Pedro A. Serena

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 ≈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.

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.

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.

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 ϕ29 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 ϕ29 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.

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.P. Garćıa-Mochales, R. Paredes, 3 S. Peláez, and P. A. Serena Departamento de F́ısica de la Materia Condensada, Facultad de Ciencias, Universidad Autónoma de Madrid, c/ Francisco Tomás y Valiente 7, Campus de Cantoblanco, E-28049-Madrid, Spain∗ Centro de F́ısica, Instituto Venezolano de Investigaciones Cient́ıficas, Apdo 20632, Caracas 1020A, Venezuela Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Cient́ıficas c/ Sor Juana Inés de la Cruz 3, Campus de Cantoblanco, E-28049-Madrid, Spain (Dated: February 2, 2008)

Evidence of shell structures in Au nanowires at room temperature

Statistical conductance properties of gold elongating nanowires at room temperature are studied experimentally. The measured conductance histogram, built with thousands of consecutive nanocontact breakage experiments, exhibits a rich structure of low-intensity peaks at high-conductance quanta values. Their position as a function of a peak index number suggests two markedly different regimes for electronic and atomic shell structures in these nanowires, as observed previously for alkali metal nanowires.

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.

Ballistic resistivity in aluminum nanocontacts

We thank J. J. Saenz for helpful discussions, and Cecalcula (Venezuela) for computer facilities. This work has been partially supported by the CSIC-IVIC researchers exchange program and the Spanish DGICyT (MEC) through Project No. BFM2003-01167/FISI.

Atomic-Scale Sliding Friction on Graphene in Water.

The sliding of a sharp nanotip on graphene completely immersed in water is investigated by molecular dynamics (MD) and atomic force microscopy. MD simulations predict that the atomic-scale stick-slip is almost identical to that found in ultrahigh vacuum. Furthermore, they show that water plays a purely stochastic role in sliding (solid-to-solid) friction. These observations are substantiated by friction measurements on graphene grown on Cu and Ni, where, oppositely of the operation in air, lattice resolution is readily achieved. Our results promote friction force microscopy in water as a robust alternative to ultra-high-vacuum measurements.

Simulations and experiments of aluminum conductance histograms

We study experimentally and numerically the statistical conductance properties of Al breaking nanocontacts at room temperature. The measured conductance histogram (CH) from hundreds of consecutive experiments exhibits peaks close to integer values in units of 2e2/h. The results are compared with minimum-cross-section histograms obtained from molecular dynamics calculations. The agreement between these atomistic simulations and experiments provides evidence that the CH is a signature of favourable atomic configurations.