Showing papers in "Journal of Computational and Theoretical Nanoscience in 2010"

Five-Input Majority Gate, a New Device for Quantum-Dot Cellular Automata

Abstract: Science and Research Branch of IAU, Tehran, IranQuantum-dot Cellular Automata (QCA) is one of the most attractive technologies for computing atnano-scale. The principle logic element in QCA is majority gate. In this paper, a novel design for5-input majority gate is presented. A 5-input majority gate study has been proposed; however thisstudy has changed the scheme of basic QCA cells. The new proposed device reduces cell countsand area and uses conventional form of QCA cells. Accuracy of this design is proven by applyingsome simple physical substantiation and QCADesigner tool is used for verifying majority circuitlayout and functionality. Furthermore, a QCA Full-Adder is constructed using the new proposeddesign. Simulation results demonstrate that the proposed design of majority gates and Full-Adderresulted in significant improvements in designing logical circuits.

Elastic Properties and Frequencies of Free Vibrations of Single-Layer Graphene Sheets

Abstract: We determine the basal plane stiffness and Poisson’s ratio of single layer graphene sheets (SLGSs) in armchair and zigzag directions by using molecular mechanics simulations of their uniaxial tensile deformations with the MM3 potential, and of their axial and bending vibrations. Both approaches give the basal plane stiffness equal to ∼340 N/m which agrees well with that reported in the literature and derived from results of indentation experiments on SLGSs and from the first principle calculations. The computed value of Poisson’s ratio equals 0.21 in both armchair and zigzag directions. Assuming that the response of a SLGS is the same as that of a plate made of a linear elastic, homogeneous, and isotropic material having Poisson’s ratio = 0.21, the in-plane stiffness of ∼340 N/m and the total mass equal to that of the SLGS, the thickness of the SLGS is found to be ∼1 A. Thus Young’s modulus and the shear modulus of a SLGS equal ∼3.4 TPa and ∼1.4 TPa, respectively. It is shown that mode shapes corresponding to the several lowest frequencies of the SLGS differ noticeably from those of an equivalent thin layer made of a linear elastic isotropic material with Young’s modulus = 3.4 TPa and the shear modulus = 1.4 TPa. Furthermore, a free– free SLGS vibrates about a plane bisecting its width rather than its thickness as predicted by the Euler Bernoulli beam theory. We also investigate the effect of pretension on the natural frequencies of SLGSs using MM simulations and correlate it to that of 1 A thick linear elastic plate found by analyzing its three-dimensional deformations. These results will help design SLGS nanomechanical resonators having frequencies in the THz range.

First-Principles Study on Physical Properties of a Single ZnO Monolayer with Graphene-Like Structure

Abstract: The elastic, piezoelectric, electronic, and optical properties of a single ZnO monolayer (SZOML) with graphene-like structure are investigated from the first-principles calculations. The phonon dispersion curves contain three acoustic and three optical branches. Atpoint, the out-of-plane acoustic mode has an asymptotic behavior ��q� = Bq 2 with B = 1� 385 × 10 −7 m 2 /s, while two in-plane acoustic modes have sound velocities 2.801 km/s and 8� 095 km/s; the other three optical modes have fre- quencies 250 cm −1 , 566 cm −1 , and 631 cm −1 . The elastic and piezoelectric constants are obtained from the relaxed ion model. It is found that the SZOML is much softer than graphene, while it is a piezoelectric material. The electronic band gap is 3.576 eV, which implies that the SZOML is a wide band gap semiconductor. Many peaks exist in the linear optical spectra, where the first peak at 3.58 eV corresponds to the band gap of SZOML.

Tunable core size of carbon nanoscrolls

Abstract: Department of Structural Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Torino, ItalyWe study the equilibrium core radius of a carbon nanoscroll (CNS) formed from spontaneous rollingof a graphene sheet. By a balance between the elastic bending energy and the van der Waalsinteraction energy in the system, we derive an analytical relation between the surface energy, thebending stiffness, the interlayer spacing, the length of a graphene sheet and the core radius of theresulting CNS. This relation is then quantitatively veri“ed by molecular dynamics simulations. Ourwork immediately suggests that the core size of a CNS can be actively controlled for applicationssuch as tunable water and ion channels, molecular sensors, as well as ”exible gene and drugdelivery systems.

Solitonic Ionic Currents Along Microtubules

Abstract: Microtubules are very important cytoskeletal structures implicated in different cellular activities. We should mention the cell division and traffic of organelles (mitochondria, vesicles and other cargos) by kinesin and dynein motor proteins. Microtubules are also playing important roles in higher neuronal functions including mechanisms of consciousness and memory. We here investigate the circumstances and the conditions enabling microtubules to act as nonlinear electrical transmission lines for ions flow along their cylinders. We established a model in which each tubulin dimmer protein is an electric element with a capacitive, resistive and negative incrementally resistive property due to polyelectrolyte nature of microtubules in cytosol. The particular attention was paid to the role of nano-pores existing between neighboring dimmers within a MT wall which exhibit properties like ionic channels. These nano-pores are candidates to explain some properties of microtubules resembling to unipolar transistors enabling the rectification and amplification of ionic currents.

The Effective Susceptibility Concept in the Electrodynamics of Nano-Systems

Abstract: The effective susceptibility concept is developed for solution of electrodynamical problems of nano-systems. General principles of introducing effective susceptibility are discussed. The effective susceptibility for different nano-systems, namely, thin films, mesoparticles and quantum dots were calculated. Some examples of effective susceptibility uses were demonstrated. In part, the absorption profiles when inhomogeneous along the thickness thin film absorbs the light, was calculated. Discussed concept was used to show the influence of the shape of nano-partiles covering the surface on dispersion of surface plasmon polaritons. It was shown that proposed approach can be useful for analysis of surface plasmon polarriton resonance experiments. The effective susceptibility concept is useful for modeling of near-field images of linear and nonlinear scanning near-field optical microscopy. The presented method can be applied for modeling of near-field images of different objects. For example, there are pyramid-like quantum dots and semiconductor surface excited by strong focused Gauss-like beam of the light.

3D Reconstruction of Carbon Nanotube Composite Microstructure Using Correlation Functions

Abstract: Reconstruction of simulated microstructure from statistical microstructure descriptors attracts strong research interest due to its importance in materials design. A new methodology is presented in this paper to reconstruct robust microstructure with large number of representative volume elements which may acts as a stable input for deterministic method to simulate performance and effective properties. It is applied in carbon nanotube composite to demonstrate the capability of this method to generate robust microstructure while incorporating more statistical information on geometry, shape, anisotropy and spatial arrangement. Not only one point based statistical information, such as size, volume fraction, is taken into consideration, but correlation function is incorporated to cover information from geometry, shape and spatial correlation. Monte Carlo method was applied in reconstruction. Instead of using discrete image matrix, the information of geometric distribution of the nanotube composite is stored with the information of location of nanotubes. In this way, robust micrographs with large number of representative volume elements were generated for the future evaluation using finite element methods.

Calculation of Fluctuations in Boundary Layers of Nanowire Field-Effect Biosensors

Abstract: Fluctuations in the biofunctionalized boundary layers of nanowire field-effect biosensors are investigated by using the stochastic linearized Poisson-Boltzmann equation. The noise and fluctuations considered here are due to the Brownian motion of the biomolecules in the boundary layer, i.e., the various orientations of the molecules with respect to the surface are associated with their probabilities. The probabilities of the orientations are calculated using their free energy. The fluctuations in the charge distribution give rise to fluctuations in the electrostatic potential and hence in the current through the semiconductor transducer of the sensor, both of which are calculated. A homogenization result for the variance and covariance of the electrostatic potential is presented. In the numerical simulations, a cross section of a silicon nanowire on a flat surface including electrode and back-gate contacts is considered. The biofunctionalized boundary layer contains single-stranded or double-stranded DNA oligomers, and varying values of the surface charge, of the oligomer length, and of the electrolyte ionic strength are investigated.

Molecular Electronics Devices: A Short Review

Abstract: Molecular electronics has recently attracted a lot of attention due to promising application in nanoscale electronic devices. In this review we highlight recent results in this field, focusing on single organic molecules working as devices and addressing important effects related with electronic transport, such as push–pull molecules, or bridges, Coulomb blockage, negative differential resistance, molecular radicals, temperature dependence, environment sensibility, strong and weak coupling, quantum interference, coherent and incoherent transport, tunneling regime, switches, and a few applications will be addressed.

Comparative Study of Polymorphous Alzheimer's A β (1-40) Amyloid Nanofibrils and Microfibers

Abstract: The class of amyloid protein materials has been associated with severe degenerative diseases, such as Parkinson’s disease, Alzheimer’s disease and type II diabetes. Moreover, they represent an intriguing class of protein molecules that show exceptional strength, sturdiness and elasticity. However, physical models that explain the structural basis of these properties remain largely elusive. This is partly due to the fact that structural models of microscale amyloid fibrils remain unknown, preventing us from pursuing bottom-up studies to describe the link between their hierarchical structure and physical properties. Here we focus on the -amyloid peptide A (1-40), which is associated with Alzheimer’s disease. Earlier experimental studies suggest that this amyloid fibril arranges in both double and triple layered -sheet structures, leading to twofold and threefold morphologies. The resulting structures are stabilized by a hydrophobic core and interprotein H-bond networks. Here we identify the atomistic coordinates of both twofold and threefold morphologies, providing a structural fiber model with lengths of hundreds of nanometers. We present a systematic comparison between the two morphologies, including energetic properties, structural changes and H-bonding patterns, for varying fibril lengths. Our results suggest that the double layered morphology is more stable than the threefold morphology. The model described here predicts the formation of twisted amyloid microfibers with a periodicity of ≈133 nm and ≈82 nm, for the twofold and threefold structures, respectively. The approach proposed here makes a direct connection from the atomistic to the mesoscale level, provides a link between the fibril geometry, the chemical interactions and the final more stable configuration, and resolves the issue of missing atomistic structures for long amyloid fibers.

Graphene-carbon nanotube composites

Abstract: The formation of graphen-nanotube composites addresses a few basic problems. First, both partners are good donors and acceptors of electrons, which significantly complicates the intermolecular interaction between them leading to a two-well shape of the ground state energy term. The second problem concerns odd-electron character of the components. Similarly to high aromatics and fullerenes, much larger C-C distances provide a considerable weakening of odd electrons interaction in nanotubes and graphene that necessitates taking the configurational interaction of odd electrons into account. Avoiding a severe complication, the broken spin-symmetry approach makes the problem feasible. Moreover, unrestricted broken-symmetry Hartree-Fock approach possesses a unique sensitivity in revealing enhanced chemical activity of the species caused by their partial radicalization in terms of atomic chemical susceptibility. The chemical susceptibility profiles along the tube and across their body as well as over graphene sheets form the ground of computational synthesis of graphen-nanotube composites in due course of the relevant addition reactions and make it possible to select two main groups of the composites, conditionally called hammer and cutting-blade structures. The final product will depend on whether both components of the composition are freely accessible or one of them is fixed. Thus, in diluted solutions where the first requirement is met, one can expect the formation of the multi-addend cutting-blade composites. Oppositely, when either nanotubes or graphene sheets are fixed on some substrates, the hammer composites will be formed. A particular "cradle" composite is suggested for an individual graphene sheet to be fixed by a pair of nanotubes.

Graphene Nanocutting Through Nanopatterned Vacancy Defects

Abstract: Graphene Nanocutting Through Nanopatterned Vacancy Defects Rhonda Jack1 2, Dipanjan Sen1 3, and Markus J. Buehler1 ∗ 1Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Mass. Ave., Room 1-235A&B, Cambridge, MA, 02139, USA 2Department of Chemical Engineering, Hampton University, Hampton VA, USA 3Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA, 02139, USA

Fourier transform light scattering (FTLS) of cells and tissues

Abstract: Fourier transform light scattering (FTLS) has been recently developed as a novel, ultrasensitive method for studying light scattering from inhomogeneous and dynamic structures. FTLS relies on quantifying the optical phase and amplitude associated with a coherent image field and propagating it numerically to the scattering plane. In this paper, we review the principle and applications of FTLS to static and dynamic light scattering from biological tissues and live cells. Compared with other existing light scattering techniques, FTLS has significant benefits of high sensitivity, speed, and angular resolution. We anticipate that FTLS will set the basis for disease diagnosis based on intrinsic tissue optical properties and provide an efficient tool for quantifying cell structures and dynamics.

Modeling of Dislocation Interaction with Solutes, Nano-Precipitates and Interfaces: A Multiscale Challenge

Abstract: We review here several multiscale methods that we have developed to determine dislocation properties and interactions in metals. The review includes: (1) dislocation core properties in fcc and bcc metals; (2) the effect of solutes or nanoprecipitates on the mobility of a screw dislocation in bcc metals; (3) the interaction between dislocations and precipitates in intermetallic compounds; and (4) the transmission of dislocations through coherent and incoherent interfaces. In the concurrent quantum mechanical (QM) and molecular mechanical (MM) coupling approach, the quantum mechanical treatment is spatially confined to a small region, surrounded by a larger classical atomistic region. This approach is particularly useful for systems where quantum mechanical interactions in a small region, such as lattice defects or chemical impurities, can affect the macroscopic properties of a material. We discuss how the coupling across the different scales can be accomplished efficiently and accurately. We have applied this method to study the core structure and mobility of an edge dislocation in Al and of a screw dislocation in Ta, which are prototypical fcc and bcc metals. We find that the local environment of W solutes in Ta has a dramatic effect both on the dislocation mobility and slip paths. Isolated W solutes enhance the dislocation mobility, W nanoclusters of triangular shape pin the dislocation, while those of hexagonal shape result in spontaneous dislocation glide. The first sequential multiscale approach is a hybrid ab initio-based approach of Suzuki’s atomic-row (AR) model, which allows the study of the dislocation core of a screw dislocation in bcc metals. The second hybrid approach, based on an extension of the Peierls-Nabarro model to study the dislocation-interface and the dislocation-precipitate interactions, integrates the atomistic nature from ab initio calculations of the generalized stacking fault energy surface (GSFS) into the parametric dislocation dynamics method. The ab initio-based calculations reveal that Cu nano-clusters in -Fe dramatically alter the core structure of a screw dislocation from non-polarized in pure Fe to polarized, in agreement with experiments. In contrast, Cr clusters do not change the core polarization and increase the Peierls stress, thus hardening Fe. The hybrid method with four different interaction models was applied to study the interaction of a superdislocation with a spherical -precipitate embedded in the � -matrix of a nickel-based superalloy. The dislocation core structure was found to play an important role in determining the critical resolved shear stress. Based on these simulations, analytical equations for the precipitate strengthening are derived. For the Cu/Ni interface, the dislocation is found to dissociate into partials in both Cu and Ni, and the dislocation core is squeezed near the interface facilitating the spreading process, and leaving an interfacial ledge. It is shown that the strength of the bimaterial can be greatly enhanced by the spreading of the glide dislocation, and also increased by the pre-existence of misfit dislocations.