Interfacial interactions between DNA and polysaccharide-coated magnetic nanoparticles: Insight from simulations and experiments.

In this work we examine the structural and energetic stability and the interactions between dextran-coated magnetic nanoparticles (MNPs) and a DNA oligonucleotide at ionic strength conditions that are relevant to physiological gene delivery processes. All-atom Molecular Dynamics simulations provided information at the atomic-level regarding the mechanisms responsible for the physical adsorption of Dextran on the magnetic surface and the conditions under which a successful DNA-Dextran complexation can be accomplished. Coulombic interactions were found to play the main role for the formation of the Dextran interfacial layer onto the magnetic surface while hydrogen bonding between the Dextran molecules enhanced the structural integrity of this layer.

Varying the degree of oxidation of graphite: effect of oxidation time and oxidant mass.

In this work, we employ a fast and less toxic modified Hummers' method to develop graphene oxide (GO) with varying degrees of oxidation and investigate the effect of the latter on the structure and the thermal properties of the synthesized materials. Two different key parameters, the time of the oxidation reaction and the mass of the oxidation agent, were systematically altered in order to fine tune the oxidation degree. All graphene oxides were characterized by a plethora of experimental techniques, like X-ray diffraction (XRD), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) as well as infrared spectroscopy (IR) and X-ray photoelectron spectroscopy (XPS) for their structural, thermal and chemical identification.

Morphology and Dynamics in Hydrated Graphene Oxide/Branched Poly(ethyleneimine) Nanocomposites: An In Silico Investigation.

Graphene oxide (GO)-branched poly(ethyleneimine) (BPEI) hydrated mixtures were studied by means of fully atomistic molecular dynamics simulations to assess the effects of the size of polymers and the composition on the morphology of the complexes, the energetics of the systems and the dynamics of water and ions within composites. The presence of cationic polymers of both generations hindered the formation of stacked GO conformations, leading to a disordered porous structure. The smaller polymer was found to be more efficient at separating the GO flakes due to its more efficient packing.

The Role of Oxidation Pattern and Water Content in the Spatial Arrangement and Dynamics of Oxidized Graphene-Based Aqueous Dispersions.

In this work, we employ fully atomistic molecular dynamics simulations to elucidate the effects of the oxidation pattern and of the water content on the organization of graphene sheets in aqueous dispersions and on the dynamic properties of the different moieties at neutral pH conditions. Analysis of the results reveals the role of the oxidation motif (peripherally or fully oxidized flakes) in the tendency of the flakes to self-assemble and in the control of key structural characteristics, such as the interlayer distance between the sheets and the average size and the distribution of the formed aggregates. In certain cases, the results are compared to a pertinent experimental system, validating further the relevant computational models.

Effects of the structure of lipid-based agents in their complexation with a single stranded mRNA fragment: a computational study.

In this work we employed fully atomistic molecular dynamics simulations, aiming towards a better understanding of the mechanisms associated with the formation and the stability of lipid-based RNA nanoassemblies, in an aqueous environment. We examined two groups of lipid-based complexation agents, differing in the degree of hydrophobicity and in the overall charge. The first group was comprised of cationic ionizable agents while the second included electrically neutral amphoteric phosphatidylcholine lipids.