Nanoscience Center

Nanoscience seminars

Seminars are arranged during the terms on weekly bases on Friday afternoons at 1 o'clock with coffee, talk starts 13:15 in YN121 in NSC. Welcome!


Friday 22.5

Coffee at 13:00 seminar 13:15 in YN341


Kunal Garg

The Chronic Manifestation Knot (CMK) Model: A holistic and unified approach to facilitate graphical data visualization and statistical predictive modelling for diseases at the microorganism level

Borrelia species are predominantly responsible for the most common form of Tick-borne diseases (TBD) which is Lyme borreliosis (LB). Episodes of Lyme arthritis (LA) is a hallmark symptom of LB patients. LA is an atypical form of reactive arthritis (ReA) that is a sub-type of Spondyloarthritis (SpA). Coinfections such as Ehrlichia chaffeensis accompany primary Borrelia species during the later stages of LB infection to induce severe symptoms. Currently, there is no holistic approach that would unify different TBD pathogens into independent and multiple TBD infection (MTBDI) combination categories to facilitate graphical and statistical analysis between any two patients groups. The chronic manifestation knot (CMK) model with its eight categories is a holistic and unified approach that facilitates data visualization and predictive statistical modelling (binary logistic regression) between two patients groups (LB and SpA patient groups). The CMK model helps to discover and clinically understand different developmental aspects of a disease at the microorganism(s) level. In order to validate the newly proposed CMK model, immune response frequencies of LB and SpA patient groups were statistically moulded to clinically understand relevant MTBDI combination(s) that may play an imperative in inducing chronic conditions. The immune response frequencies by LB and SpA patient groups (n = 54) to Borrelia burgdorferi, Borrelia burgdorferi RB, Borrelia afzelii, Borrelia garinii, and Ehrlichia chaffeensis were obtained from two independent studies that emphasized on recording the immune responses on the enzyme-linked Immunosorbent assay (ELISA) platform. The raw optical density (OD) values from both the studies were converted into the optical density index (ODI), and finally transformed into binary codes for establishing the eight CMK categories. Graphically, immune responses by both patient groups to the CMK categories revealed that the outer surface membrane proteins across both Borrelia morphologies are different. Statistically, the results revealed that Borrelia’s pleomorphic ability may play a crucial role for Borrelia spirochete to progress through the early to late stages of LB, to induce chronic conditions like arthritis together with coinfections. From statistical and experimental standpoints, the inclusion of Borrelia RB for diagnostic purposes should strongly be considered to improve the detection efficiency of the ongoing diagnostic tools. Advisor: Leona Gilbert

Keywords: Chronic manifestation knot model, Borrelia Round Body, and Lyme Borreliosis.


Sami Kinnunen

Fabrication of conducting ceramic thin films by atomic layer deposition

MAX phases are a class of ternary carbides and nitrides which possess rare combination of properties characteristic to both metals and ceramics. Many are electrically and thermally conducting but also elastically stiff and resistant to oxidation and high temperatures. Atomic layer deposition (ALD) is a method used to produce thin conformal films from gaseous precursors. MAX phases have not been fabricated by ALD before. Two different phases, Ti2AlN/Ti4AlN3 and Ti2AlC/Ti3AlC2, were selected as candidates, since ALD processes for TiN, AlN and TiC already exist. Films were deposited in different temperatures and ratio of precursor pulses were varied. Annealing at 600-1000 oC in N2 -atmosphere and vacuum was made in order to increase crystallinity of films. Deposited films were characterized by Atomic Force Microscope (AFM), Scanning Electron Microscope (SEM), Raman spectroscopy, X-ray Diffraction (XRD) and Time-of-Flight Elastic Recoil Detection Analysis (ToF-ERDA). Elemental composition showed that Ti:Al ratio is easy to control while means to control N content is challenging. AFM and SEM pictures showed polycrystallinity especially in annealed samples. However, XRD did not show hints of MAX phases. It is possible that higher deposition temperature and better control of elemental composition might yield more positive result. Advisors: Timo Sajavaara and Jari Malm

1. P. Eklund, M. Beckers, U. Jansson, H. Högberg, and L. Hultman. The Mn+1AXn phases: Materials science and thin-film processing. Thin Solid Films, 518(8):1851-1878, (2010).
2. Steven M. George. Atomic Layer Deposition: An Overview.
Chemical Reviews, 110(1):111-131, (2010)


Sami Kortet

Lycoperdic Acid and its Derivatives: Synthesis and Binding to Glutamate Receptors Based on Molecular Dynamics Simulations

Ionotropic glutamic acid receptors (iGluRs), such as AMPA (GluA) and kainate receptors (GluK), are of great interest in the area of structural biology and medicinal chemistry.1 These receptors, located in the central nervous system (CNS), are interesting targets when researching molecule-receptor – interactions and developing drug candidates for CNS disorders. In our study, the first aim was to computationally develop novel GluA2 and GluK1 binders using lycoperdic acid, a non-proteinogenic amino acid, as a core structure. The second aim was to synthesize lycoperdic acid and the most promising derivatives. In the computational part, molecular dynamics (MD) simulations of molecule-receptor–complexes were used.2 Analyses and visualisations of the simulations made it possible to estimate molecule-receptor–interactions, pharmacological profiles and binding energies for each molecule. Several derivatives that possibly bind better to the receptors than the natural molecule glutamate were found. Also some of the derivatives were found to be selective, having suitable interactions and certain pharmacological profiles only with either of the receptor types. In the synthesis part, our synthesis route to lycoperdic acid required nine steps, two of them being enantioselective organocatalytic reactions. The applicability of the synthesis route has been confirmed, yet requiring some improvements in the last step. The carbon core structure of the title compound was achieved enantioselectively when a silyloxyfuran reacted with acrolein in the presence of a chiral diphenylpyrrolidine catalyst (non-optimised yield 50 %, enantiomeric ratio 92:8).3 The results have shown that computational methods can provide useful and informative tools for novel drug development by helping to prioritize the synthesis in the lab, where modern organic synthesis methods are available. Advisors: Petri Pihko and Olli Pentikäinen

[1] S. F. Traynelis, Glutamate Receptor Ion Channels: Structure, Regulation, and Function, Pharmacol Rev., 2010, 62 (3), 405–496.

[2] P. A. Postila, M. Ylilauri, O. T. Pentikäinen, Full and Partial Agonism of Ionotropic Glutamate Receptors Indicated by Molecular Dynamics Simulations, J. Chem. Inf. Model., 2011, 51, 1037–1047.

[3] E. K. Kemppainen, G. Sahoo, A. Valkonen, P. M. Pihko, Mukaiyama–Michael Reactions with Acrolein and Methacrolein: A Catalytic Enantioselective Synthesis of the C17–C28 Fragment of Pectenotoxins, Org. Lett., 2012, 14 (4), 1086–1089.

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Thursday 28.5
Coffee at 13:00 seminar 13:15 in YN341

Utilization of selected non-conventional diagnostic techniques for materials characterization


Prof. Jozef Kaiser
Central European Institute of Technology (CEITEC),
Brno University of Technology, Czech Republic

Laser-Induced Breakdown Spectroscopy (LIBS) is an analytical technique able to perform multi- elemental diagnostic of most of the periodic table elements, including those with low atomic weight. In a matter of seconds it can analyze samples of all states without the need for any special preparation. It is based on the detection of photons emitted by the atomized sample constituents in the laser-induced plasma created during laser-ablation [1].

Another technique, the (micro-) computed tomography (µCT) can practically non-destructively reveal among others the 3D structure of e.g. powder consolidated materials or coatings with different level of porosities, distinguish in certain extent the presence of different grains/inclusions and detect local failure [2].

In the talk the selected application of these two techniques will be presented together with the overview of research activities of CEITEC´s ( Materials Characterization and Advanced Coatings research group (

[1] Kaiser J. et al., Surface Science Reports 67, 2012, 233-243.
[2] Olakanmi E.O. et al., Journal of Materials Processing Technology 211, 2011, 113-121.






Pyrophosphate Content Measurement in Cells by Simple Terpyridine-Zn+2 Dye

Removing alkylthiols from gold surface:
Molecular dynamics simulations in density function theory

Quantitative spectroscopic analysis of covalent functionalization
of gold clusters

Master students:
Gunjan Pandey

Sami Kaappa

Johanna Salmela

Tiny Metal Objects beyond Nano: Not Just with the Sizes

Katsuaki Konishi

Hokkaido University

Host-Guest Dialogue at Interfaces,
Spoken in the Language of Cavitands

Enrico Dalcanale Università di Parma

Fr at 10-12
A mini workshop on Coarse Graining Alex de Vries
University of Groningen Netherlands

27.3 Deciphering protein-protein, protein-ligand and protein-metal ion interactions with native mass spectrometry Janne Jänis
University of Eastern Finland
10.4 Manufacturing and characterisation of carbon nanotube reinforced free-standing Al2O3 films

Master students:
Kasper Leppänen


An alternative to problem-tailored global optimization algorithms:
using evolution to find the most stable structures of clusters

Detecting conformational changes in D. radiodurans bacteriophytochrome with Förster resonance energy transfer

Fabrication of suspended graphene samples

Master students:
Teemu Peltonen,

Heini Takkinen


Vesa-Matti Hiltunen

On the way to a DNA Dosimeter Stefan Sellner
Physikalisch-Technische Bundesanstalt (PTB), Germany
Jussi Toppari

master seminars
The Chronic Manifestation Knot (CMK) Model: A holistic and unified approach to facilitate graphical data visualization and statistical predictive modelling for diseases at the microorganism level
Lycoperdic Acid and its Derivatives: Synthesis and Binding to Glutamate Receptors Based on Molecular Dynamics Simulations
Fabrication of conducting ceramic thin films by atomic layer deposition

Kunal Garg


Sami Kortet


Sami Kinnunen


Utilization of selected non-conventional diagnostic techniques for materials characterization

Jozef Kaiser
Brno University of Technology
Czech Republic

Nanomaster seminars

Juuli Raivola
Kevin Roberts

Delmar Larsen

University of California, Davis, USA

11.9 Nanomaster seminars Ville Valkiala Johansson
18.9 Nanomaster seminars Niko-Ville Hakkola
Sisi Xie
Joonas Pylväinen

The previous seminars in  2014 2013 2012 2011 2010 2009 2008 2007


Seminars in:

Department of Physics Molecular Recognition

Contact Information


Nanoscience Center
P.O.Box 35
FI-40014 University of Jyväskylä
Tel: +358 50 3956 020
Fax: +358 14 617 412

Street address and office:
Survontie 9 C
40500 Jyväskylä