Research Projects Ongoing or Completed (13.01.2022):

• [2017/26/M/ST4/00044] Cezary Czaplewski (PI) 04.2018 -04.2022
  National Science Centre (Poland, NCN)
  An integrated approach to modeling protein structure and dynamics based on the UNRES coarse-grained force field and bioinformatics methods and limited experimental data.
  The goal of this project is to develop an integrated and robust protocol for the prediction of the structure and conformational transitions of proteins and protein-protein complexes based on the UNRES coarse-grained force field, bioinformatics methods and limited experimental data. .
  Role: Principal Investigator

• [EuroHPC PL] Consortium of ACK Cyfronet AGH, PCSS, CI TASK, WCSS, NCBJ, IITiS PAN, CFT PAN 01/01/2021-12/31/2023
  The European Regional Development Fund (ERDF) POIR.04.02.00-00-D014/20-00
  National Supercomputing Infrastructure for EuroHPC
  The EuroHPC PL project aims to build a specialized general-purpose infrastructure for large-scale computing, enabling the undertaking of research challenges in the key areas from the point of view of the Polish soceity, scientific community and economy.
  Role: Domain-specific expert

• [MAGENTA] Consortium of 10 partners from 7 countries 01/01/2017-12/31/2020
  Coordinator: Sawako Nakamae, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), France,
  European Commission under the H2020 Program
  MAGnetic nanoparticle based liquid ENergy materials for Thermoelectric device Applications
  MAGENTA proposes a brand new technological path in thermoelectric materials research for waste-heat recovery applications. The originality of the project is based on the newly discovered thermal-to-electric energy conversion capacity of ionic-liquids and ferrofluids; i.e., colloidal dispersions of magnetic nanoparticles in ionic liquids (IL-FFs). Both experimental and theoretical approaches will be employed to build foundational knowledge on novel magneto-thermoelectric phenomena in ferrofluids. Computational simulations will allow ‘bottom-up’ construction of IL-FFs with optimal conditions for harvesting energy.
  Role: Co-Investigator

• [2013/10/M/ST4/00640] Adam Liwo (PI) 04.2014 - 04.2017
  National Science Centre (Poland, NCN, HARMONIA5)
  An integrated approach to the prediction of the structures of proteins a protein complexes with the use of the coarse-grained UNRES force field and utilizing the information from structural data bases
  The goal of this project is to develop a method structures of proteins and their complexes, which combines physical principles of protein structure formation and folding with bioniformatics tools. It combines physics-based coarse-grained UNRES model of polypeptide chains with template-based modeling method based on global optimization of multiple sequence alignment by means of the Conformational Space Annealing (CSA).
  Role: Co-Investigator

• [2012/06/A/ST4/00376] Adam Liwo (PI) 26.03.2013 – 25.03.2018
  National Science Centre (Poland, NCN, MAESTRO3)
  A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions
  The goal of this project is the development of the Unified Coarse-Grained Model for the description and simulation of the structure and dynamics of systems containing proteins, nucleic acids, polysaccharides, and glycoproteins i aqueous and lipid environments and the development of a semi-analytical theory, which will relate regular structural patterns of biomacromolecules to mean-field local and multipole-multipole interactions.
  Role: Co-Investigator

• [PSPB-051/2010] Maciej Bobrowski and Herbert Keppner (Co-PIs) 02/02/2012 - 06/30/2015
  Polish-Swiss Research Programme
  ENERLIQ - Energy conversion based on ionic liquids and novel SOLID technology.
  The main goal of the ENERLIQ project is to develop the next generation electronic devices based on an innovative and reliable concept inspired by current solid-state energy conversion systems. The actuation of energy conversion will rely on parylene- and ionic liquids-based Peltier-like systems.
  Role: Co-Investigator

• [2011/01/B/ST4/06094 ] Wiesław Wiczk (PI) 01.12.2011 – 30.11.2014
  National Science Centre (Poland, NCN)
  Studies of structure and photophysical properties of aromatic derivatives of acetylene and diacetylene.
  The goal of this project is theoretical and experimental investigation of properties model molecular wires: aromatic derivatives of acetylene and diacetylene.
  Role: Co-Investigator

• [N N204/355240] Cezary Czaplewski (PI) 04/13/2011 -10/12/2012
  National Science Centre (Poland, NCN)
  Simulations of structure and mechanism of polymerization of poly(p-xylylene) and its derivatives.
  This project supports my PhD student Krzystof Smalara. The goal of this project is to study polymerization of p-xylylene based polymers using all-atom molecular dynamics (MD) simulations with reactive empirical force fields AIREBO and REAXX and with classical empirical force field extended with Monte Carlo step allowing for bond formation.
  Role: Principal Investigator

• [N N519/641640] Maciej Bobrowski (PI) 04/15/2011 -04/14/2014
  National Science Centre (Poland, NCN)
  Hybrid calculation of growth of polymer films on solid and liquid substrates in Chemical Vapor Deposition method.
  The overall aim of the project is to design a new computational method of simulation of growth of polymer thin films based on all atom and coarse grained hybrid molecular dynamics and Monte Carlo method.
  Role: Co-Investigator

• [N N204/169738] Cezary Czaplewski (PI) 03/23/2010 -03/22/2013
  Polish Ministry of Science and Higher Education (MNiSW/NCN)
  Development of effective methods of simulation of protein folding thermodynamics, kinetics and folding pathways.
  The goal of this project is to extend replica-exchange methods based on molecular dynamics, Monte Carlo and Hybrid Monte Carlo and implement it using parallel programming on CPU (with OpenMP extension) and GPU (using CUDA library).
  Role: Principal Investigator

• [MPD] International PhD Projects Programme
  Jarosław Marszałek (consortium coordinator) 09/01/2010 -06/30/2015
  Foundation for Polish Science (FNP)
  The overall objective of the programme is to increase the level of research carried out in Poland performed by young scientists during the preparation of their PhD theses. Within the scope of the programme the Foundation covers the stipends for PhD students and research grants including the costs resulting from international cooperation.
  Role: Member of the consortium and graduate adviser of two PhD students

• [PARYLENS] Consortium of 12 partners from 8 countries 10/01/2010-09/30/2013
  Coordinator: Herbert Keppner, HES-SO, Switzerland,
  European Commission under the 7th Framework Program
  PARYLENE based artificial smart LENSes fabricated using a novel solid-on-liquid deposition proces
  The main goal of the PARYLENS project is to develop the next generation optical devices. The development of these devices relies on recent advances in nanotechnology combined with SOLID (Solid On Liquid) parylene deposition. The actuation of the tuneable lenses will rely on Parylene-based electroactive polymers and liquid crystals.
  Role: Co-Investigator

• [BW8370-5-0449-0] Cezary Czaplewski (PI) 03/31/2010 -31/12/2010
  University of Gdańsk
  Molecular modeling of poli(p-xylylene) and its derivatives.
  The goal of this project is to investigate mechanism of polymerization and deposition of p-xylylene based polymers on selected substrates using quantum chemistry and molecular simulation techniques.
  Role: Principal Investigator

• [EGI] International Project Not Cofunded
  (Projekty Międzynarodowe Niewspółfinansowane PMN) 2010
  Polish Ministry of Science and Higher Education
  Academic Computer Centre CYFRONET AGH
  Standardisation and integration of the Polish National Grid with European Grid Infrastructure
  Role: Co-Investigator

• [N N204/049035] Adam Liwo (PI) 08/28/2008 -09/27/2011
  Polish Ministry of Science and Higher Education
  Optimization of the mezoscopic UNRES force field for prediction of the structure and the thermodynamic and kinetic characteristics of proteins.
  The goal of this project is to perform thermodynamical and kinetic experiments on selected proteins and use these data to optimize UNRES force field for both protein structure prediction and protein folding simulations.
  Role: Co-Investigator

• [STREP 033201] Consortium of 10 partners from 8 countries 01/01/07-12/31/09
  Coordinator: Herbert Keppner, HES-SO, Switzerland,
  European Commission under the 6th Framework Program
  MULTIPOL: Multifunctional Polymer Materials and Systems with Tailored Mechanical, Electrical and Optical Properties.
  The overall aim of the MULTIPOL project is to create new multifunctional parylene-based polymers and systems with the following properties: conductivity, insulation, size, weight, density, biocompatibility, toxicity, environmentally friendly synthesis and processing, dielectric, optical, magnetic, and integrate them in the chosen electronic devices.
  Role: Paid consultant