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Panagiotis Kolokathis
Nova Mechanics

Panagiotis D. Kolokathis, PhD, is a computational scientist who graduated from the Chemical Engineering School of National Technical University of Athens (NTUA). He holds a Master's Degree in Quality Management and Technology and a PhD in the field of material science and engineering. After completing his studies, he worked for 5 years as a postdoctoral researcher at NTUA in collaboration with Fahrenheit GmbH, Fraunhofer ISE, and the University of Leipzig on the  development of next-generation solar cooling adsorbers. He then worked as a R&D plastics’ engineer at Lalizas SA before joining NovaMechanics as a computational scientist. Kolokathis' research interests  focus on density functional theory, statistical mechanics, atomistic and coarse-grained simulations,  transition state theory, computational fluid dynamics, Lagrangian Dynamics, Rietveld refinement,  machine learning, design of experiments, and invention of new scientific algorithms/methodologies.  He has expertise in simulations of Nanocomposite Materials. Some of his notable accomplishments  include identifying and determining the hydrated ALPO-5 structure for the first time, providing an  analytical solution for the Master Equation for calculating the diffusion coefficient inside periodic  materials, and conceiving and developing the KoBra software. He speaks Greek, English, French, and  German.

Abstract for OpenTox Summer School 2023

Nanoinformatics models and tools available through Enalos Cloud Platform and  ΝanoPharos Database 

Models and in silico tools developed for drug and material design can greatly underpin the efforts for  assessing the risk of small molecules and (engineered) nanomaterials (ENMs), reducing the time and  resources spend in experimental activities. While several predictive models have been built for  assessing the toxic side-effects of small molecules and ENMs, these remain unexploited by the wider  community as they have not been properly disseminated. These models should be integrated within  a simple and user-friendly environment to reach all interested users and facilitate decisions making.  Enalos Cloud Platform ( is a cutting-edge cloud  platform that provides an innovative solution for cheminformatics and nanoinformatics modeling.  Through Enalos Cloud Platform, models can be made available under the technology of Software as a  Service (SaaS). Enalos Cloud Platform offers a user-friendly environment that is specifically designed  for non-informatics experts. The platform has been designed to reduce the time and resources spent  on experimental activities and to provide researchers with a highly efficient and effective way of  predicting toxicity and property calculations for chemical structures or ENMs. The platform is an  invaluable tool for researchers in the fields of drug design, materials science, patient stratification,  and in ENMs risk assessment. The platform is available online and free of charge, making it accessible  to researchers and scientists globally. 

During this session, the attendees will learn to use computational tools powered by the Enalos Cloud  Platform to predict the properties of a range of nanomaterials. In more details, the attendees will  be trained to use: 

  • a) the NanoXtract image analysis tool for the calculation of several image descriptors based on  Transmission Electron Microscopy (TEM) images of nanomaterials: 
  • b) In vivo nanoparticle delivery general model: A tool comprising of a compartmental kinetics model  and the accompanying equations to describe the targeted delivery of nanomedicines in vivo: 
  • c) the Nanomaterials lung exposure dose simulation tool for the computation of the deposition dose  of nanomaterials in various human's respiratory regions using as input the evolution over time of the  nanomaterials' concentration in an indoor space 
  • d) Uptake and bioaccumulation of nanomaterials models Powered by the Enalos DIAGONAL Cloud  Platform: A tool to model the uptake and bioaccumulation of nanomaterials in invertebrate organisms. 
  • e) the Nanotube construction tool for the digital construction of energy-minimized nanotubes of single-layer materials and calculation of their atomic descriptors 
  • f) the NanoConstruct tool for the digital reconstruction of energy minimised nanoparticles based on their CIF files and the calculation of their atomistic descriptors 
  • g) NanoPharos database: ready to modelling curated and enriched datasets