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HYPERBIO

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

Total Cost €

EC-Contrib. €

Partnership

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Outcomes and
results

HYPERBIO project word cloud

Explore the words cloud of the HYPERBIO project. It provides you a very rough idea of what is the project "HYPERBIO" about.

formulating researcher continuous computation parallelization charged bacteria constitute accuracy soft polymer time particle hybrid bottlenecks environments positive computational consistent proteins limits career electrostatic electrostatics biological outer despite rigorous combine intermolecular international magnitude heavily amphiphilic moieties polymers methodology tested linear resolution break advantages nucleic simulations size progress scaling resistance computer fast biomolecular nowadays gram polysaccharides date players multidisciplinary explicit membranes formalism stage molecules treatment antibiotic popular lipopolysaccharide self chemically orders feasibility polyelectrolyte acids molecular opening mixtures membrane particles interactions applicative

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 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.	NO (OSLO)	coordinator	196˙400.00

Map

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

List of publications.
year	authors and title	journal	last update
2018	Hima Bindu Kolli, Antonio de Nicola, SigbjÃ¸rn LÃ¸land Bore, Ken SchÃ¤fer, Gregor Diezemann, JÃ¼rgen 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 Î±-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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