IMTIMT-Bucharest Scientific R-Bucharest Scientific Report 2010eport 201042

L9: Laboratory for Molecular NanotechnologyL9: Laboratory for Molecular Nanotechnology

Laboratory Head — Dr. Radu Popa (radu.popa@imt.ro)Laboratory Head — Dr. Radu Popa (radu.popa@imt.ro)

Centre of Nanotechnologies

Mission: Interdisciplinarylaboratory established in2009, relying on state of theart equipments (belonging tovarious labs). We work on

functional integration of biological components, such aspeptides, proteins, antibodies, nucleotides, DNAfragments, etc., with micro-nano processed and patternedinorganic structures, targeting various micro-nano-bio-infoapplications. We combine substrate preparation andprocessing, micro-nano scale lithography and controlledmolecular deposition, adsorption and manipulation ofbiomolecules, nanoscale microscopy techniques, andequilibrium/non-equilibrium quantum mechanicalnumerical analysis, aiming at developing unifiedexperimental and theoretical frameworks for the study offunctional properties obtained from the interaction ofbiomolecules with nano/micro objects. Controlling andinvestigating the chemical and physical properties of newnanomaterials is another key research orientation. Weaddress health and environmental applications focused ondeveloping advanced solutions for (bio)sensors and(bio)sensor arrays using chemical and physical principles.

Main areas of expertise:• Electrochemistry: investigation of redox mechanisms;design and development of electro-chemical sensors,electrochemical biosensors, immunosensors, DNA sensors,etc.; • Materials chemistry and surface functionalization: -chemical modification of carbon allotropes (carbon

nanotubes, graphene and carbon nanoparticles) andmetallic nanoparticles; - development of advanced carbon nanocomposites forthermal, electrical and biomedical applications; • Analytical investigations and characterizations (UV-Vis,fluorescence, HPLC, FT-IR, etc.): - nanoscale microscopy and patterning (SPM, dip-pennanolithography). • Substrate preparation and processing for molecularnanotechnology applications (micro-nanolithography,metal deposition, plasma etching, annealing). • ELISA based techniques for the detection of food toxins(domoic acid, ochratoxins, mycotoxins, etc.). • Modeling and simulation: ab-initio calculations ofelectronic structure optical response and electronictransport in materials; ab-initio molecular dynamics withCar-Parrinello method; quantum dynamics of electronicstates strongly interacting with electromagnetic fields orvibrations; dielectric response of heterogeneous materialslike suspensions of biological cells; light interaction withmetallic nanoparticles; coupled field analysis.

� Research Team: 6 senior researchers, 1 researchassistant; multidisciplinary expertise (physics, chemistry,engineering, HPC).

� Main tools: • Modeling and simulation: - SIESTA/TRANSIESTA: packages for ab-initio moleculardynamics and electronic structure calculations (moleculesand solids) • Processing and characterization available in various IMT-Bucharest laboratories.

�Mission�Main areas of expertise�Research Team�Main tools

Efficient electrochemical catalysis and regeneration of nicotinamide adenine dinucleotide at layer-by-layer self-assembled doped membranes

Nanostructured materials exhibit interesting properties which enhance the electrochemical detection of NADH. Relevantissues in the effective use of nicotinamideadenine dinucleotide are the need of highoverpotentials for direct oxidation orreduction of the cofactor, electrode fouling,dimerization of the cofactor, etc.Nevertheless, to promote economicallyefficient processes, the regeneration of thepyridine cofactor remains a key problem tosolve. A platform for variousdehydrogenase based bioassays should beobtained by developing an electrochemicalprobe based on layer-by-layer self-assembled doped metallic nanoparticlesmembranes. When using nanoparticles forcatalysis two main aspects are relevant:the stabilization of particles while retainingsufficient catalytic activity and theproblematic separation of the catalyticparticles from the reaction product. Onesolution may be the immobilization of thenanoparticles in thin membranes,minimizing the mass transfer limitations. Ageneric platform offering a fastregeneration and an efficient catalysis ofcoenzyme is the goal of this project.

Financed by the National UniversityResearch Council (PNII-TE 2010- 2013)

Project director: Dr. Antonio Radoi, antonio.radoi@imt.ro.Coordinator: IMT-Bucuresti

Gold nanosized particles on carbon nanotubes.

Synthesis of spherical (left) and square (right) Pt nanoparticles.

Main projects - Results Main projects - Results

L9: Laboratory for Molecular NanotechnologyL9: Laboratory for Molecular Nanotechnology

Centre of Nanotechnologies

IMTIMT-Bucharest Scientific R-Bucharest Scientific Report 2010eport 2010 43

ResultsResults

Synthesis and Molecular Assembly of Functional Nanomaterials

The novel properties and associatedfunctionalities arising from graphene, a singlelayer of sp2 hybridized carbon atoms, hasgenerated considerable attention and pavedthe way towards applications ranging fromgraphene-based composits, sensors, andbiomedicines to nanodevices. However, aswas the case in the early days of carbonnanotubes research, graphene suffers from aproblem that is common to many novelmaterials, there is no method for the mass-production of this material. Thus, the focus ofthis project is to produce colloidal suspensions ofmonodisperse graphene sheets without the helpof stabilizers or surfactants, with fewer defectswhich are amenable to surface chemistry.

Financed by the European Social FundHuman Resource Development byPostdoctoral Research on Micro andNanotechnologies(POSDRU/89/1.5/S/63700, 2010-2013)Project Director: Dr. Lucia Monica Veca,monica.veca@imt.ro

Interaction of low-dimension systems with electromagnetic/phonon fields via plasmon resonances

The interaction of electromagnetic/ phonon fields with heterogeneous systems is a central topic in physics with a largevariety of applications in: photonic and phononic crystals, plasmonics or sensing like surface-enhanced Raman scatteringand surface-enhanced infrared scattering. Metallic nanoparticles interact with electromagnetic fields via particle polarizability. The response of metallic nanoparticlesdepends on their resonant behaviour with respect to the incident radiation field. The resonances of metallic nanoparticlesare localized plasmon resonances which are placed in the ultraviolet-visible and near- or mid-infrared range of theelectromagnetic spectrum. The response to electromagnetic fields can be calculated analytically only for high-symmetrystructures like spheres, spheroids, ellipsoids, etc. For more general shapes the response to electromagnetic fields can becalculated only numerically with complex computational schemes like the discrete-dipole approximation or finite-differencetime domain method, which offer little inside into the physics of plasmon resonances. It has been developed a methodthat calculates the electrostatic resonances of metallic nanoparticles. The main advantage of the method is the eigenmodedecomposition of particle polarizability. The eigenmode decomposition permits the extraction of dielectric and geometricinformation about the nanoparticle and the surrounding medium which, in turn, can be used in designing plasmonicstructures. The following figure shows the imaginary part of dielectric polarizability for various nanoparticle shapes. Thereare either individual nanoparticles or dimers. The imaginary part of polarizability is proportional with light extinction ofmetallic nanoparticles.

Financed by the European Social Fund Human Resource Development by Postdoctoral Research on Micro andNanotechnologies (POSDRU/89/1.5/S/63700, 2010-2013)Project director: Dr. Titus Sandu, titus.sandu@imt.ro

Graphene obtained by liquid phase exfoliation of graphite in organicsolvents whose surface energies match that of graphene.

(a) Extinction spectra of metallic nanoparticles and metallicdimers as a function of shape. The shape of metallic

nanoparticles and dimers is determined by the aspect ratioa/A, where 2A is the cross-section diameter and 2a is the axial

length of the nanoparticle. The metallic tight junction in thedimer is characterized by h, its cross-section radius.-

L9: Laboratory for Molecular NanotechnologyL9: Laboratory for Molecular Nanotechnology

Centre of Nanotechnologies

IMTIMT-Bucharest Scientific R-Bucharest Scientific Report 2010eport 201044

Main projects - Results Main projects - Results Theoretical and Experimental Study of Polynucleotides:

Controlled Immobilization and Scanning Tunneling Microscopy Investigation

Developing alternative methods for fast and low-cost DNA sequencing is an increasingly active area of research. In thiscontext we are focusing both on experimental and theoretical investigations on the feasibility of STM-based reading of thenucleobase sequence. Experimentally, we have obtained very high quality (atomically flat: 3Å roughness/200nm terraces,at single-crystal grade) Au layers on mica substrate based on TSG - template stripped gold - technique, as well as uniformdepositions of alkanethiol layers for strand immobilization. YOYO-1 marked, λ-phage DNA strands were also linearized andimmobilized on APTES/glass substrates using a controlled mechanical stretching (molecular combing) approach. We alsorealized the immobilization of Cy3-marked 25-base-long single-strand DNA sequences with end thiol modifications on Ausubstrate and preliminary experiments of controlled depositions of MHA thiols on Au substrate using dip pennanolithography process.

The theoretical experiments are based on ab-initio calculations under the DFT paradigm, as implemented in theSIESTA/Transiesta/Inelastica packages. We concentrate on assessing the molecule identification potential offered bytunneling spectroscopic signatures, with the latest accent on the inelastic electron tunneling spectroscopy (IETS) extensionimplemented in the Inelastica package. We place single A/G/C/T-based nucleotides in various orientations between metallicelectrodes at fixed inter-electrode clearance and calculate the IETS spectra, aiming at identifying selectivity features inthese spectral signatures in low-coupling, off-resonance regime. As a major computational bottleneck of these studies isdetermined by the initial relaxation of these "large" molecules (33-36 atoms), we inserted in the original SIESTA code anacceleration procedure consisting in successive temporary "freezing" sequences of quasi-relaxed portions of the molecule- this solution proved to significantly stabilize and speed-up the relaxation phase.

Financed by the National Authority for Scientific Research (2009- 2011) – core fundingProject director: Dr. Radu Popa, radu.popa@imt.ro, Coordinator: IMT-Bucuresti

dCMP-LUMO

STM confirmation of Auterraces:

RMS roughness=3Å.

Other IETS simulations: CO moleculeadsorbed on Cu-111, and BDT moleculeadsorbed between Au-111 electrodes.

Simulated IETS spectra for CO adsorbed on Cu-111, andBDT molecule adsorbed between Au-111 electrodes.

Tunneling model for dAMP, dCMP nucleotidesbetween 15Å-spaced Au 111 electrodes.

AFM image of λ-phage sequences combing-stretchedand immobilized on APTES/glass substrate,

at 10 μg/ml concentration.

Localized DOS integrated aroundmolecular HOMO, LUMO levelsfor dAMP, dCMP nucleotides:

localization on atoms ofnucleobases and major

contributions of π-orbitals.

dAMP-HOMO dCMP-HOMOdAMP-LUMO

Projected DOS spectraconfirm dominant

π-orbital localization.