Andrea Danani

Solution of the tunneling-percolation problem in the nanocomposite regime

We noted that the tunneling-percolation framework is quite well understood at the extreme cases of percolation-like and hopping-like behaviors but that the intermediate regime has not been previously discussed, in spite of its relevance to the intensively studied electrical properties of nanocomposites. Following that we study here the conductivity of dispersions of particle fillers inside an insulating matrix by taking into account explicitly the filler particle shapes and the inter-particle electron tunneling process. We show that the main features of the filler dependencies of the nanocomposite conductivity can be reproduced without introducing any a priori imposed cut-off in the inter-particle conductances, as usually done in the percolation-like interpretation of these systems. Furthermore, we demonstrate that our numerical results are fully reproduced by the critical path method, which is generalized here in order to include the particle filler shapes. By exploiting this method, we provide simple analytical formulas for the composite conductivity valid for many regimes of interest. The validity of our formulation is assessed by reinterpreting existing experimental results on nanotube, nanofiber, nanosheet and nanosphere composites and by extracting the characteristic tunneling decay length, which is found to be within the expected range of its values. These results are concluded then to be not only useful for the understanding of the intermediate regime but also for tailoring the electrical properties of nanocomposites.

PAMAM Dendrimers for siRNA Delivery: Computational and Experimental Insights

Short double-stranded RNAs, which are known as short interfering RNA (siRNA), can be used to specifically down-regulate the expression of the targeted gene in a process known as RNA interference (RNAi). However, the success of gene silencing applications based on the use of synthetic siRNA critically depends on efficient intracellular delivery. Polycationic branched macromolecules such as poly(amidoamine) (PAMAM) dendrimers show a strong binding affinity for RNA molecules and, hence, can provide an effective, reproducible, and relatively nontoxic method for transferring siRNAs into animal cells. Notwithstanding these perspectives, relatively few attempts have been made so far along these lines to study in detail the molecular mechanisms underlying the complexation process between PAMAMs and siRNAs. In this work we combine molecular simulation and experimental approaches to study the molecular requirements of the interaction of RNA-based therapeutics and PAMAM dendrimers of different generations. The dendrimers and their siRNA complexes were structurally characterized, and the free energy of binding between each dendrimer and a model siRNA was quantified by using the well-known MM/PBSA approach. DOSY NMR experiments confirmed the structural in silico prediction and yielded further information on both the complex structure and stoichiometry at low N/P ratio values. siRNA/PAMAM complex formation was monitored at different N/P ratios using gel retardation assays, and a simple model was proposed, which related the amount of siRNA complexed to the entropy variation upon complex formation obtained from the computer simulations.

Lattice-Gas Theory of Collective Diffusion in Adsorbed Layers

A general theory for collective diffusion in interacting lattice-gas models is presented. The theory is based on the description of the kinetics in the lattice gas by a master equation. A formal solution of the master equation is obtained using the projection-operator technique, which gives an expression for the relevant correlation functions in terms of continued fractions. In particular, an expression for the collective dynamic structure factor Sc is derived. The collective diffusion coefficient Dc is obtained from Sc by the Kubo hydrodynamic limit. If memory effects are neglected (Darken approximation), it turns out that Dc can be expressed as the ratio of the average jump rate and of the zero-wavevector static structure factor S(0). The latter is directly proportional to the isothermal compressibility of the system, whereas is expressed in terms of the multisite static correlation functions gn. The theory is applied to two-dimensional lattice systems as models of adsorbates on crystal surfaces. Three examples are considered. First, the case of nearest-neighbour interactions on a square lattice (both repulsive and attractive). Here, the theoretical results for Dc are compared to those of Monte Carlo simulations. Second, a model with repulsive interactions on the triangular lattice. This model is applied to NH3 adsorbed on Re(0001) and the calculations are compared to experimental data. Third, a model for oxygen on W(110). In this case, the complete dynamic structure factor is calculated and the width of the quasi-elastic peak is studied. In the third example the gn are calculated by means of the discretized version of a classical equation for the structure of liquids (the Crossover Integral Equation), whereas in the other examples they are computed using the Cluster Variation Method.

Elucidating the molecular mechanism of PAMAM-siRNA dendriplex self-assembly: effect of dendrimer charge density.

Dendrimers are attractive vehicles for nucleic acid delivery due to monodispersity and ease of chemical design. The purpose of this study was to elucidate the self-assembly process between small interfering RNA (siRNA) and different generation poly(amidoamine) dendrimers and to characterize the resulting structures. The generation 4 (G4) and G7 displayed equal efficiencies for dendriplex aggregate formation, whereas G1 lacked this ability. Nanoparticle tracking analysis and dynamic light scattering showed reduced average size and increased polydispersity at higher dendrimer concentration. The nanoparticle tracking analysis indicated that electrostatic complexation results in an equilibrium between differently sized complex aggregates, where the centre of mass depends on the siRNA:dendrimer ratio. Isothermal titration calorimetric data suggested a simple binding for G1, whereas a biphasic binding was evident for G4 and G7 with an initial exothermic binding and a secondary endothermic formation of larger dendriplex aggregates, followed by agglomeration. The initial binding became increasingly exothermic as the generation increased, and the values were closely predicted by molecular dynamics simulations, which also demonstrated a generation dependent differences in the entropy of binding. The flexible G1 displayed the highest entropic penalty followed by the rigid G7, making the intermediate G4 the most suitable for dendriplex formation, showing favorable charge density for siRNA binding.

Targeting the Blind Spot of Polycationic Nanocarrier-Based siRNA Delivery

Polycationic nanocarriers attract increasing attention to the field of siRNA delivery. We investigated the self-assembly of siRNA vs pDNA with polycations, which are broadly used for nonviral gene and siRNA delivery. Although polyethyleneimine (PEI) was routinely adopted as siRNA carrier based on its efficacy in delivering pDNA, it has not been investigated yet why PEI efficiently delivers pDNA to cells but is controversially discussed in terms of efficacy for siRNA delivery. We are the first to investigate the self-assembly of PEI/siRNA vs PEI/pDNA and the steps of complexation and aggregation through different levels of hierarchy on the atomic and molecular scale with the novel synergistic use of molecular modeling, molecular dynamics simulation, isothermal titration calorimetry, and other characterization techniques. We are also the fist to elucidate atomic interactions, size, shape, stoichiometry, and association dynamics for polyplexes containing siRNA vs pDNA. Our investigation highlights differences in the hierarchical mechanism of formation of related polycation-siRNA and polycation-pDNA complexes. The results of fluorescence quenching assays indicated a biphasic behavior of siRNA binding with polycations where molecular reorganization of the siRNA within the polycations occurred at lower N/P ratios (nitrogen/phosphorus). Our results, for the first time, emphasize a biphasic behavior in siRNA complexation and the importance of low N/P ratios, which allow for excellent siRNA delivery efficiency. Our investigation highlights the formulation of siRNA complexes from a thermodynamic point of view and opens new perspectives to advance the rational design of new siRNA delivery systems.

Quantifying the Effect of Surface Ligands on Dendron–DNA Interactions: Insights into Multivalency through a Combined Experimental and Theoretical Approach

We report the synthesis, DNA binding ability and preliminary gene delivery profiles of dendrons with different amine surface groups, 1,3-diaminopropane (DAP), N,N-di-(3-aminopropyl)-N-(methyl)amine (DAPMA) and spermine (SPM). By using a combination of ethidium bromide displacement, gel electrophoresis and transfection assays, it is shown that the dendrons with SPM groups are the most effective DNA binders, while the DAPMA-functionalised dendrons were the most effective systems for gene delivery (although the gene delivery profiles were still modest). In order to provide deeper insight into the experimental data, we performed a molecular dynamics simulation of the interactions between the dendrons and DNA. The results of these simulations demonstrated that, in general terms, the enthalpic contribution to binding was roughly proportional to the dendron surface charge, but that dendrons with DAP (and DAPMA) surface amines had significant entropic costs of binding to DNA. In the case of DAP, this is a consequence of the fact that the entire dendron structure has to be organised in order for each individual monoamine charge to make effective contact with DNA. For SPM, however, each surface ligand is already a multivalent triamine, therefore, each individual charge has a much lower entropic cost of binding. For DAPMA, we observed that strong binding of the hindered tertiary amine to the DNA double helix led to ligand back-folding and significant geometric distortion of DNA. Although this weakens the overall binding, we suggest that this distortion might be an explanation for the experimentally observed enhanced gene delivery, in which DNA compaction is an important step. Overall, this paper demonstrates how structure-activity relationships can be developed for multivalent dendritic ligands and provides insights into the thermodynamics of multivalent interactions.

Validation of a novel molecular dynamics simulation approach for lipophilic drug incorporation into polymer micelles.

Polymer micelles can be used to facilitate the aqueous solubilization of lipophilic, poorly water-soluble compounds and drugs. Even if the evaluation of the efficiency of drug incorporation into such micelles can be tested experimentally, a theoretical approach based on molecular simulation can constitute a useful tool that reduces time and cost. Here we present a promising method, based on molecular dynamics simulation, for the calculation of the Flory-Huggins interaction parameters as a measure of the potential for drug incorporation into polymer micelles. The data from modeling are validated on four drug compounds with different physical-chemical properties by means of a comparison with the data obtained from experiments.

Catalytic chameleon dendrimers.

Dendrimers with boronic ester end-groups and an iron porphyrin core were synthesized and characterized. The dendrimer termini were reversibly exchanged by the addition of appropriate diol molecules. According to molecular dynamics (MD) simulations, the exchange of termini may lead to changes in the conformational behavior of the dendrimer, specifically regarding the average position of the end groups relative to the core. The spatial steric disposition attained with different termini was shown to significantly affect epoxidation reaction activity and selectivity with various alkenes, thus allowing for an original way to control and adjust catalytic behavior under alternating environments.

Ion-Selective Controlled Assembly of Dendrimer-Based Functional Nanofibers and Their Ionic-Competitive Disassembly

The construction of hierarchical materials through controlled self-assembly of molecular building blocks (e.g., dendrimers) represents a unique opportunity to generate functional nanodevices in a convenient way. Transition-metal compounds are known to be able to interact with cationic dendrimers to generate diverse supramolecular structures, such as nanofibers, with interesting collective properties. In this work, molecular dynamics simulation (MD) demonstrates that acetate ions from dissociated Cd(CH(3)COO)(2) selectively generate cationic PPI-dendrimer functional fibers through hydrophobic modification of the dendrimers surface. The hydrophobic aggregation of dendrimers is triggered by the asymmetric nature of the acetate anions (AcO(-)) rather than by the precise transition metal (Cd). The assembling directionality is also controlled by the concentration of AcO(-) ions in solution. Atomic force (AFM) and transmission electron microscopy (TEM) prove these results. This well-defined directional assembly of cationic dendrimers is absent for different cadmium derivatives (i.e., CdCl(2), CdSO(4)) with symmetric anions. Moreover, since the formation of these nanofibers is controlled exclusively by selected anions, fiber disassembly can be consequently triggered via simple ionic competition by NaCl salt. Ions are here reported as a simple and cost-effective tool to drive and control actively the assembly and the disassembly of such functional nanomaterials based on dendrimers.

Generation-Dependent Molecular Recognition Controls Self-Assembly in Supramolecular Dendron−Virus Complexes

In this work molecular dynamics simulation identifies a clear link between the dendron-virus multivalent molecular recognition and the nature of the consequent self-assembly. Data demonstrate how a weak hydrophobic association is transformed in an electrostatic self-assembly, orders of magnitude stronger, depending on the dendron generation used to assemble the viruses. This opens a new frontier in the engineering of hierarchical self-assemblies, potentially enabling the control of the supramolecular properties by acting at the single-molecule level.