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HYPERBIO

Hybrid Particle-Field Approach Including Electrostatics for Large-Scale Simulations of Biological Systems

Total Cost €

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EC-Contrib. €

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Partnership

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Project "HYPERBIO" data sheet

The following table provides information about the project.

Coordinator
UNIVERSITETET I OSLO 

Organization address
address: PROBLEMVEIEN 5-7
city: OSLO
postcode: 313
website: www.uio.no

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Norway [NO]
 Project website https://www.ctcc.no/news/2016/marie-curie-grant-awarded-to-hima-bindu-kolli.html
 Total cost 196˙400 €
 EC max contribution 196˙400 € (100%)
 Programme 1. H2020-EU.1.3.2. (Nurturing excellence by means of cross-border and cross-sector mobility)
 Code Call H2020-MSCA-IF-2015
 Funding Scheme MSCA-IF-EF-ST
 Starting year 2016
 Duration (year-month-day) from 2016-09-01   to  2018-08-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    UNIVERSITETET I OSLO NO (OSLO) coordinator 196˙400.00

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 Project objective

Despite the continuous progress in computer simulations, the typical time and size bottlenecks are nowadays still heavily affecting the feasibility of large-scale simulations of complex biological systems at the molecular resolution accuracy. The current proposal aims at formulating a new hybrid particle-field approach including explicit treatment of electrostatic interactions for computational modelling of complex biological environments. The proposed method will combine the computational advantages of a self-consistent field approach (linear scaling cost for computation of intermolecular interactions, easy parallelization), becoming increasingly popular in polymer and soft-matter simulations, with a rigorous treatment of particles and explicit electrostatics. The proposed approach will allow fast and reliable simulations of polyelectrolyte mixtures, including biological charged membranes, multi-phase systems, and biological polymers (polysaccharides, proteins, nucleic acids etc), and it will make it possible to break by orders of magnitude the current limits for biomolecular simulations both in time and size. The project will have a main development part, where the self-consistent field formalism with electrostatics will be derived and implemented, and an applicative part, where the new methodology will be tested on lipopolysaccharide moieties. These large amphiphilic and chemically complex molecules constitute the outer membrane of Gram- bacteria, and are to date one of the major research targets to in antibiotic resistance studies. This project is multidisciplinary and involves international collaboration. This project would have a great positive impact on the applicant’s early stage researcher career, identifying her as one of the key players in the opening a new pathway into molecular simulations of biological systems.

 Publications

year authors and title journal last update
List of publications.
2018 Hima Bindu Kolli, Antonio de Nicola, Sigbjørn Løland Bore, Ken Schäfer, Gregor Diezemann, Jürgen Gauss, Toshihiro Kawakatsu, Zhong-Yuan Lu, You-Liang Zhu, Giuseppe Milano, Michele Cascella
Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in an Aqueous Environment
published pages: 4928-4937, ISSN: 1549-9618, DOI: 10.1021/acs.jctc.8b00466
Journal of Chemical Theory and Computation 14/9 2019-05-09
2018 Raphael Mathias Peltzer, Hima Bindu Kolli, Achim Stocker, Michele Cascella
Self-Assembly of α-Tocopherol Transfer Protein Nanoparticles: A Patchy Protein Model
published pages: 7066-7072, ISSN: 1520-6106, DOI: 10.1021/acs.jpcb.8b05936
The Journal of Physical Chemistry B 122/28 2019-05-09

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The information about "HYPERBIO" are provided by the European Opendata Portal: CORDIS opendata.

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