Related papers: Mesoscopic model for nano-channel confined DNA
We propose a model for DNA dynamics by introducing the helical structure through twist deformation in analogy with the structure of helimagnet and cholesteric liquid crystal system. The dynamics in this case is found to be governed by the…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
In many physical systems, degrees of freedom are coupled \emph{via} hydrodynamic forces, even in the absence of Hamiltonian interactions. A particularly important and widespread example concerns the transport of microscopic particles in…
We consider the folding of a self-avoiding homopolymer on a lattice, with saturating hydrogen bond interactions. Our goal is to numerically evaluate the statistical distribution of the topological genus of pseudoknotted configurations. The…
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. In this work, we study the fundamental limits and trade-offs of DNA-based storage systems by introducing a new channel model, which we…
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…
The properties of nucleon-nucleon scattering inside dense nuclear matter are investigated. We use the relativistic Brueckner-Hartree-Fock model to determine on-shell and half off-shell in-medium transition amplitudes and cross sections. At…
We propose a model Hamiltonian for describing charge transport through short homogeneous double stranded DNA molecules. We show that the hybridization of the overlapping pi orbitals in the base-pair stack coupled to the backbone is…
We study the coupled rotation-vibration levels of a hydrogen molecule in a confining potential with cylindrical symmetry. We include the coupling between rotations and translations and show how this interaction is essential to obtain the…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
Methane hydrate nucleation under nanoconfinement remains poorly understood due to the complex interplay between geometric restriction and molecular ordering. Here, we investigate the structural organization of water-methane systems confined…
Deformations that conserve the parallelism and the distances --between layers, in smectic phases; between columns, in columnar phases-- are commonplace in liquid crystals. The resulting deformed textures have the same mass density as in the…
The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to…
Quartz nanopipettes are an important emerging class of electric single-molecule sensors for DNA, proteins, their complexes as well as other biomolecular targets. However, in comparison to other resistive pulse sensors, nanopipettes…
We present an elastic model of B-form DNA as a stack of thin, rigid plates or base pairs that are not permitted to deform. The symmetry of DNA and the constraint of plate rigidity limit the number of bulk elastic constants contributing to a…
We propose to use sub-wavelength confinement of light associated with the near field of plasmonic systems to create nanoscale optical lattices for ultracold atoms. Our approach combines the unique coherence properties of isolated atoms with…
DNA denaturation has long been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear, structural transition. Many aspects of this phenomenon, however, remain poorly understood.…
Diffusive transport of particles or, more generally, small objects is a ubiquitous feature of physical and chemical reaction systems. In configurations containing confining walls or constrictions transport is controlled both by the…