Related papers: Structure of DNA-Functionalized Dendrimer Nanopart…
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…
DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and…
Using a bead-spring model of bacterial DNA polymers of {\em C. crescentus} and {\em E. coli} we show that just $33$ and $38$ effective cross-links at special positions along the chain contour of the DNA can lead to the large-scale…
Many industrial soft materials often include oil-in-water (O/W) emulsions at the core of their formulations. By using tuneable interface stabilizing agents, such emulsions can self-assemble into complex structures. DNA has been used for…
The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4]…
We study the elastic response of a worm-like polymer chain with reversible kink-like structural defects. This is a generic model for (a) the double-stranded DNA with sharp bends induced by binding of certain proteins, and (b) effects of…
Conformations of isolated homo- dendrimers of G=1-7 generations with D=1-6 spacers have been studied in the good and poor solvents, as well as across the coil-to-globule transition, by means of a version of the Gaussian self-consistent…
We study, via DEM simulations, the apparent mass $m$ and loss factor $\eta$ of particle dampers (PD) attached to a vertically driven, single degree of freedom mechanical system. Although many studies focus on $\eta$, less work has been…
We have extended our analytically derived PDB-NMA formulation, ATMAN [1], to include protein dimers using mixed internal and Cartesian coordinates. A test case on a 1.3\AA\ resolution model of a small homodimer, ActVA-ORF6, consisting of…
Confinement has been suggested as a tool to tune the self-assembly properties of nanoparticles, surfactants, polymers and colloids. In this way, we explore the phase diagram of Janus nanoparticles using Molecular Dynamics simulations. The…
Graphene-based nanofolds (GNFs) are edge-connected 2D stacked monolayers originated from single-layer graphene. Graphene-based nanoscrolls (GNSs) are nanomaterials with geometry resembling graphene layers rolled up into a spiral…
We present a new simulation technique to study systems of polymers functionalized by reactive sites that bind/unbind forming reversible linkages. Functionalized polymers feature self-assembly and responsive properties that are unmatched by…
We investigate the mechanical stability of a segment of DNA wrapped around a histone in the nucleosome configuration. The assumption underlying this investigation is that the proper model for this packaging arrangement is that of an elastic…
The effective interaction between two parallel strands of helical bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using computer simulations of the "primitive" model of electrolytes. In particular we study a simple…
From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA…
The giant dipole resonance (GDR) in deformed nuclei is analyzed using the self-consistent separable random-phase-approximation (SRPA) with Skyrme forces SkT6, SkM$^*$, SLy6 and SkI3. The deformed nuclei $^{150}$Nd and $^{238}$U are used as…
Jammed disordered packings of non-spherical particles show significant variation in the packing density as a function of particle shape for a given packing protocol. Rotationally symmetric elongated shapes such as ellipsoids,…
We report extensive numerical simulations of different models of 2D polymer rings with internal elasticity. We monitor the dynamical behavior of the rings as a function of the packing fraction, to address the effects of particle deformation…
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…
Here we derive and experimentally test a free energy functional that captures the adhesion of DNA-coated emulsion droplets. Generalizing previous approaches, the theory combines important energetic and entropic effects of microscopic DNA…