arXiv subjects

D. S. Galvao

Publications and source records attributed to D. S. Galvao.

17 recordsLinked to original sources

arXiv2022

Quantum Biochemical Analysis of the TtgR Regulator and Effectors

The recent expansion of multidrug-resistant (MDR) pathogens poses significant challenges in treating healthcare-associated infections. Although antibacterial resistance occurs by numerous mechanisms, active efflux of the drugs is a critical concern. A single species of efflux pump can produce a simultaneous resistance to several drugs. One of the best-studied efflux pumps is the TtgABC: a tripartite resistance-nodulation-division (RND) efflux pump implicated in the intrinsic antibiotic resistance in Pseudomonas putida DOT-T1E. The expression of the TtgABC gene is down-regulated by the HTH-type transcriptional repressor TtgR. In this context, by employing quantum chemistry methods based on the Density Functional Theory (DFT) within the Molecular Fragmentation with Conjugate Caps (MFCC) approach, we investigate the coupling profiles of the transcriptional regulator TtgR in complex with quercetin (QUE), a natural polyphenolic flavonoid, tetracycline (TAC), and chloramphenicol (CLM), two broad-spectrum antimicrobial agents. Our quantum biochemical computational results show the: [i] convergence radius, [ii] total binding energy, [iii] relevance (energetically) of the ligands regions, and [iv] most relevant amino acids residues of the TtgR-QUE/TAC/CLM complexes, pointing out distinctions and similarities among them. These findings improve the understanding of the binding mechanism of effectors and facilitate the development of new chemicals targeting TtgR, helping in the battle against the rise of resistance to antimicrobial drugs.

physics.bio-ph↗

arXiv2020

Carbon Nanotube Peapods Under High-Strain Rate Conditions: A Molecular Dynamics Investigation

New forms of carbon-based materials have received great attention, and the developed materials have found many applications in nanotechnology. Interesting novel carbon structures include the carbon peapods, which are comprised of fullerenes encapsulated within carbon nanotubes. Peapod-like nanostructures have been successfully synthesized, and have been used in optical modulation devices, transistors, solar cells, and in other devices. However, the mechanical properties of these structures are not completely elucidated. In this work, we investigated, using fully atomistic molecular dynamics simulations, the deformation of carbon peapods under high-strain rate conditions, which are achieved by shooting the peapods at ultrasonic velocities against a rigid substrate. Our results show that carbon peapods experience large deformation at impact, and undergo multiple fracture pathways, depending primarily on the relative orientation between the peapod and the substrate, and the impact velocity. Observed outcomes include fullerene ejection, carbon nanotube fracture, fullerene, and nanotube coalescence, as well as the formation of amorphous carbon structures.

cond-mat.mtrl-sci↗

arXiv2019

Elastic Properties of Graphyne-based Nanotubes

Graphyne nanotubes (GNTs) are nanostructures obtained from rolled up graphyne sheets, in the same way carbon nanotubes (CNTs) are obtained from graphene ones. Graphynes are 2D carbon-allotropes composed of atoms in sp and sp2 hybridized states. Similarly to conventional CNTs, GNTs can present different chiralities and electronic properties. Because of the acetylenic groups (triple bonds), GNTs exhibit large sidewall pores that influence their mechanical properties. In this work, we studied the mechanical response of GNTs under tensile stress using fully atomistic molecular dynamics simulations and density functional theory (DFT) calculations. Our results show that GNTs mechanical failure (fracture) occurs at larger strain values in comparison to corresponding CNTs, but paradoxically with smaller ultimate strength and Young's modulus values. This is a consequence of the combined effects of the existence of triple bonds and increased porosity/flexibility due to the presence of acetylenic groups.

cond-mat.mtrl-sci↗

arXiv2015

Surface Effects on the Mechanical Elongation of AuCu Nanowires: De-alloying and the Formation of Mixed Suspended Atomic Chains

We report here an atomistic study of the mechanical deformation of AuxCu(1-x) atomic-size wires (NWs) by means of high resolution transmission electron microscopy (HRTEM) experiments. Molecular dynamics simulations were also carried out in order to obtain deeper insights on the dynamical properties of stretched NWs. The mechanical properties are significantly dependent on the chemical composition that evolves in time at the junction; some structures exhibit a remarkable de-alloying behavior. Also, our results represent the first experimental realization of mixed linear atomic chains (LACs) among transition and noble metals; in particular, surface energies induce chemical gradients on NW surfaces that can be exploited to control the relative LAC compositions (different number of gold and copper atoms). The implications of these results for nanocatalysis and spin transport of one-atom-thick metal wires are addressed.

cond-mat.mtrl-sci↗

arXiv2015

A Brief Review on Syntheses, Structures and Applications of Nanoscrolls

Nanoscrolls are papyrus-like nanostructures which present unique properties due to their open ended morphology. These properties can be exploited in a plethora of technological applications, leading to the design of novel and interesting devices. During the past decade, significant advances in the synthesis and characterization of these structures have been made, but many challenges still remain. In this mini review we provide an overview on their history, experimental synthesis methods, basic properties and application perspectives.

cond-mat.mes-hall↗

arXiv2014

Site-dependent hydrogenation on graphdiyne

Graphene is one of the most important materials in science today due to its unique and remarkable electronic, thermal and mechanical properties. However in its pristine state, graphene is a gapless semiconductor, what limits its use in transistor electronics. In part due to the revolution created by graphene in materials science, there is a renewed interest in other possible graphene-like two-dimensional structures. Examples of these structures are graphynes and graphdiynes, which are two-dimensional structures, composed of carbon atoms in sp2 and sp-hybridized states. Graphdiynes (benzenoid rings connecting two acetylenic groups) were recently synthesized and some of them are intrinsically nonzero gap systems. These systems can be easily hydrogenated and the relative level of hydrogenation can be used to tune the band gap values. We have investigated, using fully reactive molecular dynamics (ReaxFF), the structural and dynamics aspects of the hydrogenation mechanisms of graphdiyne membranes. Our results showed that the hydrogen bindings have different atom incorporation rates and that the hydrogenation patterns change in time in a very complex way. The formation of correlated domains reported to hydrogenated graphene is no longer observed in graphdiyne cases.

cond-mat.mtrl-sci↗

arXiv2014

Mechanical Properties and Fracture Dynamics of Silicene Membranes

As graphene became one of the most important materials today, there is a renewed interest on others similar structures. One example is silicene, the silicon analogue of graphene. It share some the remarkable graphene properties, such as the Dirac cone, but presents some distinct ones, such as a pronounced structural buckling. We have investigated, through density functional based tight-binding (DFTB), as well as reactive molecular dynamics (using ReaxFF), the mechanical properties of suspended single-layer silicene. We calculated the elastic constants, analyzed the fracture patterns and edge reconstructions. We also addressed the stress distributions, unbuckling mechanisms and the fracture dependence on the temperature. We analysed the differences due to distinct edge morphologies, namely zigzag and armchair.

cond-mat.mes-hall↗

arXiv2014

Graphene-like Membranes: From Impermeable to Selective Sieves

Recently, it was proposed that graphene membranes could act as impermeable atomic structures to standard gases. For some other applications, a higher level of porosity is needed, and the so-called Porous Graphene (PG) and Biphenylene Carbon (BPC) membranes are good candidates to effectively work as selective sieves. In this work we have used classical molecular dynamics simulations to study the dynamics of membrane permeation of He and Ar atoms and possible selectivity effects. For the graphene membranes we did not observe any leakage through the membrane and/or membrane/substrate interface until a critical pressure limit, then a sudden membrane detachment occurs. PG and BPC membranes are not impermeable as graphene ones, but there are significant energy barriers to diffusion depending on the atom type. Our results show that this kind of porous membranes can be effectively used as selective sieves for pure and mixtures of gases.

cond-mat.mes-hall↗

arXiv2014

Mechanical Properties of Graphene Nanowiggles

In this work we have investigated the mechanical properties and fracture patterns of some graphene nanowiggles (GNWs). Graphene nanoribbons are finite graphene segments with a large aspect ratio, while GNWs are nonaligned periodic repetitions of graphene nanoribbons. We have carried out fully atomistic molecular dynamics simulations using a reactive force field (ReaxFF), as implemented in the LAMPPS (Large-scale Atomic/Molecular Massively Parallel Simulator) code. Our results showed that the GNW fracture patterns are strongly dependent on the nanoribbon topology and present an interesting behavior, since some narrow sheets have larger ultimate failure strain values. This can be explained by the fact that narrow nanoribbons have more angular freedom when compared to wider ones, which can create a more efficient way to accumulate and to dissipate strain/stress. We have also observed the formation of linear atomic chains (LACs) and some structural defect reconstructions during the material rupture. The reported graphene failure patterns, where zigzag/armchair edge terminated graphene structures are fractured along armchair/zigzag lines, were not observed in the GNW analyzed cases.

cond-mat.mes-hall↗

arXiv2014

Violation of the Universal Behavior of Membranes Inside Cylindrical Tubes at Nanoscale

Recently, it was proposed based on classical elasticity theory and experiments at macroscale, that the conformations of sheets inside cylindrical tubes present a universal behavior. A natural question is whether this behavior still holds at nanoscale. Based on molecular dynamics simulations and analytical modeling for graphene and boron nitride membranes confined inside carbon nanotubes, we show that the class of universality observed at macroscale is violated at nanoscale. The precise origins of these discrepancies is addressed and proven to be related to both surface and atomistic effects.

cond-mat.mes-hall↗

arXiv2012

Correlation between Quantum Conductance and Atomic Arrangement of Silver Atomic-Size Nanowires

We have studied the effect of thermal effects on the structural and transport response of Ag atomic-size nanowires generated by mechanical elongation. Our study involves both time-resolved atomic resolution transmission electron microscopy imaging and quantum conductance measurement using an ultra-high-vacuum mechanically controllable break junction. We have observed drastic changes in conductance and structural properties of Ag nanowires generated at different temperatures (150 and 300 K). By combining electron microscopy images, electronic transport measurements and quantum transport calculations, we have been able to obtain a consistent correlation between the conductance and structural properties of Ag NWs. In particular, our study has revealed the formation of metastable rectangular rod-like Ag wire (3/3) along the (001) crystallographic direction, whose formation is enhanced. These results illustrate the high complexity of analyzing structural and quantum conductance behaviour of metal atomic-size wires; also, they reveal that it is extremely difficult to compare NW conductance experiments performed at different temperatures due to the fundamental modifications of the mechanical behavior.

cond-mat.mtrl-sci↗

arXiv2007

Is it possible to grow amorphous normal nanosprings ?

Nanosprings have been object of intense investigations in recent years. They can be classified as normal or binormal depending on the geometry of their cross-section. Normal amorphous nanosprings have not been observed experimentally up to now, and only recently the synthesis of a crystalline ZnO normal nanohelix has been reported. We discuss the shape of the catalyst in terms of the cross-sectional shape of the nanospring, and show that, within the vapor-liquid-solid model, the growth of amorphous normal nanospring is not energetically favoured.

cond-mat.mtrl-sci↗

arXiv2007

Molecular Recognition Effects in the Surface Diffusion of Large Organic Molecules: The Case of Violet Lander

Violet Lander (VL) (C108H104) is a large organic molecule that when deposited on Cu (110) exhibited lock-and-key like behavior (Otero et al., Nature Mater. 3, 779 (2004)). In this work we report on a detailed fully atomistic molecular dynamics study of this phenomenon. Our results show that it has its physical basis in the interplay of the molecular hydrogens and the Cu(110) atomic spacing, which is a direct consequence of an accidental commensurability between molecule and surface dimensions. This knowledge could be used to engineer new molecules capable of displaying lock-and-key behavior with new potential applications in nanotechology.

cond-mat.mtrl-sci↗

arXiv2006

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↗

arXiv2006

On the Formation of Copper Linear Atomic Suspended Chains

We report high resolution transmission electron microscopy and classical molecular dynamics simulation results of mechanically stretching copper nanowires conducting to linear atomic suspended chains (LACs) formation. In contrast with some previous experimental and theoretical work in literature that stated that the formation of LACs for copper should not exist our results showed the existence of LAC for the [111], [110], and [100] crystallographic directions, being thus the sequence of most probable occurence.

cond-mat.mtrl-sci↗

arXiv2006

Nanowires and Suspended Atom Chains from Metal alloys

We present a study of the elongation and rupture of gold-silver alloy nanowires. Atomistic details of the evolution were derived from time-resolved atomic resolution transmission electron microscopy and molecular dynamics simulations. The results show the occurrence of gold enrichment at the nanojunction region, leading to a gold-like structural behavior even for alloys with minor gold content. Our observations have also revealed the formation of mixed (Au and Ag) linear atomic chains.

cond-mat.mtrl-sci↗

arXiv2002

Molecular Dynamics Simulations of Carbon Nanotubes as Gigahertz Oscillators

Recently Zheng and Jiang [PRL 88, 045503 (2002)], based on static models, have proposed that multiwalled carbon nanotubes could be the basis for a new generation of nanooscilators in the several gigahertz range. In this work we present the first molecular dynamics simulation for these systems. Different nanotube types were considered in order to verify the reliability of such devices as gigahertz oscillators. Our results show that these nanooscillators are dynamically stables when the radii difference values between inner and outer tubes are of ~ 3.4 A. Frequencies as large as 38 GHz were observed, and the calculated force values are in good agreement with recent experimental investigations. Moreover, our results contradict some predictions made by Zheng and Jiang.

cond-mat.mtrl-sci↗