I have visited the University of Gdansk, Poland for seven months (14.05.2014-12.12.2014) in connection with the NanoBridges Work Package-3 (Development of novel structural descriptors for nanoparticles). I have built the 7 standalone and open accessible C++ programs for the nano-QSAR modeling work. The programs are free for all (eg. Personal, academic, non-profit, non-commercial, govt, commercial etc) to use.
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From 17th November to 30th December 2014 I was seconded to National Institute for Environmental Sciences (NIES) in Tsukuba, Japan, within the NanoBRIDGES project. During this 1.5 month period I was fulfilling the WP4: Development of novel Nano-QSAR methodologies. I was hosted by fate modeling specialist – Dr. Noriyuki Suzuki and his group.
The aim of the internship at National Institute for Environmental Sciences (NIES) was to fulfill the tasks of NanoBRIDGE project (i.e. WP4 task). The main task during cooperation with NIES researchers was to learn fate modeling techniques along with the methods of their proper validation. This knowledge will allow in the future to design an integral approach in order to characterize the environmental behavior and threats caused by nanomaterials, and allow their better and more precise classification, with less labor input during screening process.
Throughout the whole period of the internship, the theory of fate modeling was constantly introduced to me. Hosting researchers explained me the exact purpose of using such models (fate models), and the course of conducting simulations with their use. They explained the structural differences between specific models which is the consequence of their different purpose. They clarified the modeling process for me, explained the mathematical mechanisms used widely in fate modeling and introduced the main rules of models validation process. They also explained, how to collect and preprocess accurate data for modeling.
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I stayed at the Lawrence Berkeley National Laboratory, LBNL, (Berkeley, California, USA) for 10 months – between November 2013 and August 2014). I had the privilege of working under the supervision of Dr. Maciej Haranczyk at the Department of Computational Science, Computational Research Division (CRD).
Thanks to Dr. Haranczyk, I have started a cooperation with Daniela Ushizima from the CAMERA: Center for Applied Mathematics for Energy Research Applications, an expert in image analysis and data visualization. Our goal was is to quantify the risks posed by engineered nanoparticles, particularly hydroxyapatites.
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I have visited the National Institute for Environmental Studies in Tsukuba (Japan) for 3 months (16.09.2014 – 15.12.2014). My work was related to the Work Package 3 Development of novel structural descriptors for nanoparticles. The aim of the research secondment was to indicate the interactions between the small sized zinc oxide nanoparticles and various proteins.
During the stay in Tsukuba in order to achieve the objective of the research was performed the following steps: the parameterization of the zinc oxide particle in the AMBER force field; modeling the small-sized zinc oxide nanoparticles on the structure of the wurtzite; modeling the systems of the proteins and the nanoparticles; performing the molecular dynamics of the systems (contains one of the proteins and one of the zinc oxide nanoparticles) in water in the AMBER force field using the AMBER software package (approx. 200ns); performing the molecular dynamics of the proteins in water in the AMBER force field using the AMBER software package (approx. 200ns); the investigation of the interactions. read more >>
I came to the Interdisciplinary Center for Nanotoxicity, Jackson State University for three months (Sep 15th –Dec 15th 2014) to perform research within the WP 2 – “Carrying out experiments to produce necessary (missing) data for nanoparticles.”
My main scientific interest has been focused on carbon nanotubes’ (CNT) interactions with proteins, with particular regard to the effect on CNT dispersibility. This property is considered an important factor in potential CNT toxicity. During my work I developed a large library of CNT (27 various items), characterized their morphological properties with the use of transmission electron microscopy (TEM) and identified their chemical functionalization by means of Fourier transform infrared spectroscopy (FT-IR). Next, I investigated the stability of CNT dispersions in water and model protein solution (bovine serum albumin, BSA) by means of UV-VIS spectroscopy, dynamic light scattering (DLS) and zeta-potential measurement. Additionally, all CNT were investigated for their hydrophobicity index based on octanol/water partitioning. read more >>