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Alexandre F. da Fonseca

Publications and source records attributed to Alexandre F. da Fonseca.

9 recordsLinked to original sources

Energy barriers for collapsing large-diameter carbon nanotubes

Single-wall carbon nanotubes (SWNTs) are best known in their hollow cylindrical shapes, but the ground state of large-diameter tubes actually corresponds to a collapsed dumbbell-like structure, where the opposite sides of the nanotube wall are brought in contact and stabilized by van der Waals attraction. For those tubes, the cylindrical shape is metastable and it is interesting to investigate the energy barrier for jumping from one configuration to another. We calculate the energy barrier for SWNT collapse by considering a transition pathway that consists of an initial local deformation that subsequently propagates itself along the SWNT axis. This leads to finite and physically meaningful energy barriers in the limit of infinite nanotubes. Yet, such barriers are surprisingly large (tens of eV) and therefore virtually unsurmountable, which essentially prevents the thermal collapse of a metastable cylindrical at any reasonable temperatures. Moreover, we show that collapse barriers increase counterintuitively with SWNT diameter. Finally, we demonstrate that, despite such huge barriers, SWNTs may collapse relatively easily under external radial forces and we shed light on recent experimental observations of collapsed and cylindrical SWNTs of various diameters.

cond-mat.mes-hall

Mechanical properties of amorphous nanosprings

Helical amorphous nanosprings have attracted particular interest due to their special mechanical properties. In this work we present a simple model, within the framework of the Kirchhoff rod model, for investigating the structural properties of nanosprings having asymmetric cross section. We have derived expressions that can be used to obtain the Young's modulus and Poisson's ratio of the nanospring material composite. We also address the importance of the presence of a catalyst in the growth process of amorphous nanosprings in terms of the stability of helical rods.

cond-mat.mtrl-sci

Circular and helical equilibrium solutions of inhomogeneous rods

Real filaments are not perfectly homogeneous. Most of them have various materials composition and shapes making their stiffnesses not constant along the arclength. We investigate the existence of circular and helical equilibrium solutions of an intrinsically straight rod with varying bending and twisting stiffnesses, within the framework of the Kirchhoff model. The planar ring equilibrium solution only exists for a rod with a given form of variation of the bending stiffness. We show that the well known circular helix is not an equilibrium solution of the static Kirchhoff equations for a rod with non constant bending stiffness. Our results may provide an explanation for the variation of the curvature seen in small closed DNAs immersed in a solution containing Zn^{2+}, and in the DNA wrapped around a nucleosome.

physics.class-ph

Elastic Properties of Nanowires

We present a model to study Young's modulus and Poisson's ratio of the composite material of amorphous nanowires. It is an extension of the model derived by two of us [Da Fonseca and Galvao, Phys. Rev. Lett. 92, 175502 (2004)] to study the elastic properties of amorphous nanosprings. The model is based on twisting and tensioning a straight nanowire and we propose an experimental setup to obtain the elastic parameters of the nanowire. We used the Kirchhoff rod model to obtain the expressions for the elastic constants of the nanowire.

cond-mat.mtrl-sci

Lancret helices

Helical configurations of inhomogeneous symmetric rods with non-constant bending and twisting stiffness are studied within the framework of the Kirchhoff rod model. From the static Kirchhoff equations, we obtain a set of differential equations for the curvature and torsion of the centerline of the rod and the Lancret's theorem is used to find helical solutions. We obtain a free standing helical solution for an inhomogeneous rod whose curvature and torsion depend on the form of variation of the bending coefficient along the rod. These results are obtained for inhomogeneous rods without intrinsic curvature, and for a particular case of intrinsic curvature.

physics.bio-ph

Kirchhoff rods with nonhomogeneous cross section

The Kirchhoff's theory for thin, inextensible, elastic rods with nonhomogeneous cross section is studied. The Young's and shear moduli of the rod are considered to vary radially, and it is shown that an analytical solution for the constitutive relations can be obtained for circular cross section and constant Poisson's ratio. We comment on possible applications of our results.

cond-mat.mtrl-sci

Resonant helical deformations in nonhomogeneous Kirchhoff filaments

We study the three-dimensional static configurations of nonhomogeneous Kirchhoff filaments with periodically varying Young's modulus. This type of variation may occur in long tandemly repeated sequences of DNA. We analyse the effects of the Young's modulus frequence and amplitude of oscillation in the stroboscopic maps, and in the regular (non chaotic) spatial configurations of the filaments. Our analysis shows that the tridimensional conformations of long filaments may depend critically on the Young's modulus frequence in case of resonance with other natural frequencies of the filament. As expected, far from resonance the shape of the solutions remain very close to that of the homogeneous case. In the case of biomolecules, it is well known that various other elements, besides sequence-dependent effects, combine to determine their conformation, like self-contact, salt concentration, thermal fluctuations, anisotropy and interaction with proteins. Our results show that sequence-dependent effects alone may have a significant influence on the shape of these molecules, including DNA. This could, therefore, be a possible mechanical function of the ``junk'' sequences.

physics.bio-ph

Helical filaments with varying cross section radius

The tridimensional configuration and the twist density of helical rods with varying cross section radius are studied within the framework of the Kirchhoff rod model. It is shown that the twist density increases when the cross section radius decreases. Some tridimensional configurations of helix-like rods are displayed showing the effects of the nonhomogeneity considered here. Since the helix-like solutions of the nonhomogeneous rods do not present constant curvature and torsion a set of differential equations for these quantities is presented. We discuss the results and possible consequences.

physics.bio-ph

Solving the boundary value problem for finite Kirchhoff rods

The Kirchhoff model describes the statics and dynamics of thin rods within the approximations of the linear elasticity theory. In this paper we develop a method, based on a shooting technique, to find equilibrium configurations of finite rods subjected to boundary conditions and given load parameters. The method consists in making a series of small changes on a {\it trial} solution satisfying the Kirchhoff equations but not necessarily the boundary conditions. By linearizing the differential equations around the trial solution we are able to push its end point to the desired position, step by step. The method is also useful to obtain configurations of rods with fixed end points but different mechanical parameters, such as tension, components of the moment or inhomogeneities.

physics.bio-ph