Related papers: Structure of DNA-Functionalized Dendrimer Nanopart…
In this work, Na isotopes with mass varying from $A=$ 20 to 31 have been studied using DJ16A, JISP16 and N3LO microscopic effective interactions in the $sd$-shell. These effective interactions are derived for $sd$-shell using no-core shell…
Depletion forces play a role in the compaction and de-compation of chromosomal material in simple cells but it remains debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics…
This dissertation presents an investigation into the electrical properties of two types of G4-DNA and several DNA-based molecules, targeting them as candidates for molecular wires and devices. Atomic force microscopy (AFM) and electrostatic…
Single molecule experiments on single- and double stranded DNA have sparked a renewed interest in the force-extension of polymers. The extensible Freely Jointed Chain (FJC) model is frequently invoked to explain the observed behavior of…
The phase behaviour of a single large semiflexible polymer immersed in a suspension of spherical particles is studied. All interactions are simple excluded volume interactions and the diameter of the spherical particles is an order of…
Branched molecules of deoxyribonucleic acid (DNA) can self-assemble into nanostructures through complementary cohesive strand base pairing. The production of DNA nanostructures is valuable in targeted drug delivery and biomolecular…
Determination of sizes and flexibilities of RNA molecules is important in understanding the nature of packing in folded structures and in elucidating interactions between RNA and DNA or proteins. Using the coordinates of the structures of…
We report the results of molecular dynamics simulations of the properties of a pseudo-atom model of dodecane thiol ligated 5-nm diameter gold nanoparticles (AuNP) in vacuum as a function of ligand coverage and particle separation in three…
Phenyl-disubstituted polyacetylene (PDPA) is an organic semiconductor which has been studied during the last years for its efficient photo-luminescence. In contrast, the molecular geometry, providing the basis for the electronic and optical…
Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…
We developed new parameterizations of local regularized finite-range pseudopotentials up to next-to-next-to-next-to-leading order (N3LO), used as generators of nuclear density functionals. When supplemented with zero-range spin-orbit and…
Translocation of a single stranded DNA (ssDNA) through an alpha-hemolysin channel in a lipid membrane driven by applied transmembrane voltage V was extensively studied recently. While the bare charge of the ssDNA piece inside the channel is…
The electrical conduction properties of G4-DNA are investigated using a hybrid approach, which combines electronic structure calculations, molecular dynamics (MD) simulations, and the formulation of an effective tight-binding model…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
Electrically conducting polymers with mechanical adaptability are essential for flexible electronics, yet most suffer structural degradation under rapid deformation. In this study, multiscale coarse-grained (MSCG) simulations are used to…
We develop a robust coarse-grained model for single and double stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
The response of a semiflexible polyelectrolyte chain to stretching in the regimes of moderate and weak screening is studied theoretically, with a special focus on DNA experiments. By using the nonlinear Poisson--Boltzmann description of…
We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid…
We formulate the configurational partition function for dendrimers, taking explicit account of their conformations and segmental interactions. Two approximate schemes are presented, one based on the effective dendrimer-dendrimer…