Publications

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Presentations

    • H. Wolff, The Potential Carcinogenicity of Carbon Nanotubes(CNTs): Similarities and Differences with the Pathogenesis of Asbestos Related Cancers, The International Congress of Occupational Health (ICOH), 29 April-4 May 2018, Dublin, Ireland (oral)
    • C. Contini, N. Quirke, Inorganic nanoparticles and lipids interaction, MRS Spring meeting 2018, 2-6 April 2018, Phoenix, Arizona, USA (poster)
    • U. Vogel, Health effects of inhaled nanomaterials, NOSA-FAAR Aerosol Symposium 2018, 26-28 March 2018, Helsinki, Finland (invited talk)
    • U. Vogel, Cardiovascular disease as a particle-induced occupational disease, 2nd International Occupational and Environmental Diseases Congress, 4-8 March 2018, Antalya, Turkey (invited talk)
    • O. Joubert, Z.M. Doumandji, S. Nahle, L. Ferrari, C. Seidel, L. Gate, B. Rihn, Transcriptomic, the help for in vivo and in vitro nanotoxicology, 2nd Nanomedicine & Nanosafety Conference (NMNS 2017), Tehran, Iran, 29-30 November 2017 (oral)
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  • O. Joubert, Smartnanotox: Smart tools for gauging nano – hazards, Asia-Europe Dialogue on Nanosafety & Nanocertification Workshop, Tehran, Iran, 28 November 2017 (oral)
  • H. Lopez, S. Poggio, D. Power, E. Brandt, A. Lyubartsev, V. Lobaskin. Modelling of bio-nano interactions for predictive toxicology, OpenTox Euro 2017, Basel, Switzerland, 21-23 November 2017 (invited talk)
  • U. Vogel, Safe use of graphene nanomaterials, “Graphene Flagship” 2nd Division 2 “Health, medicine & sensors” meeting, 2 Novermber 2017, Delft, The Netherlands (invited talk)
  • U. Vogel, Safe use of nanomaterials – Good examples from Denmark, SweNanoSafe meeting, 24 October 2017, Stockholm, Sweden (invited talk)
  • S. Poggio, Coarse-grained modelling of protein-nanoparticle interactions, 9th International Conference on Nanomaterials – Research & Application (NANOCON 2017), 18-20 October 2017 Brno, Czech Republic (oral)
  • J. Štrancar, V. Lobaskin, SmartNanoTox project presentation, 9th International Conference on Nanomaterials – Research & Application (NANOCON 2017), 18-20 October 2017 Brno, Czech Republic (invited talk)
  • Y. Ding, P. Mayer, P. Weindl, T. Krebs, A.-G. Lenz, T. Stöger, O. Schmid, Comparing nanomaterial toxicity with lung cells cultured under air-liquid interface and submerged conditions, Inhaled Particles XII Conference, 25-27 September 2017, Glasgow, UK (oral)
  • T. Stoeger, Nanoparticles and persistent virus infection – a dangerous liaison for the development of chronic lung disease(s)? Inhaled Particles XII Conference, 25-27 September 2017, Glasgow, UK (oral)
  • U. Vogel, Development of an adverse outcome pathway based on toxicogenomic data for EMN-induced risk of developing atherosclerotic plaques, Inhaled Particles XII Conference, 25-27 September 2017, Glasgow, UK (oral)
  • U. Vogel, Nanomaterial-induced pulmonary acute phase response constitutes a causal link between inhalation of nanomaterials and risk of cardiovascular disease, Inhaled Particles XII Conference, 25-27 September 2017, Glasgow, UK (oral)
  • H. Cassidy, V. Zhernovkov, T. Santra, O. Rukhlenko, B.N. Kholodenko, D. Matallanas, SmartNanoTox: assesing a modern danger, Conway festival of Research and Innovation, 13 September 2017, Dublin, Ireland (poster)
  • L. Agosta, E.G. Brandt, A. Lyubartsev, Diffusion and reaction pathways of water near fully hydrated Tio2 surfaces from ab-initio molecular dynamics, CCP5 annual meeting “Materials modelling: Simulation Meets Experiment”, 11-13 September 2017, Glasgow, Scotland (poster)
  • A. Lyubartsev, Nanosafety-How do we ensure safety of the future nanotechnique , SweNanoSafe workshop, 5 September 2017, Stockholm, Sweden (oral)
  • B.N. Kholodenko, Catching signals surfing the net, MASSCAUSAL, The invitation-only 2nd International Workshop on causal discovery from single cell data, 1-3 September 2017, Heraklion, Crete, Greece (keynote talk)
  • I. Urbančič, M. Garvas, B. Kokot, H. Majaron, P. Umek, M. Škarabot, F. Schneider, S. Galiani, Z. Arsov, T. Koklič, A. Mertelj, I. Muševič, C. Eggeling, J. Štrancar, Lipid wraping as a molecular initiating event in nanotoxicology through fluorescence microspectroscopy and super-resolution microscopy, Photonica 2017 conference, 28 August-1 September 2017, Belgrade, Serbia (invited talk)
  • O. Schmid, Dosimetric considerations for designing toxicological studies with aerosolized nanoparticles: On the role of dose metric and tissue-delivered dose, European Aerosol Conference (EAC), 27 August–1 September 2017, Zurich, Switzerland (oral)
  • Y. Ding, P. Weindl, C. Wimmer, P. Mayer, T. Krebs, O. Schmid, Characterization of the air-liquid interface cell exposure (ALICE-CLOUD) system for in-vitro toxicological studies of engineered nanomaterials (ENMs), European Aerosol Conference (EAC), 27 August–1 September 2017, Zurich, Switzerland (poster)
  • S. Constant, A. Stelzl, K. Wieland, O. Schmid, In vitro testing of aerosolized substances with PRIMARY 3D Human Airway Epithelia: Application of ALICE-Cloud technology to eLiquids (e-cigarettes), European Aerosol Conference (EAC), 27 August–1 September 2017, Zurich, Switzerland (oral)
  • U. Vogel, Safe Use of Nanomaterials; Inflammation and genotoxicity following pulmonary exposure to graphene nanomaterials, 1st European Conference on Chemistry of Two-Dimensional Materials (Chem2DMat), 22-26 August 2017, Strasbourg, France (invited talk)
  • B. Kokot, Z. Urh, I. Urbancic, J. Štrancar, Lipid affinity to nanoparticles – possible molecular initiating event for nanoparticle toxicity, European Biophysical Society Association conference & International union for pure and applied biophysics (EBSA & IUPAB 2017), 16-20 July 2017, Edinburg, UK (poster)
  • H. Majaron, B. Kokot, I. Urbančič, P. Umek, T. Koklič, M. Garvas, J. Štrancar, Fluorescent labelling of nanoparticles for reliable bio-nano interactions study, European Biophysical Society Association conference & International union for pure and applied biophysics (EBSA & IUPAB 2017), 16-20 July 2017, Edinburg, UK (poster)
  • I. Urbančič, M. Garvas, B. Kokot, H. Majaron, P. Umek, M. Škarabot, F. Schneider, S. Galiani, Z. Arsov, T. Koklič, A. Mertelj, I. Muševič, C. Eggeling, J. Štrancar, Exploring high affinity of TiO2 nanotubes to lipid membranes, European Biophysical Society Association conference & International union for pure and applied biophysics (EBSA & IUPAB 2017), 16-20 July 2017, Edinburg, UK (poster)
  • S. Poggio, D. Power, E. Brandt, V. Lobaskin, A. Lyubartsev, A flexible and scalable package for protein/surface interactions, CECAM workshop “Extended Software Development Workshop in meso and multiscale methods”, 3-14 July 2017, Barcelona, Spain (oral)
  • V. Lobaskin, SmartNanoTox – Smart tools for gauging nano hazards, Nanotexnology 2017, 3-7 July 2017, Thessaloniki, Greece (oral)
  • V. Lobaskin, New tools for safety assessment, Workshop “Delivering Safe Nanotechnology to Market”, EuroNanoForum 2017, 21-23 June 2017, Valletta, Malta (oral) (poster 1, poster 2)
  • A. Lyubartsev, Multiscale simulations of DNA and nucleosome core particles, The 9-th International Symposium “Molecular Mobility and Order in Polymer Systems”, 19-23 June, St.Petersburg, Russia (oral)
  • L. Agosta, E. Brandt, A. Lyubartsev, Diffusion and reaction pathways of water near fully hydrated TiO2 surfaces from ab-initio molecular dynamics, CECAM workshop “Tackling complexity of the nano/bio interface – computational and experimental approaches”, 12-16 June 2017, Bremen, Germany (poster)
  • S. Constant, A. Stelzl, O. Schmid, ALICE-Cloud Technology for in vitro testing of Aerosolized substances with PRIMARY 3D Human Airway Epithelia: Application to e-liquids (e-cigarettes), 21th Conference of the International Society of Aerosols and Medicine (ISAM), 3–7 June 2017, Santa Fe, USA (poster)
  • W. Möller, Y. Ding, A. Stelzl, O.V. Amarie, A.Ö. Yildirim, O. Schmid, Dose-controlled aerosol-lung delivery and standardized airway hyperresponsiveness (AH) measurements in mice, 21th Conference of the International Society of Aerosols and Medicine(ISAM), 3–7 June 2017, Santa Fe, USA (poster)
  • O. Schmid, Nanomaterial dosimetry in inhalation toxicology: Bridging the gaps between in vitro and in vivo models as well as real world exposure, 8th International Symposium on NanoTechnology, Occupational and Environmental Health (NanoEH), 29 May-1 June 2017, Elsinor, Denmark (oral)
  • Y. Ding, Dispersion and aerosolization of engineered nanoparticles in liquid suspension for in-vitro toxicity testing, 8th International Symposium on NanoTechnology, Occupational and Environmental Health (NanoEH), 29 May-1 June 2017, Elsinor, Denmark (oral)
  • T. Stoeger, Macrophage response to particles, 8th International Symposium on NanoTechnology, Occupational and Environmental Health (NanoEH), 29 May-1 June 2017, Elsinor, Denmark (oral)
  • K.B. Knudsen, Physicochemical predictors of MWCNT-induced pulmonary histopathology and toxicity 1 year after pulmonary deposition of 11 different MWCNT in C57BL/6N mice, 8th International Symposium on NanoTechnology, Occupational and Environmental Health (NanoEH), 29 May-1 June 2017, Elsinor, Denmark (oral)
  • S. Søs Poulsen, Developing an adverse outcome pathway based on toxicogenomic data for ENM-induced risk of developing atherosclerotic plaques, 8th International Symposium on NanoTechnology, Occupational and Environmental Health (NanoEH), 29 May-1 June 2017, Elsinor, Denmark (oral)
  • Y. Ding, P. Weindl, C. Wimmer, A. Schröppel, T. Krebs, O.Schmid, Dispersion and aerosolization of engineered nanoparticles in liquid suspension for in-vitro toxicity testing, 8th International Symposium on NanoTechnology, Occupational and Environmental Health (NanoEH), 29 May-1 June 2017, Elsinor, Denmark (poster)
  • K. Ganguly, D. Ettehadieh, S. Upadhyay, S. Takenaka, T. Adler, E. Karg, F. Krombach, W.G. Kreyling, H. Schulz, O. Schmid, T. Stoeger, Carbon nanoparticle and lung interaction is crucial for systemic effects: Lessons learnt from inhalation versus intra-arterial infusion exposures in mice, 8th International Symposium on NanoTechnology, Occupational and Environmental Health (NanoEH), 29 May-1 June 2017, Elsinor, Denmark (poster)
  • Y. Yu, H. Adler, T. Stoeger, In vitro study of nanoparticle induced gammaherpesvirus reactivation in macrophages, 8th International Symposium on NanoTechnology, Occupational and Environmental Health (NanoEH), 29 May-1 June 2017, Elsinor, Denmark (poster)
  • N.R. Jacobsen, T. Stoeger, S. van den Brule, A.T. Saber, A. Beyerle, G. Vietti, A. Mortensen, J. Szarek, A. Kermanizadeh, A. Banerjee, N. Ercal, U. Vogel, H. Wallin and P. Moller, ZnO Nanoparticles: Pulmonary Toxicity and Mortality in Mice after Intratracheal Instillation in Three Laboratories, 8th International Symposium on NanoTechnology, Occupational and Environmental Health (NanoEH), 29 May-1 June 2017, Elsinor, Denmark (poster)
  • J. B. Sørli, Prediction of acute lung toxicity of impregnation products using an in vitro, 8th International Symposium on NanoTechnology, Occupational and Environmental Health (NanoEH), 29 May-1 June 2017, Elsinor, Denmark (poster)
  • C. Seidel, S. Sébillaud, M. Lorcin, L. Chézeau, C. Darne, S. Bau, S. Grossmann, S. Viton, H. Nunge, L. Douteau, S. Michaux, F. Cosnier, L. Gaté, Inhaled multi-walled carbon nanotubes-induced gene expression in rat lung, 8th International Symposium on NanoTechnology, Occupational and Environmental Health (NanoEH), 29 May-1 June 2017, Elsinor, Denmark (poster)
  • S. Poggio, H. Lopez, V. Lobaskin, Coarse-grained modeling of protein-nanoparticle interactions, CECAM workshop “State of the art in mesoscale and multiscale modeling”, 29-31 May 2017, Dublin, Ireland (poster)
  • D.Power, S. Poggio, H. Lopez, V. Lobaskin, Coarse graining of human serum albumin, CECAM workshop “State of the art in mesoscale and multiscale modeling”, 29-31 May 2017, Dublin, Ireland (poster)
  • A. Lyubartsev, Methodologies of systematic structure-based coarse-graining, CECAM workshop “State of the art in mesoscale and multiscale modeling”, 29-31 May 2017, Dublin, Ireland (oral)
  • Z.M. Doumandji, Etude toxicologique de nanoparticules de Zinc sur cellules de rat en culture, Presentation at Biological Sciences and Environment doctoral school, 15 May 2017, Vittel, France
  • B.N. Kholodenko, Molecular communications in four dimensions, 2nd International Workshop on Molecular Communications, 9-11 May 2017, Dublin, Ireland (keynote talk)
  • B.N. Kholodenko, Why kinase dimerization conveys drug resistance: thermodynamic principles and a structure-based dynamic modeling give the answer, National Cancer Institute’s Workshop Systems Biology of Metastasis, MD Anderson Cancer Center, 24-25 April 2017, Houston, USA (invited talk)
  • B.N. Kholodenko, Getting insights into cell biology by modelling of cellular networks, BioSB (Bioinformatics and Systems Biology) Conference, 4 April 2017, Lunteren, The Netherlands (keynote talk)
  • H. Lopez, S. Poggio, D. Power, V. Lobaskin, Modelling bionan interactions for predictive toxicology, Nanomaterial Safety Assessment Conference, 7-9 February 2017, Malaga, Spain (poster)
  • O. Joubert, Z. Doumandji, R. Safar, Smartnanotox: Smart tools for gauging nano-hazards, Nanomaterial Safety Assessment Conference, 7-9 February 2017, Malaga, Spain (oral)
  • H. Lopez, S. Poggio, D. Power, V. Lobaskin, Multiscale modelling of nanoparticle protein corona, Lorentz Workhsop “Structured Soft Interfaces: Caught Between Multi-Scale Simulation and Application”, 23-27 January 2017, Leiden, The Netherlands
  • O. Joubert, Nanoparticles: update on their hazard assessment, 6th Congress of the Association Tunisienne de Toxicologie, January 2017, Tabarka, Tunisia (invited lecture)
  • M. Schneemilch, N. Quirke, Free energy of adsorption of supported lipid bilayers from molecular dynamics simulation, The 4th International Conference on Molecular Simulation (ICMS-2016), 23-26 October 2016, Shanghai, China (oral)
  • M. Meunier, Molecular modelling of polymers and nanocomposites. The 4th International Conference on Molecular Simulation (ICMS-2016), 23-26 October 2016, Shanghai, China (oral)
  • H. Lopez, V. Lobaskin, Bionano interactions: A key to understanding toxicity of nanomaterials, UCD Conway Festival of Research & Innovation, 13-15 September 2016, Dublin, Ireland (invited lecture)
  • V. Lobaskin, Proteins at solid interfaces: A coarse-grained simulation, CECAM Workshop “Controlling food protein folding and aggregation: Challenges and perspectives in industry, experiments and simulation”, 18-20 August 2016, Dublin, Ireland (oral)
  • Z. Arsov, I. Urbancic, M. Garvas, R. Podlipec, B. Kokot, T. Koklic, J. Štrancar, Interaction of materials with model and cell membranes studied by fluorescence microscopy and microspectroscopy, Regional Biophysics Conference RBC2016, 25-28 August 2016, Trieste, Italy (invited talk)
  • U. Vogel, N.R. Jacobsen, K.B. Knudsen, S.S. Poulsen, S. Bengtson, A.T. Saber, H. Wallin, Nanomaterial-induced genotoxicity in mice, EEMGS Annual Meeting, 14-18 August 2016, Copenhagen, Denmark (poster)
  • U. Vogel, S.S. Poulsen, A.T. Saber, N.R. Jacobsen, C. Yauk, H. Wallin, S. Halappanavar, Global gene expression profiling in nanosafety – for hazard identification, grouping and ranking and risk assessment, The 8th International Nanotoxicology Congress, 1-4 June 2016, Boston, USA (poster)
  • H. Lopez, V. Lobaskin, Bionano interactions: A key to understanding toxicity of nanomaterials, Public Seminar, May 2016, Chemistry Department, University of Leeds, Leeds, UK (oral)
  • O. Schmid, Evidence from rodent studies on the most relevant dose metric for partico-(nano) toxicological studies, COST Modena (Modelling Nanomaterial Toxicity) Workshop, 4-5 May 2016, Tallinn, Estonia
  • N. Quirke, Some challenges in the simulation of biological membranes, International Molecular Simulation Workshop, April 2016, Xian Jiaotong University, China (oral)
  • N. Quirke, Nanoscale phenomena, April 2016, Department of Chemistry, Shaanxi Normal University, Xian, China (invited lecture)
  • D. Matallana, Characterisation of novel lats1 pro-apoptotic effectors, Scientific meeting “The Hippo pathway in health and disease”, December 2016, Oxford Martin School, Oxford, UK (oral)

Other Dissemination

 

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    • O. Schmid. Talks at Trade fair/User Group Meeting. Results on the VITROCELL® CLOUD 6 with Quartz Crystal Microbalance for real-time measurement of cell-delivered aerosol dose, VITROCELL User Group Meeting, Baltimore, USA, 10 March 2017
    • Vitrocell Booth with the SmartNanoTox presentation, The Society of Toxicology’s 56th Annual Meeting and ToxExpo, Baltimore, Maryland, USA (13th -15th March 2017)
    • Vitrocell Booth with the SmartNanoTox presentation, The Society of Toxicology’s VITROCELL User Group Meeting, Baltimore, Maryland, USA (13th -15th March 2017)
    • O. Schmid, Talks at institutes/companies.  Dose-controlled delivery of aerosolized substances to mice, Host: Prof. Wayne Mitzner, Johns Hopkins University, Maryland, USA, 14 March 2017
    • Vitrocell Booth with the SmartNanoTox presentation, 7th Conference of Alternative Methods, Guangzhou, China (11-14 April 2017)
    • Z. M. Doumandji, Etude toxicologique de nanoparticules de Zinc sur cellules de rat en culture, Presentation at Biological Sciences and Environment doctoral school, Vittel, France, May 2017
    • A booth with the SmartNanoTox role-up, including paper hand-outs of the project description, was manned by Vladimir Lobaskin at the EuroNanoForum 2017, 21-23 June 2017, Valletta, Malta
    • A booth with the SmartNanoTox role-up, including paper hand-outs of the project description, was manned by Kristina B. Knudsen and Jorid B. Sørli during the poster sessions at the 8th International Symposium on NanoTechnology, Occupational and Environmental Health (NanoEH), 29 May -1 June 2017, Elsinor, Denmark
    • Vitrocell Booth with the SmartNanoTox presentation, 8th International Symposium on NanoTechnology, Occupational and Environmental Health (NanoEH) conference in Elsinor, Denmark (29th of May-1st of June 2017)
    • Vitrocell Booth with the SmartNanoTox presentation, 21. ISAM-Congress, Santa Fe, New Mexico, USA (3rd -7th June 2017)
    • Vitrocell Booth with the SmartNanoTox presentation, 3rd International Conference on Toxicological Alternatives & Translational Toxicology 2017, Nanjing, China (9th -12th July 2017)
    • Vitrocell Booth with the SmartNanoTox, 10th World Congress on Alternatives and Animals in the Life Sciences (WC10), Seattle, Washington, USA (20th -24th August 2017)
    • Vitrocell Booth (#39) with the SmartNanoTox presentation, 53rd Congress of the European Societies of Toxicology (EUROTOX), Bratislava, Slovak Republic (10th – 13th of September 2017)
    • Janez Štrancar. Press conference about the “Lipid wrapping as molecular initiating event” on Jozef Stefan Institute (News on www.ijs.si , Twits on @StrancarLab and @SmartNanoTox) (15th of September 2017
    • Janez Štrancar. Interview about the “Towards better understanding of nanoparticles toxicity” for National Slovenian Radio (Look into science), (15th of September 2017)
    • Janez Štrancar. TV report about our lipid wrapping on the news (Slovenian national channel 1, at 13:14). 19th of September 2017

Codes

    • Software package to perform systematic coarse-graining of molecular system using the Inverse Monte Carlo or iterative inverse Boltzmann approaches: this package includes also utilities to transfer atomistic trajectories to coarse-grained ones, an user-friendly interface to compute all reference distribution functions, perform post-simulation analysis and to export computed coarse-grained potentials to Gromacs format thus enabling their direct use in subsequent mesoscale simulations, and the user manual in pdf and on-line formats. The code can be downloaded from here or here
    • Convert PDB files to 1 bead per aminoacid model: This script can be used to convert a PDB structure to a CG model in which one bead is used to represent each amino acid. See Lopez and Lobaskin for more details [J. Chem. Phys. 143, 243138 (2015)]
    • Coarse-grained model of adsorption of blood plasma proteins onto nanoparticles: This file contains the scripts and data needed to calculate the interaction of HSA for a given orientation with a 50 nm negative charged hydrophobic NP. See Lopez and Lobaskin for more details [J. Chem. Phys. 143, 243138 (2015)] The coarse-grained simulation of NP interaction with proteins and lipids can be performed using ESPResSo MD package. The source code can be downloaded from here.
    • Coarse-grained DMPC and Nanoparticle model: This file contains all the input files needed to run the simulation of a 10, 15, 20 or 25 nm particle adsorbing onto bilayers a DMPC bilayer. The simulation are performed with Gromacs which can be downloaded from here
    • Slipids model for lipid bilayer interacting with Gold nanoparticles: This file contains all the input files needed to run a simulation of a 3nm, 5nm or 10 nm gold particles adsorbing onto bilayers of various size. Also included are the files for a single lipid PMF as it adsorbs onto a gold surface. The simulation are performed with Gromacs which can be downloaded from here