Nanoscale Modeling – TechConnect Briefs

Influence of His-195 on the nitrogenase FeMo-cofactor activity

Cavallotti C., Moscatelli D., Carrà S., Politecnico di Milano, IT

Mo-nitrogenase is the enzyme responsible for the conversion of atmospheric nitrogen to ammonia. Its active site is the iron-molibdenum cofactor, FeMo-co, which is composed by two incomplete cubes, Fe4S3 and MoFe3S3, connected through three bridging [...]

Denaturation of hen egg white lysozyme in electromagnetic fields: a molecular dynamics study

English N.J., Mooney D.A., University College Dublin, IE

Nonequilibrium molecular dynamics simulations of hen egg white lysozyme have been performed in the canonical ensemble at 298 K in the presence of external electromagnetic fields of varying intensity in the microwave to far-infrared frequency [...]

Investigation of dsDNA Molecule Mechanical Behavior using Atomistic Continuum Mechanics Method

Han C-N, Chou C.Y., Wu C-J, Chiang K.N., National Tsing Hua University, TW

In this research, an atomistic continuum model of dsDNA based on equivalent-spring method would be first conducted and the simulation result would be further validated by the experimental result. A spring element is chosen to [...]

Theoretical Studies on the Ozonization at the Capped-end of a Single-walled Carbon Nanotube: The Effect of the Finite Length

Sawangphruk M., Sirijaraensre J., Pantu P., Limtrakul J., Kasetsart University, TH

Since the discovery in 1991, single-walled carbon nanotubes (SWNTs) have been investigated for numerous potential applications in nanotechnology. However, the insolubility and high chemical stability obstruct the purification and the applications of the nanotubes. The [...]

Structure and Electronic Properties of “DNA-Gold-Nanotube” Systems: A Quantum Chemical Analysis

Pannopard P., Sirijaraensre J., Nokbin S., Khongpracha P., Limtrakul J., Kasetsart University, TH

The idea of chemical sensing based on molecular recognition is known as one of the most promising concepts for single-molecule detection, even though it still remains in an early developmental stage. The approach requires probes [...]

Molecular Dynamic investigation of the interaction of supported affinity ligands with Monoclonal Antibodies

Zamolo L., Busini V., Moiani D., Moscatelli D., Cavallotti C., Politecnico di Milano, IT

Monoclonal antibodies are gaining an increasing importance in diagnostic and therapeutic treatment of grave diseases such as immunodeficiency, Alzheimer’s syndrome and cancer. The production of these pharmaceuticals and especially the purification step, however, are still [...]

Adsorption of glycine and phenylalanine in H-ZSM-5 zeolite: an embedded QM/MM study

Boekfa B., Sirijaraensre J., Limtrakul J., Limtrakul P., Pantu P., Limtrakul J., Limtrakul P., Kasetsart University, TH

Zeolites are crystalline aluminosilicate microporous materials whose pore diameters are in the range of 2 to 10 Å. Zeolites have numerous important applications in catalysis, adsorption, drug delivery, and chemical separations. Recently, zeolites have received [...]

Scanning Tunneling Microscopy Images of Au Adsorbed on GaAs(111)B surface

Yi H., Kratzer P., Hilner E., Mikkelsen A., KISTI, KR

We have studied the GaAs(111)B surface with Au deposited either homogeneously or as nanoparticles, and found the presence of Au in either form to give rise to a $(sqrt{3} !times! sqrt{3} )$ Au-induced surface reconstruction. [...]

New Pair Force Evaluation Method for Parallel Molecular Dynamics in Arbitrary Geometries

Macpherson G.B., Reese J.M., University of Strathclyde, UK

We develop a new molecular dynamics algorithm for pair force evaluation of molecules occupying arbitrary polyhedral, unstructured mesh geometries. This is designed for hybrid MD/continuum simulation of nanofluidic systems. We show that the conventional MD [...]

Electric Filed Modulation on the Geometric and Electronic Structures of Diblock Molecule

Wi Li Y., Yin G.P., Zhao J.W., Harbin Institute of Technology, CN

Theoretical investigations on the diblock molecule, thiophene-thiazole compound, have been carried out at Hartree-Fock (HF) level by considering the interaction from the external electric field (EF). It demonstrates the external EF modifies both the geometric [...]

Nonequilibrium molecular dynamics simulation for size effects on thermal conductivity of silicon nanostructures

Liu X.J., Yang J.P., Yang Y-W, Yang J.P., Yang Y-W, Nanyang Technological University, SG

The thermal conductivity of silicon nanostructures was investigated using the Tersoff potential based Nonequilibrium molecular dynamics (NEMD) simulation approach. In such bond-order NEMD simulation model, the quality of the Tersoff potential for heat transport of [...]

Deformation of Carbon Nanotube Oscillators Encapsulating Cu Nanowires

Lee J-H., Kang J-W, Hwang H-J., Sangmyung University, KR

Pure carbon nanotube (CNT) oscillators are compared to CNT oscillator encapsulating copper nanowire (M@CNT) by molecular dynamics simulations. The excess forces of the Cu@CNT oscillator are slightly higher than that of the CNT oscillator and [...]

Molecular Dynamics Simulations of Nonvolatile Carbon Nanotube Shuttle Memory

Kwon O-K., Lee J-H., Kang J-W, Hwang H-J., Semyung University, KR

We propose a novel carbon-nanotube (CNT)-based nonvolatile memory, which can serve as a key building block for molecular-scale computers and perform molecular dynamics simulations to investigate the dynamic operations of a double-walled CNT memory. We [...]

The Innitial Reverse-Bias Injecting P+-N Junction Mode in P+-N-P+- Structures with Punch-Through

Mats I., Diatex, Selected Texno-Fix, CA

The Volt-Ampere Characteristics (VAC)s of P+NP+-structures in the schemes with floating base and short-cut p+-n junction (emitter) in punch-through modes were calculated before. It is important to research a behavior for similar structures but with [...]

Computational Screening of Metallofullerenes for Nanoscience

Slanina Z., Nagase S., Institute for Molecular Science, JP

The objects of fullerene science - fullerenes, metallofullerenes & other fullerene endohedrals, and nanotubes - represent promising candidates for nanoscience and nanotechnology applications. The emerging concepts are illustrated on C74-based endohedrals, especially Ca@C74, Sr@C74, and [...]

Efficient DSMC Modeling Techniques for Micro/Nano Gas Flows

Masters N., Ye W., Georgia Institute of Technology, US

An efficient DSMC technique for modeling of low-speed gas flows has been developed. THis technique greatly reduces the inherent DSMC noise and thus is suitable for modeling micro/nano gas flows whose typical velocities are below [...]

Investigation of Mechanical Strength of the Nanoshell of Bacteriophage Phi-29

Han C-N, Chou C.Y., Chiang K.N., National Tsing Hua University, Taiwan, TW

In this research, by using the analytical solution (method 1, method 2) and finite element method that include three approaches were proposed to find the stress in the nanoshell when phi-29 packages the dsDNA. Method [...]

Quantum Design of Complex Nanostructured Electronic Materials

Williamson A.J., Lawrence Livermore National Laboratory, US

Over the last decade, our ability to predict the fundamental properties of nanoscale building blocks such as quantum dots, wires, and slabs has improved dramatically. In particular, first principles modeling techniques can now routinely predict [...]

Pseudopotential theory of electronic excitations in semiconductor nanostructures

Franceschetti A., Troparevsky M.C., National Renewable Energy Laboratory, US

The calculation of the optical and electronic properties of semiconductor nanopstructures is still based for the most part on highly approximated, continuum-like models such as the effective-mass approximation. These models do not take into account [...]

Conduction Properties of BN-doped Fullerene Chain Obtained by Density Functional Calculations

Krainara N., Luksirikul P., Sirijaraensre J., Pantu P., Limtrakul J., Kasetsart University, TH

Carbon-based molecules such as fullerenes and carbon nanotubes, have attracted the attention of researchers because of their unique mechanical, and electronic properties and potential applications in a wide variety of areas of nanotechnology. The substitution [...]

Atomistic Simulation of Cracktip Failure Pathways in Fe and Fe Alloys

Gordon P.A., Neeraj T., Li Y., Luton M.J., ExxonMobil Research & Engineering, US

This work employs transition pathway analysis to examine the activation barriers associated with failure of atomically sharp cracktips in Fe. The effect of structual and compositional heterogeneities are explored, as it is speculated that these [...]

Dielectric Response in Silicon Nanostructures from first principles

Hamel S., Williamson A., Wilson H., Gygi F., Galli G., Ratner E., Wack D., Lawrence Livermore National Laboratory, US

In the next few years, the typical size of finFET devices used in the microchip industry is expected to be of the order of a few nanometers. This poses formidable challenges, including for optical metrology, [...]

A Temperature-related Homogenization Technique for Nanoscale Continuum Approximation

Xiao S.P., Yang W.X., The University of Iowa, US

A new homogenization technique, the temperature-related Cauchy-Born (TCB) rule, is proposed in this paper with the consideration of the free energy instead of the potential energy. The TCB rule is verified via stress analyses of [...]

Mechanics of silicon nanowires: size-dependent elasticity from first principles

Rudd R.E., Lee B., Lawrence Livermore National Laboratory, US

We have conducted a detailed study of the size dependence of the mechanical properties of silicon nanowires using first principles quantum mechanical calculation together with continuum mechanics theory and atomistic simulation based on empirical potentials. [...]

Molecular Simulation and Theory for Nanosystems

Sadus R.J., Swinburne University of Technology, AU

A knowledge of self-assembling molecules such as DNA and dendritic systems can provide beneficial insights for the development of tailor-made nano-scale devices. In this context, molecular simulation and theory have an important role in both [...]

Interaction of DNA with Single-Walled Carbon Nanotubes: Implication to the Bio-Sensors

Kong K-J, Chang H., Lee J-O, Korea Research Institute of Chemical Technology, KR

Here, we have briefly introduced the recent progresses in experiments of DNA sensing with CNT-FET sensors and theoretical investigations to explore the sensing mechanism.

A Kinetic Study of the MOCVD of GaN

Moscatelli D., Cavallotti C., Politecnico di Milano, IT

Quantum chemistry investigations have been performed to study the gas phase chemistry active during the MOVPE of GaN when Ga(CH3)3 and NH3, diluted in a H2 carrier gas, are used as precursors. Optimized molecular geometries, [...]

A Multiscale investigation of the influence of surface morphology on thin films CVD deposition

Barbato A., Rondanini M., Cavallotti C., Politecnico di Milano, IT

Growth rates and morphology of thin solid films deposited through Chemical Vapor Deposition processes are strongly dependent on chemical-physical events that occur at time and length scales differing by several orders of magnitudes. Models adopted [...]

Bridging Domain Multiscale Method

Xiao S.P., Hou W.Y., The University of Iowa, US

A bridging domain method for coupling continuum models with molecular models is described. In this method, the continuum and molecular domains are overlapped in a bridging subdomain, where the Hamiltonian is taken to be a [...]

Atomistic-Continuum Simulations of Carbon Nanotubes in LIquids

Koumoutsakos P., Kotsalis E., Walther J.H., Dupuis A., ETH Zürich, CH

We consider atomistic continuum simulations of carbon nanotube configurations embedded in flows of dense liquids. We consider Schwartz domain decompositions algorithms implying that non-periodic boundary conditions are imposed on the molecular system. In these algorithms, [...]

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