Poster Abstracts

Area of Advance Nano

Community Building

Bohusgarden, Uddevalla, June 16-18

1

Chemical vapor deposition of nanocrystalline graphenedirectly on arbitrary high-temperature insulators

Jie Sun1, Niclas Lindvall1, and August Yurgens1

1 MC2, Chalmers University of Technology, Sweden 41296

CVD is a scalable technique for production of large-area graphene [1]. Forpractical application, there is a need to develop a metal-catalyst-free tech-nique for production of graphene directly on insulators because the graphenegrown on metal foils needs to be transferred which often results in damagedgraphene [2]. We have discovered that graphene can be deposited directlyon Si3N4 and HfO2 by CVD without metal catalyst. We also predict thatgraphene can be synthesized on any insulator withstanding ∼1000C [3]. In-deed, here we show that continuous large-area graphene with no observablepin-holes can be grown on SiO2, Al2O3, MgO, BN, SiC, GaN, Si, mica, etc.The films are sp2-bonded as evidenced by the G, D and 2D peaks in Ra-man spectroscopy. Four-probe measurements show that the sheet resistanceof the graphene is a few kΩ/. The transparency is similar to exfoliatedgraphene (2-3% of absorption), measured by transmission spectroscopy. On300 nm SiO2/Si substrates, the thin films show a similar optical interfer-ence effect as that of Cu-catalyzed graphene. The thickness is controlledfrom submonolayer to thick graphite. The films are nanocrystalline with atypical domain size of ∼10 nm, as confirmed by transmission electron mi-croscopy (TEM). Converged e-beam diffraction on the SiO2-grown sampleshows monolayer graphene’s hexagonal pattern. We note that our films arenot only novel, but also of high quality. The carrier mobility, determinedby Hall measurements, is ∼40 cm2/Vs, the best reported value on metal-freeproduced graphene. The as-synthesized thin films remain their metallic lusterresembling oriented graphite even at hundreds of layers [4], in contrast withcarbon black thin films which are dull black (similar to industrial graphite)when they are thick. Finally, a model for the noncatalytic deposition mech-anism is proposed. Hydrocarbons readily decompose and self-assemble intographene nanoflakes at ∼1000C without the need of any catalyst. Normally,these nanographene will aggregate and form porous bumps known as carbonblack and used in car tires. Nevertheless, under our conditions, these flakes

self-organize into textured two-dimensional nanocrystalline graphene on hotflat substrates.

[1] J. Sun et al, IEEE Transactions on Nanotechnology, 11, 255, (2012)

[2] C. Rosa et al, Applied Physics Letters, 102, 022101, (2013)

[3] J. Sun et al, Applied Physics Letters, 98, 252107, (2011)

[4] J. Sun et al, Applied Physics Letters, 100, 022102, (2012)

2

Electromagnetic response of graphene

Tobias Wenger1, Mikael Fogelstrom1, and Jari Kinaret2

1 Department of Microtechnology and Nanoscience (MC2), Chalmers Uni-versity of Technology, SE-412-96 Goteborg, Sweden2 Department of Applied Physics, Chalmers University of Technology, SE-412-96 Goteborg, Sweden

We theoretically investigate the linear response of large sheet graphene andgraphene nanoribbons. The linear response is calculated within the RandomPhase Approximation (RPA) and the focus is on the plasmon mode dispersionand the electromagnetic properties of the systems.

For both cases we calculate the polarizability and this allows us to find thedielectric function and the conductivity. Using this we calculate the plasmonmode dispersion and in particular investigate the long wavelength behaviour.This far our calculations follow closely those of [1] and [2] for large sheetgraphene and [3] for the graphene nanoribbon. We then proceed to calculatethe reflection, transmission and absorption coefficients of the two systems,highlighting the tunable nature of the graphene EM response. This tunabil-ity could be of considerable interest in e.g. the field of photovoltaics.

[1] E.H. Wang and S. Das Sarma, Dielectric function, screening, and plasmonsin two-dimensional graphene, PRB 75, 205418 (2007)

[2] B. Wunsch, T. Stauber, F. Sols and F. Guinea, Dynamical polarizationof graphene at finite doping, New J. Phys. 8, 318 (2006)

[3] L. Brey and H.A. Fertig, Elementary electronic excitations in graphenenanoribbons, PRB 75, 125434 (2007)

3

Scattering of flexural acoustic phonons at graphene grainboundaries

Edit Helgee1 and Andreas Isacsson1

1 Chalmers University of Technology, Department of Applied Physics

We have studied the scattering of long-wavelength flexural phonons againstgrain boundaries in graphene using molecular dynamics. The grain bound-aries consist of arrays of dislocations, where the size of each dislocation is ofthe order of magnitude of the lattice constant. The small size of the dislo-cations suggests that long-wavelength phonons should be unaffected by theboundary. However, the dislocations also cause out-of-plane buckling of thegraphene sheet. The width of the buckles can be on the order of tens ofAngstroms, large enough to interact with long-wavelength vibrations. Of thetwo grain boundaries considered here, one shows no buckling while the otherdisplays an out-of-plane buckling 6 A high and approximately 17 A wide.For the flat grain boundary, the phonon transmission approaches unity atlong wavelengths. The buckled grain boundary, on the other hand, yieldstransmission coefficients between 0.4 and 0.7 for wavelengths exceeding 10A. Also, the flexural vibrations couple to longitudinal modes at the buckledgrain boundary. This indicates that grain boundaries scatter long-wavelengthflexural phonons, provided that the boundary causes out of plane buckling ofthe graphene sheet. A continuum mechanical model of the scattering processhas been developed, providing further insights into the scattering mechanism.

4

Measurement of quantum dot decay rates

Jens Schulenborg, Janine Splettstoßer, Michele Governale, and L. D. Contreras-Pulido

Due to potential applications in nanoelectronics, metrology and quantum in-formation, the study of the dynamics of quantum dots has attracted greatinterest over the past years. Recently, the relaxation rates in the dynamicalresponse of an interacting single-level quantum dot (QD), weakly tunnel cou-pled to an electronic reservoir and initially brought out of equilibrium, havebeen investigated [1, 2].

The theoretical study presented on this poster focuses on the readout ofthe dynamic response of the quantum dot, capacitively coupled to a sensorquantum dot (SQD) detector. In particular, the influence of measurementback-action effects on the dot’s time-evolution is addressed. Starting froma master equation approach for the quantum dot coupled to the measuringdevice, the relaxation behavior of the dot (influenced by the measurement) isextracted. The result shows that the back-action of the measurement leadsto a significant reduction of the dot charge relaxation rates for certain criticalgate voltages. Additionally, further rates, which are more closely related tothe characteristics of the SQD, govern the time-evolution of the quantum dot.Nevertheless, a readout of the unmodified dot decay rates is still theoreticallypossible.

[1] Janine Splettstoesser, Michele Governale, Jurgen Konig, and Markus But-tiker. Charge and spin dynamics in interacting quantum dots. Phys. Rev.B, 81:165318, Apr 2010.

[2] L. Debora Contreras-Pulido, Janine Splettstoesser, Michele Governale,Jurgen Konig, and Markus Buttiker. Time scales in the dynamics of aninteracting quantum dot. Phys. Rev. B, 85:075301, Feb 2012.

5

Optical mapping of single DNA molecules in nanochan-nels: A novel method for identification and characteriza-tion of antibiotics resistance

Lena K. Nyberg1, Gustav Emilsson1, Adam Nilsson2, Erik Lagerstedt2, CharlestonNoble2, Liselotte Svensson Stadler3, Nahid Karami3, Fei Sjoberg3, EdwardR. B. Moore3, Joachim Fritzsche1, Erik Kristiansson1, Jonas O. Tegenfeldt2,Tobias Ambjornsson2, and Fredrik Westerlund1

1 Chalmers University of Technology, Sweden2 Lund University, Sweden3 Goteborg University, Sweden

The use, and overuse, of antibiotics has, during the last decade, led to adramatic increase in antibiotic resistant bacteria. Here, we present opticalmapping of single DNA-molecules in nanofluidic channels as a novel approachfor characterization of resistance genes located in bacterial plasmids. Due tothe miniscule amounts of sample needed for nanofluidics experiments it ispossible to omit the time-consuming cultivation and amplification steps thatare normally required for plasmid identification, when using standard tech-niques like Pulsed-Field Gel Electrophoresis (PFGE) and Next-GenerationSequencing (NGS). Furthermore, we map full-length plasmids and therebydirectly acquire information about the size distribution of the sample as wellas the sequence for each molecule, in one single experiment.

The optical mapping assay is based on our previous work on competitivebinding of two molecules to DNA, resulting in an intensity distribution alongthe DNA, a barcode, which reflects the underlying basepair sequence withkilobasepair (kbp) resolution [1]. We are currently developing automatedsoftware for analysis of experimentally generated barcodes as well as cre-ation of theoretical barcodes of sequenced plasmids for comparison with ex-perimental results. Our preliminary results show that optical mapping ofplasmids using competitive binding can have several applications: Firstly, itcan be used for size determination of plasmids, similarly to what is tradi-tionally done using Pulsed Field Gel Electrophoresis, PFGE. Secondly, wecan generate theoretically calculated barcodes for sequenced plasmids thatcan be compared with experimental barcodes for identification of plasmids.

Thirdly, our assay can be used for characterization of unsequenced plasmidsand potentially serve as a guide for de novo assembly of plasmid genomes incombination with Next Generation Sequencing techniques.

We believe that our optical mapping assay has the potential of becominga useful clinical diagnostics tool for identification of resistance genes. Theassay is based on commercially available reagents in combination with flu-orescence microscopy, which is standard equipment in most hospitals, andonly requires minute amounts of sample which means that no cultivation oramplification steps are needed. Furthermore, our nanofluidic assay is fullycompatible with lab-on-a-chip devices.

[1] “A single-step competitive binding assay for mapping of single DNAmolecules,” Lena Nyberg, et al., Biochemical and Biophysical Research Com-munications, 417, 404-408, (2012)

6

Near- and far-field microscopy of non-linear plasmonic en-hancement effects

Michael Stuhrenberg1, Nisha Rani Agarwal1,2, Juris Kiskis1, Mahesh Namboodiri1,and Annika Enejder1

1 Molecular microscopy, Department of Chemical and Biological Engineering,Chalmers University of Technology, Goteborg, Sweden2 Neuro-plasmonics, Istituto Italiano di Tecnologia, Genova, Italy

Plasmons are created by excitation of collective electron oscillations on thesurface of metallic nanostructures which provide unique and effective meansof manipulating light. While a vast amount of literature deals with linearplasmons, the field of non-linear plasmonics remains relatively unexplored.The study of non-linear effects of plasmons provides a wide variety of at-tractive properties such as generation of coherent light-fields, frequency con-version and non-linear enhancement effects. Significant for the non-linear,multiphoton regime of plasmons is that excitation is achieved with two ormore electromagnetic fields resulting in a frequency-upconverted, hence, blue-shifted emission.

By combining a high-power pico-second pulsed laser set up (HighQ LasersGmbH, APE GmbH), a far-field laser scanning microscope (Nikon) and a100 nm-sized open aperture scanning probe (Nanonics Ltd.), the near-fieldof individual nanostructures can be probed and compared with the resultingnonlinear signals in the farfield. This unique combination of instrumentationand approach allows us to analyze the interference and coherence of surfaceplasmons and their nonlinear effects. Nanostructures studied, nanoholes andcup like nanocrescents, are manufactured by colloidal lithography which of-fers a cost-effective way of covering vast areas (cm2) with tunable propertiessuch as density and resonance frequency. By optimizing their geometries sothat their plasmon resonances match the excitation and/or emission wave-lengths, enhanced nonlinear emission (four-wave mixing/coherent anti-StokesRaman Scattering/second harmonic generation etc.) is supported. We en-vision that these structures can be used for few-molecule sensing as well ashigh-resolution imaging.

7

Electrochemical Detection of Acetylcholine Using EnzymeFunctionalized Nanoparticles

Jacqueline D. Keighron1, Michael E. Kurczy1, Joakim Wigstrom1, and Ann-Sofie Cans1

1 Department of Chemical and Biological Engineering, Chalmers Universityof Technology, 41296 Gothenburg, Sweden

Acetylcholine is a highly important non-electroactive neurotransmitter inthe mammalian central nervous system. Its function is linked to memoryand sleep, and it regulates, in part, mood and action via its connection todopamine. A fast, sensitive method to detect the release of acetylcholine atthe surface of a single cell is needed to gather data about the kinetics ofexocytosis events in these systems.

To this end, carbon fiber electrodes have been modified with electrodepositedgold nanoparticles to increase the effective electrode surface area and providea high curvature surface for enzyme attachment. Acetylcholinesterase andcholine oxidase were then deposited onto the gold surfaces to catalyze acetyl-choline to hydrogen peroxide for electrochemical detection. The function-alized electrodes have been characterized to determine the KM and Vmaxof the enzymes as well as the total enzyme coverage and gold nanoparticlesurface area in order to optimize retained enzyme activity. This optimizeddesign has proven capable of detecting release events from an artificial exo-cytotic system on a sub-second time scale.

8

Electrical Detection of Spin Polarized Current in Topo-logical Insulator Bi2Se3

Andre Dankert1, Johannes M. Geurs1, Mutta V. Kamalakar1, and Saroj P.Dash1

1 Chalmers University of Technology, Department of Microtechnology andNanoscience, Quantum Device Laboratory; Goteborg, Sweden

Topological insulators are a new class of quantum materials that possesstopologically protected metallic surface states with massless Dirac fermions,while the bulk is semiconducting. [1] It possess a strong spin-orbit couplingconstraining the spin to be coupled to its momentum and perpendicular indirection. [2] This spin-momentum locking causes a spin polarized charge cur-rent when the carriers have a finite momentum by applying an electric field.So far, the detection of such spin- momentum locking has been limited to us-ing angle-resolved photoemission [3] and optical spectroscopic techniques.[4]Recently, electrical measurement techniques have been explored to probe thespin polarized surface currents. [5, 6]

Here we demonstrate the electrical detection of spin polarized currents onthe surface of exfoliated Bi2Se3 flakes by ferromagnetic tunnel contacts. Wecreate a spin polarized charge current in Bi2Se3 via spin-momentum locking.The ferromagnetic electrodes detect the spin current yielding a hystereticmagnetoresistance effect while sweeping a magnetic field in parallel configu-ration. The spin signal is also found to reverse sign with bias current direc-tions. These observations can be understood as a spin-valve effect betweenthe ferromagnetic contact and the spin-current on the Bi2Se3 surface due tospin-momentum locking. The signal amplitude increases linearly with biascurrent and can be observed over a wide temperature range. Our resultsshow the possibility of electrical creation and detection of spin currents intopological insulators and indicate its applicability in future spintronic de-vices based on two-dimensional heterostructures.

[1] Ando, Y. Topological Insulator Materials. J. Phys. Soc. Japan 82, 102001(2013).

[2] Hasan, M. Z. & Kane, C. Colloquium: topological insulators. Rev. Mod.Phys. 82 (2010).

[3] Pan, Z.-H. et al. Electronic Structure of the Topological Insulator Bi2Se3Using Angle-Resolved Photoemission Spectroscopy: Evidence for a NearlyFull Surface Spin Polarization. Phys. Rev. Lett. 106, 257004 (2011).

[4] McIver, J. W., Hsieh, D., Steinberg, H., Jarillo-Herrero, P. & Gedik, N.Control over topological insulator photocurrents with light polarization. Nat.Nanotechnol. 7, 96–100 (2012).

[5] Li, C. H. et al. Electrical detection of charge-current-induced spin po-larization due to spin-momentum locking in Bi2Se3. Nat. Nanotechnol.218–224 (2014).

[6] Tian, J. et al. Topological insulator based spin valve devices: Evidence forspin polarized transport of spin-momentum-locked topological surface states.Solid State Commun. 191, 1–5 (2014).

9

From 2D to 3D anisotropy engineering in magnetoplas-monic nanoparticles

Kristof Lodewijks1, Nicolo Macafferi2, Surya Prakash Gurunarayanan1, IrinaZubritskaya1, Addis Mekonnen Adamu1, Randy Dumas3, Johan Akerman3,Paolo Vavassori2, and Alexandre Dmitriev1

1 Department of Applied Physics, Chalmers University of Technology, 41296Gothenburg, Sweden2 Nanomagnetism Group, CIC nanoGUNE Consolider, 20018 Donostia-SanSebastian, Spain3 Department of Physics, University of Gothenburg, 41296 Gothenburg, Swe-den

In recent years the magnetoplasmonic response of ferromagnetic nanoparti-cles has been studied extensively in 2D geometries. Nowadays it is well es-tablished that even pure ferromagnetic particles show pronounced plasmonicresonances that can be exploited to obtain very broadband tunability of themagneto-optical Kerr effect (MOKE) response. In this work we show howthe third dimension plays a critical role in the observed effects and how it canbe exploited in order to enhance the effects observed before in 2-dimensionalstructures. We studied various 3-dimensional ferromagnetic nanoparticles inlongitudinal spectral MOKE measurements and show how phase retardationbecomes a crucial parameter when the particle geometries are changed fromin-plane 2D structures to full 3-dimensional structures. As such, the nanopar-ticles support localized surface plasmon resonances (LSPRs) along all 3 majorsymmetry axes, which each have their specific contribution to the observedMOKE spectra. All of these modes can be easily excited in P-polarization,where the out-of-plane and one of the in-plane modes can be directly excited.The second in-plane plasmonic mode (perpendicular to the excitation direc-tion) is excited by means of the spin-orbit interaction that couples stronglyto the out-of-plane LSPR mode. On top of that, the magnetic behavior ofthe nanostructures is altered substantially, as depending on the particle di-mensions along all symmetry directions, the magnetic easy/hard axes can bearbitrarily changed to be in- or out-of-plane, allowing for active control overthe magnetoplasmonic behavior by means of the applied external field.

10

Photon generation in a doubly tunable resonator

Ida-Maria Svensson1, Mathieu Pierre1, Michael Simoen1, Chris Wilson1, GoranJohansson1, Per Delsing1

1 Department of Microtechnology and Nanoscience (MC2), Chalmers Uni-versity of Technology, SE-412-96 Goteborg, Sweden

The dynamical Casimir effect [1] tells us that when a perfectly reflectingmirror is moved with a speed close to the speed of light and with a non-uniform acceleration, photons are generated. This mirror can be mimickedby a boundary condition for the electromagnetic field in a superconductingresonator. By using a SQUID, superconducting quantum interference de-vice, we can move the boundary condition with relativistic speeds and hencemeasure photon generation [2].

In this system a half-wavelength resonator with a SQUID in each end is used.These two boundary conditions can be controlled individually, which meansthat the cavity length can be modulated (breathing mode) as well as thecavity position (translational mode). Modulation at high speeds generatesphotons and when playing with modulation frequencies and phase differencesbetween the two mirror motions interference effects occur.

With modulation frequencies equal to even multiples of the fundamental cav-ity frequency theory predicts constructive interference in the breathing modeand destructive in the translational. However at modulation frequencies equalto odd multiples of the resonance frequency, the constructive interference isin the translational mode and destructive in the breathing mode respectively[3-6].

We have fabricated a high quality doubly tunable resonator. With this wehave measured an interference pattern dependent on modulation frequencyand phase offset between the two mirrors in agreement with theoretical pre-dictions.

[1] G.T. Moore, Journal of Mathematical Physics, 1970

[2] C. M. Wilson et al., Nature

[3] A. Lambrecht et al., Physical Review Letters, 1996

[4] J-Y. Ji et al., Physical Review A, 1998

[5] A. Lambrecht et al., The European Physical Journal D, 1998

[6] D.A.R. Dalvit et al., Physical Review A, 1999

[7] V. V. Dodonov, Journal of Physics A: Mathematical and General, 1998

11

Mechanical cleaning of graphene using an atomic forcemicroscope and chemical cleaning by Cl-based solvents

Niclas Lindvall1, Alexey Kalabukhov1, and August Yurgens1

1 Chalmers University of Technology, SE-41296, Gothenburg, Sweden

Being only two surfaces and no bulk, graphene is easily affected by its en-vironment. To achieve clean graphene devices with controlled doping is inmany cases essential in order to bring graphene from the lab to real devices.Surface adsorbents play an important role on the properties of a graphenedevice. Polymers used in microfabrication are one of the dominant sources ofsuch adsorbents. Traditional solvents are not sufficient to completely removethose contaminants. In order to efficiently remove them, we use two differentapproaches. First, we use the tip of an atomic force microscope (AFM) tomechanically clean graphene devices and obtain atomically smooth graphene.By appropriate choice of the AFM cantilever and contact force, a root meansquare roughness of around 0.1 nm, less than that of our pristine SiO2, canbe achieved. In addition, we observe a shift of the Dirac voltage towardszero and improved carrier mobility. This method is convenient for singledevices of limited size. For cleaning large area graphene cleaning we investi-gate a second approach, the use of Cl-based solvents, such as chloroform anddichloroethane. The result is highly dependent on the polymer used and thebaking conditions. We compare the results of the mechanical- and chemicalcleaning approaches.

[1] N. Lindvall, A. Kalabukhov, and A. Yurgens, J Appl Phys, 111 (2012)064904-064904.

[2] N. Lindvall, J. Sun, G. Abdul, and A. Yurgens, Micro Nano Lett, 7 (2012)749-752.

[3] J. Svensson, N. Lindahl, H. Yun, M. Seo, D. Midtvedt, Y. Tarakanov, N.Lindvall, O. Nerushev, J. Kinaret, S. Lee, and E. E. B. Campbell, Nano Lett,11 (2011) 3569-3575.

[4] N. Lindahl, D. Midtvedt, J. Svensson, O. A. Nerushev, N. Lindvall, A.Isacsson, and E. E. B. Campbell, Nano Lett, 12 (2012) 3526-3531.

12

Characterization and evaluation of surface functionalizedsilica nanoparticles

S. Bjorkegren1,2, L. Nordstierna1, A. Torncrona2, M. Persson1,2, A. Palmqvist1

1 Chemical and Biological Engineering, Applied Surface Chemistry, ChalmersUniversity of Technology, Gothenburg, Sweden2 AkzoNobel Pulp and Performance Chemicals, Bohus, Sweden

Colloidal particles can spontaneously accumulate at the interface of two im-miscible liquids and thereby stabilize disperse systems such as emulsions andfoams. Properly designed particles can adsorb irreversibly at the interfaceof an emulsion droplet, providing an unusually high stability of the system.In emulsion and foam applications surface modified silica nanoparticles withcontrolled hydrophobicity and surface activity have great potential. Thecontrol of the surface chemistry of the particles opens up to interesting op-portunities.

In this work, colloidal silica is functionalized through attaching both hy-drophobic and hydrophilic moieties, with the aim of creating particles withan amphiphilic character. The particles are evaluated and characterized toobtain a deeper knowledge of how they behave not only in emulsion and dis-persion systems, but also in terms of stability of the modification and stericstabilization effects. NMR diffusometry is used to evaluate the surface mod-ification and is an essential tool in the characterization of the surface, sinceone obtains the proportion of functionalities attached to the particle, withslower diffusion compared to the functionalities free in solution, with fasterdiffusion.

13

Conjugated Materials for Organic Electronics

Ergang Wang1

1 Department of Chemical and Biological Engineering, Polymer Technology,Chalmers University of Technology, 412 96 Goteborg, Sweden

Our research focus is on development of conjugated materials for organicelectronics including organic solar cells, photodetectors, light-emitting diodes(LED) and field effect transistors (FET). Moreover, we are also interested inexploring new materials system such as Graphene chemistry.

Polymer solar cells (PSCs) are promising sustainable solar energy convert-ers, which are attracting more and more attention because of their uniqueadvantages of low cost, light weight, and potential use in flexible devices.We have developed a lot of conjugated polymers as donor for solar cells,which can give efficiency about 8% in solar cells with PCBM as acceptor. Asthe morphology of the active layers in solar cells, consisting of a blend of apolymer as donor and PCBM as acceptor, is the key in determining the pho-tovoltaic performance of the solar cells, it is highly important to investigateand control the morphology.

Photodetectors are used primarily as an optical receiver to convert light intoelectricity. Photodetectors have broad applications such as radiation detec-tion, smoke detection, flame detection and to switch on relays for streetlighting. We have more interest in detecting light in near IR region, whichcan be realized by conjugated polymers.

LED is a reverse device of photodetectors, which convert electricity into light.Apart from the application for display and illumination, we can also makeLED with emission in near IR region, which can be used for infrared signalingand displays, telecommunications, biosensing, night vision displays.

Due to the unique properties of Graphene, it has attracted a lot of attention.We are interested in synthesis of Graphene-like materials and exploring theirapplications in solar cells and LED as interfacial layers and electrodes.

14

FRETmatrix: A new tool for exploring DNA

Moa Sandberg1, Anke Dierckx1, Søren Preus2, L. Marcus Wilhelmsson1

1 Department of Chemical and Biological Engineering/Chemistry and Bio-chemistry, Chalmers University of Technology, Gothenburg, S-41296, (Swe-den)2 Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, DK-8000,(Denmark)

Today several fluorescent nucleobase analogues, FBAs, are available for thestudy of DNA and RNA[1]. We have previously reported on the first FBAForster Resonance Energy Transfer (FRET)-pair consisting of the tricycliccytosine analogues, tC or tCO as donor and tCnitro as acceptor[2] andthe Matlab-based software FRETmatrix,[3] designed to resolve DNA 3D-structures from lifetime measurements on FBAs positioned within DNA. Thesoftware can resolve the DNA 3D-structure due to the rigid positioning ofthe FBAs relative to the DNA framework, meaning both that the bases haverestricted rotational freedom on the timescale of the measurement and thattheir relative position in space is correlated to the structure of the DNA inwhich they are incorporated.

Our tricyclic cytosine analogues in combination with FRETmatrix now allowus to study the interaction between the small bacterial protein IHF (Integra-tion Host Factor), and DNA in solution. IHF is involved in several cellularprocesses through its architectural function, which aids in the formation ofdifferent nucleo-protein-complexes. An X-ray crystallography study of theIHF-DNA complex, by Rice et al., showed that the protein bends DNA morethan 160, however, to form crystals the DNA needs to be nicked.[4] Our workaims at studying the IHF-DNA complex in solution and without nicking theDNA. As the study of Rice et al. showed that most of the bending occursat two specific sites within the DNA we chose to model the DNA as threeB-from helices separated by two kinks. Incorporating tCO and tCnitro atvarious positions relative to these kinks, still being careful not to change theconsensus sequences, and measuring the corresponding FRET-efficiencies al-lows us to use FRETmatrix to retrieve the geometrical parameters of the twokinks. The preliminary solution structure, obtained in this way, shows the

same general features as the crystal structure. Our study both provides thestructure of un-nicked DNA when bound to IHF in solution and highlightsthe great potential of our recently developed method.

A second study we are working on at the moment, using the same tools asabove, concerns the structure of A-DNA in solution. It is known that B-formDNA is converted to the less conventional A-form in solutions containing 78% ethanol.[5] By incorporating the tC-tCnitro FRET pair and subjectingthe DNA to 78 % ethanol, we aim to resolve the structure of a 38 bp longA-DNA sequence in solution. This would yield unique data since, to the bestof our knowledge, only X-ray crystallography data on short (10 mer) A-DNAduplexes and NMR data for DNA-RNA hybrid structures have been reported.

[1] L. M. Wilhelmsson, Q Rev Biophys. 43 (2010) 159.

[2] K. Borjesson, et al., J. Am. Chem. Soc. 131 (2009) 4288.

[3] S. Preus, et al,. Nucleic Acids Res. 41(1) (2013) e18.

[4] P. A. Rice, et al., Cell. 87 (1996) 1295.

[5] V.I. Ivanov, J. Mol. Biol. 87(4) (1974) 817

15

Off-resonance Excitation of Graphene Oscillators

Axel M. Eriksson1, Marina Voinova1, and Leonid Gorelik1

1 Department of Applied Physics, Chalmers University of Technology, S-412 96 Gothenburg, Sweden

We investigate high frequency off-resonance driving of a doped graphenemembrane suspended between two electrodes. The periodic electrical drivingfield applied from symmetrically placed capacitor plates induces charge os-cillations in the membrane with components proportional to the deflection ofthe membrane and its velocity. With increasing driving frequency the phaseshift of the latter drives the charge component out of phase with the electricalfield. The result is negative effective damping and exponential mechanicalenergy growth which is saturated by nonlinear damping.

16

Using nanofluidic channels to probe the dynamics of Rad51-filaments

Louise Fornander1, Fredrik Persson2, Joachim Fritzsche1, Joshua Araya3,Philip Nevin3, Penny Beuning3, Erik Werner4, Ali Cakir4, Bernhard Mehlig4,Mauro Modesti5, Karolin Frykholm1 and Fredrik Westerlund1

1 Chalmers University of Technology, Gothenburg, Sweden2 Science for Life Laboratory, Uppsala University, Uppsala, Sweden3 Northeastern University, Boston, USA4 University of Gothenburg, Gothenburg, Sweden5 Universite Aix-Marseille, Marseille, France

Rad51 is a key protein involved in the strand exchange reaction, a reactionwhere genetic material is transferred between two homologous DNA strands.Strand exchange is initiated by Rad51 forming a helical filament aroundsingle-stranded DNA (ssDNA), and the strand exchange is thereafter exe-cuted with a homologous double-stranded DNA (dsDNA). The structure ofRad51-DNA filaments, and also the activity of the strand exchange reaction,is dependent on the presence of ATP and dications, where Ca2+ has beenshown to promote a higher degree of strand exchange than Mg2+.

In the present study we have investigated the dynamic behavior of singleRad51-DNA filaments formed with Rad51, dsDNA/ssDNA and Ca2+/Mg2+

using nanofluidic channels and fluorescence microscopy. Nanofluidic channelsallow us to probe the filaments at a different force regime than that tradition-ally obtained in for example optical tweezers experiments. We note that theformed Rad51-DNA filaments have both rigid and flexible sections. We spec-ulate that the rigid regions stem from when two adjacent filament patchesmeet on a DNA but cannot merge together to form a continuous filament,probably since the naked DNA between the patches is too short to accom-modate another protein monomer. Moreover, dsDNA has no directionality,meaning that the filaments can grow in both directions, thus two filamentscan grow in opposite directions resulting in them two being out-of-phase attheir point of contact. Supporting our hypothesis, when filaments are formedat low protein concentration, which result a lower number of filaments perDNA, we see less rigid regions.

The results also demonstrate the general applicability of nanochannels forstudies of DNA-protein complexes at extremely low forces not easily ob-tained using other techniques.

Fornander, L. H. et al. Nucleic acids research (2012), 40(11), 4904-4913. doi:10.1093/nar/gks140

Frykholm, K. et al. Small (2014), 1-4. doi:10.1002/smll.20130228

17

Plasmonic nanopores in metal-insulator-metal

Kunli Xiong1, Mokhtar Mapar1, Fredrik Hook1, Takumi Sannomiya2, An-dreas B. Dahlin1

1 Dept. of Applied Physics, Chalmers University of Technology, Goteborg,Sweden2 Dept. of Metallurgy and Ceramics Science, Tokyo Institute of Technology,Tokyo, Japan

I focus on fabrication of nanomaterials and research the optical propertiesof different nanostructures. Right now, I am interested in fabrication ofnanopores in Metal-Insulater-Metal layers. Based on this special structure, Itry to build an electrochemisty sensor to detect low concentration and smalltargets. Meanwhile, after binding polymers, we also want to make a nano-channel with nano- entrapment to manipulate the molecular movements.

A.B. Dahlin, M. Mapar, K. Xiong, F. Mazzotta, F. Hook, T. Sannomiya.Plasmonic nanopores in metal-insulator-metal films. Advanced Optical Ma-terials 2014.

M. Virk & K. Xiong, M. Svedendahl, M. Kall, A.B. Dahlin. A thermalplasmonic sensing platform: Resistive heating of nanohole arrays. NanoLetters 2014.

18

Second harmonic promotion in a ballistic graphene high-frequency transistor

Yevgeniy Korniyenko1, Vitaly Shumeiko1, and Tomas Lofwander1

1 Department of Microtechnology and Nanoscience (MC2), Chalmers Uni-versity of Technology, SE-412-96 Goteborg, Sweden

We report on a theoretical study of time-dependent transport in a ballisticgraphene field effect transistor. Based on Floquet theory, we model Diracelectron transmission through a harmonically driven potential barrier. Qua-sibound states in the barrier, formed due to phonon-assisted tunneling, leadto transmission resonances which are of the Fano form for the main trans-mission channel and of the Breit-Wigner form otherwise . We discuss thepossibility of utilizing the resonances for promotion of higher harmonics inprospective high-frequency devices, particularly in frequency multipliers.

19

Designing frequency-dependent relaxation rates and Lambshift for a giant artificial atom

Anton Frisk Kockum1, Per Delsing1, and Goran Johansson1

1 Department of Microtechnology and Nanoscience (MC2), Chalmers Uni-versity of Technology, SE-412-96 Goteborg, Sweden

In traditional quantum optics, where the interaction between atoms and lightat optical frequencies is studied, the atoms can be approximated as point-like when compared to the wavelength of light. So far, this relation hasalso been true for artificial atoms made out of superconducting circuits orquantum dots, interacting with microwave radiation. However, recent andongoing experiments using surface acoustic waves show that a single artificialatom can be coupled to a bosonic field at several points wavelengths apart.Here, we theoretically study this type of system. We find that the multiplecoupling points give rise to a frequency dependence in the coupling strengthbetween the atom and its environment, and also in the Lamb shift of theatom. The frequency dependence is given by the discrete Fourier transformof the coupling point coordinates and can therefore be designed. We discuss anumber of possible applications for this phenomenon, including tunable cou-pling, single-atom lasing, and other effects that can be achieved by designingthe relative coupling strengths of different transitions in a multi-level atom.