Albumin (BSA) Adsorption over Graphene in Aqueous Environment: Influence of Orientation, Adsorption Protocol, and Solvent Treatment.

We report 150 ns explicit solvent MD simulations of the adsorption on graphene of albumin (BSA) in two orientations and using two different adsorption protocols, i.e., free and forced adsorption. Our results show that free adsorption occurs with little structural rearrangements. Even taking adsorption to an extreme, by forcing it with a 5 nN downward force applied during the initial 20 ns, we show that along a particular orientation BSA is able to preserve the structural properties of the majority of its binding sites. Furthermore, in all the cases considered in this work, the ibuprofen binding site has shown a strong resilience to structural changes. Finally, we compare these results with implicit solvent simulations and find that the latter predicts an extreme protein unfolding upon adsorption. The origin of this discrepancy is attributed to a poor description of the water entropic forces at interfaces in the implicit solvent methods.

The capillarity of nanometric water menisci confined inside closed-geometry viral cages.

We present an investigation of water menisci confined in closed geometries by studying the structural effects of their capillary forces on viruses during the final stage of desiccation. We used individual particles of the bacteriophage phi29 and the minute virus of mice. In both cases the genomic DNA was ejected from the capsid. However, although the structural integrity of the minute virus of mice was essentially preserved, the phi29 capsid underwent a wall-to-wall collapse. We provide evidence that the capillary forces of water confined inside the viruses are mainly responsible for these effects. Moreover, by performing theoretical simulations with a lattice gas model, we found that some structural differences between these 2 viruses may be crucial to explain the different ways in which they are affected by water menisci forces confined at the nanoscale.

Built-in mechanical stress in viral shells.

Mechanical properties of biological molecular aggregates are essential to their function. A remarkable example are double-stranded DNA viruses such as the φ29 bacteriophage, that not only has to withstand pressures of tens of atmospheres exerted by the confined DNA, but also uses this stored elastic energy during DNA translocation into the host. Here we show that empty prolated φ29 bacteriophage proheads exhibit an intriguing anisotropic stiffness which behaves counterintuitively different from standard continuum elasticity predictions. By using atomic force microscopy, we find that the φ29 shells are approximately two-times stiffer along the short than along the long axis. This result can be attributed to the existence of a residual stress, a hypothesis that we confirm by coarse-grained simulations. This built-in stress of the virus prohead could be a strategy to provide extra mechanical strength to withstand the DNA compaction during and after packing and a variety of extracellular conditions, such as osmotic shocks or dehydration.

Assessing the Accuracy of Different Solvation Models To Describe Protein Adsorption.

In protein adsorption, the surrounding solvent has an important role in mediating protein-surface interactions. Therefore, it is of paramount importance that the solvent methods employed to model these kinds of processes are able to correctly capture the complex mechanisms occurring in the protein-water-surface interface. Here, we test the suitability of the two most popular implicit solvent methods based on the Generalized Born formalism to describe the adsorption process of the immunoglobulin G (IgG) on a hydrophobic graphene surface. Our results show that in both cases, IgG experiences an extreme and early (in less than 40 ns) unfolding as a result of the adsorption to the surface in contrast with previous experimental findings. A detailed energy decomposition analysis of explicit and implicit solvent simulations reveals that this discrepancy arises from the ill-characterization of two energy components in implicit solvent methods. These findings help to elucidate how implicit solvent models may be improved to accurately characterize the protein adsorption process.

Adsorption orientations and immunological recognition of antibodies on graphene.

Large-scale molecular dynamics (MD) simulations and atomic force microscopy (AFM) in liquid are combined to characterize the adsorption of Immunoglobulin G (IgG) antibodies over a hydrophobic surface modeled with a three-layer graphene slab. We consider explicitly the water solvent, simulating systems with massive sizes (up to 770 000 atoms), for four different adsorption orientations. Protocols based on steered MD to speed up the protein diffusion stage and to enhance the dehydration process are combined with long simulation times (>150 ns) in order to make sure that the final adsorption states correspond to actual stable configurations. Our MD results and the AFM images demonstrate that the IgG antibodies are strongly adsorbed, do not unfold, and retain their secondary and tertiary structures upon deposition. Statistical analysis of the AFM images shows that many of the antibodies adopt vertical orientations, even at very small coverages, which expose at least one Fab binding site for recognition events. Single molecule force spectroscopy experiments demonstrate the immunological response of the deposited antibodies by recognizing its specific antigens. The above properties together with the strong anchoring and preservation of the secondary structure, make graphene an excellent candidate for the development of immunosensors.

Statistical analysis of the breaking processes of Ni nanowires.

We have performed a massive statistical analysis on the breaking behaviour of Ni nanowires using molecular dynamic simulations. Three stretching directions, five initial nanowire sizes and two temperatures have been studied. We have constructed minimum cross-section histograms and analysed for the first time the role played by monomers and dimers. The shape of such histograms and the absolute number of monomers and dimers strongly depend on the stretching direction and the initial size of the nanowire. In particular, the statistical behaviour of the breakage final stages of narrow nanowires strongly differs from the behaviour obtained for large nanowires. We have analysed the structure around monomers and dimers. Their most probable local configurations differ from those usually appearing in static electron transport calculations. Their non-local environments show disordered regions along the nanowire if the stretching direction is [100] or [110]. Additionally, we have found that, at room temperature, [100] and [110] stretching directions favour the appearance of non-crystalline staggered pentagonal structures. These pentagonal Ni nanowires are reported in this work for the first time. This set of results suggests that experimental Ni conducting histograms could show a strong dependence on the orientation and temperature.

DNA-mediated anisotropic mechanical reinforcement of a virus.

In this work, we provide evidence of a mechanism to reinforce the strength of an icosahedral virus by using its genomic DNA as a structural element. The mechanical properties of individual empty capsids and DNA-containing virions of the minute virus of mice are investigated by using atomic force microscopy. The stiffness of the empty capsid is found to be isotropic. Remarkably, the presence of the DNA inside the virion leads to an anisotropic reinforcement of the virus stiffness by approximately 3%, 40%, and 140% along the fivefold, threefold, and twofold symmetry axes, respectively. A finite element model of the virus indicates that this anisotropic mechanical reinforcement is due to DNA stretches bound to 60 concavities of the capsid. These results, together with evidence of biologically relevant conformational rearrangements of the capsid around pores located at the fivefold symmetry axes, suggest that the bound DNA may reinforce the overall stiffness of the viral particle without canceling the conformational changes needed for its infectivity.

From favorable atomic configurations to supershell structures: a new interpretation of conductance histograms.

Simulated minimum cross-section histograms of breaking Al nanocontacts are produced using molecular dynamics. The results allow a new interpretation of the controverted conductance histogram peaks based on preferential geometrical arrangements of nanocontact necks. As temperature increases, lower conductance peaks decrease in favor of broader and higher conductance structures. This reveals the existence of shell and supershell structures favored by the increased mobility of Al atoms.

Ionic shell and subshell structures in aluminum and gold nanocontacts.

Conductance histograms of aluminum and gold nanocontact rupture are studied experimentally and simulated using embedded atom potentials to assess the interplay between electronic and structural properties at room temperature. Our results reveal a crossover from quantized conductance structures to crystalline faceting or geometric shell/subshell structures at 300 K. The absence of electronic shell structure in gold and aluminum is in stark contrast with the behavior of alkaline metal nanowires which emulate their cluster counterparts. Semiclassical arguments suggest why rapid dominance of ionic structures takes place, and possible nanowire architectures are proposed in consistency with both the experimental and simulated nanocontact data.

Nonlinear resistance versus length in single-walled carbon nanotubes.

In this work fundamental properties of the electrical transport of single-walled carbon nanotubes as a function of their length are investigated. For this purpose, we have developed a new technique that allows us to characterize electronic transport properties of single-walled carbon nanotubes by probing them at different spots. This technique uses scanning force microscopy to make mechanical and electrical nanocontacts at any selected spot of a given image. We have applied this technique to molecules with high intrinsic resistance. The results show a nonlinear resistance vs distance behavior as the nanotube is probed along its length. This is an indication of elastic electronic transport in one-dimensional systems.

Conductance distributions in quasi-one-dimensional disordered wires.

A detailed analysis of the distribution of conductances P(g) of quasi-one-dimensional disordered wires in the metal-insulator crossover is presented. P(g) obtained from a Monte Carlo solution of the Dorokhov, Mello, Pereyra, and Kumar (DMPK) scaling equation is in full agreement with "tight-binding" numerical calculations of bulk disordered wires. Perturbation theory is shown to be valid even for mean dimensionless conductances of the order of 1. In the crossover regime <, similar 1, P(g) presents a sharp feature at g=1 which is different from that observed in surface disordered wires.