowing for the first time nanometer and femtosecond resolution at the same time in plasma diagnostics. Plasma…
Ultrafast lasers, with pulse durations below a few picoseconds, are of significant interest to the industry, offering a cutting-edge approach to enhancing manufacturing processes and enabling the fabrication of intricate components with…
Molecular combing is a powerful and simple method for aligning DNA molecules onto a surface. Using this technique combined with fluorescence microscopy, we observed that the length of lambda-DNA molecules was extended to about 1.6 times…
The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried…
Biomolecules couple to their aqueous environment through a variety of noncovalent interactions. Local structures at the surface of DNA and RNA are frequently determined by hydrogen bonds with water molecules, complemented by non-specific…
We solve the orientation recovery of a tumbling protein in the gas phase from single-event measurements of the spatial positions of its ions after an X-ray laser induced explosion. We simulate diffracted X-ray signal and ion dynamics under…
We present a new method for calculating internal forces in DNA structures using coarse-grained models and demonstrate its utility with the oxDNA model. The instantaneous forces on individual nucleotides are explored and related to model…
We study the optical properties of glass exposed to ionizing radiation, as it occurs in the space environment. 24 glass types have been considered, both space qualified and not space qualified. 72 samples (3 for each glass type) have been…
Radiation damage in high-temperature cuprate superconductors represents one of the main technological challenges for their deployment in harsh environments, such as fusion reactors and accelerator facilities. Their complex crystal structure…
Engineered electromagnetic fields in plasmonic nanopores enable enhanced optical detection and their use in single molecule sequencing. Here, a plasmonic nanopore prepared in a thick nanoporous film is used to investigate the interaction…
The cations, in form of salt, present in the solution containing DNA play a crucial role in the opening of two strands of DNA. We use a simple non linear model and investigate the role of these cations on the mechanical unzipping of DNA.…
We present a theoretical agent-based model of cell evolution under the action of cytotoxic treatments, such as radioteraphy or chemoteraphy. The major features of cell cycle and proliferation, cell damage and repair, and chemical diffusion…
The adsorption of DNA or other polyelectrolyte molecules on charged membranes is a recurrent motif in soft matter and bionanotechnological systems. Two typical situations encountered are the deposition of single DNA chains onto substrates…
The effective force between two parallel DNA molecules is calculated as a function of their mutual separation for different valencies of counter- and salt ions and different salt concentrations. Computer simulations of the primitive model…