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VARMET SIGNED

Variational Metadynamics

Total Cost €

0

EC-Contrib. €

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Partnership

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Project "VARMET" data sheet

The following table provides information about the project.

Coordinator
UNIVERSITA DELLA SVIZZERA ITALIANA 

Organization address
address: VIA LAMBERTENGHI 10 A
city: LUGANO
postcode: 6904
website: www.usi.ch

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 Switzerland [CH]
 Project website http://www.parrinello.ethz.ch/research/variationally-enhanced-sampling.html
 Total cost 2˙488˙827 €
 EC max contribution 2˙488˙827 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2014-ADG
 Funding Scheme ERC-ADG
 Starting year 2016
 Duration (year-month-day) from 2016-01-01   to  2020-12-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    UNIVERSITA DELLA SVIZZERA ITALIANA CH (LUGANO) coordinator 2˙488˙827.00

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 Project objective

We propose to extend the time scale accessible to atomistic-based simulation methods from the current range to millisecond and beyond without special-purpose machines. We shall do this by combining and extending two recent developments: a recent reformulation of the enhanced sampling problem into a powerful variational principle that opens a wealth of possibilities and provides a novel and fruitful standpoint for new developments; and a procedure for extracting rates from enhanced runs. We shall apply the methods thus developed to two major problems of great practical interest. One is the lifetime of a ligand-protein bound state. This quantity is not easily accessible experimentally and yet it is crucial in drug design to determine the potency of a drug. We plan to develop a viable and widely applicable way to compute it. The other is a study of crystallization from solution, for which we wish to determine the nucleation mechanism and nucleation rates and understand and control crystal growth. These are all issues of great relevance in engineering, pharmacology and nanotechnology. Besides being relevant on their own merits, these two applications present different challenges to the enhanced methods. We also believe that new methods should not be developed in an abstract way but in close interaction with real-life applications.

 Publications

year authors and title journal last update
List of publications.
2018 Luigi Bonati, Michele Parrinello
Silicon Liquid Structure and Crystal Nucleation from Ab Initio Deep Metadynamics
published pages: , ISSN: 0031-9007, DOI: 10.1103/PhysRevLett.121.265701
Physical Review Letters 121/26 2019-08-30
2018 Yong Wang, Omar Valsson, Pratyush Tiwary, Michele Parrinello, Kresten Lindorff-Larsen
Frequency adaptive metadynamics for the calculation of rare-event kinetics
published pages: 72309, ISSN: 0021-9606, DOI: 10.1063/1.5024679
The Journal of Chemical Physics 149/7 2019-08-30
2018 Dan Mendels, Giovannimaria Piccini, Z. Faidon Brotzakis, Yi I. Yang, Michele Parrinello
Folding a small protein using harmonic linear discriminant analysis
published pages: 194113, ISSN: 0021-9606, DOI: 10.1063/1.5053566
The Journal of Chemical Physics 149/19 2019-08-30
2018 Z. Faidon Brotzakis, Vittorio Limongelli, Michele Parrinello
Accelerating the Calculation of Protein–Ligand Binding Free Energy and Residence Times Using Dynamically Optimized Collective Variables
published pages: 743-750, ISSN: 1549-9618, DOI: 10.1021/acs.jctc.8b00934
Journal of Chemical Theory and Computation 15/1 2019-08-30
2018 Yi Isaac Yang, Haiyang Niu, Michele Parrinello
Combining Metadynamics and Integrated Tempering Sampling
published pages: 6426-6430, ISSN: 1948-7185, DOI: 10.1021/acs.jpclett.8b03005
The Journal of Physical Chemistry Letters 9/22 2019-08-30
2017 Vinita Jagannath, Zacharias Faidon Brotzakis, Michele Parrinello, Susanne Walitza, Edna Grünblatt
Controversial Effects of D-Amino Acid Oxidase Activator (DAOA)/G72 on D-Amino Acid Oxidase (DAO) Activity in Human Neuronal, Astrocyte and Kidney Cell Lines: The N-methyl D-aspartate (NMDA) Receptor Hypofunction Point of View
published pages: , ISSN: 1662-5099, DOI: 10.3389/fnmol.2017.00342
Frontiers in Molecular Neuroscience 10 2019-08-30
2018 Claudio Perego, Omar Valsson, Michele Parrinello
Chemical potential calculations in non-homogeneous liquids
published pages: 72305, ISSN: 0021-9606, DOI: 10.1063/1.5024631
The Journal of Chemical Physics 149/7 2019-08-30
2018 Haiyang Niu, Pablo M. Piaggi, Michele Invernizzi, Michele Parrinello
Molecular dynamics simulations of liquid silica crystallization
published pages: 5348-5352, ISSN: 0027-8424, DOI: 10.1073/pnas.1803919115
Proceedings of the National Academy of Sciences 115/21 2019-08-30
2018 Yi Isaac Yang, Michele Parrinello
Refining Collective Coordinates and Improving Free Energy Representation in Variational Enhanced Sampling
published pages: 2889-2894, ISSN: 1549-9618, DOI: 10.1021/acs.jctc.8b00231
Journal of Chemical Theory and Computation 14/6 2019-08-30
2017 Pablo M. Piaggi, Michele Parrinello
Entropy based fingerprint for local crystalline order
published pages: 114112, ISSN: 0021-9606, DOI: 10.1063/1.4998408
The Journal of Chemical Physics 147/11 2019-08-30
2018 Dan Mendels, GiovanniMaria Piccini, Michele Parrinello
Collective Variables from Local Fluctuations
published pages: 2776-2781, ISSN: 1948-7185, DOI: 10.1021/acs.jpclett.8b00733
The Journal of Physical Chemistry Letters 9/11 2019-08-30
2018 J. Runeson, M. Nava, M. Parrinello
Quantum Symmetry from Enhanced Sampling Methods
published pages: , ISSN: 0031-9007, DOI: 10.1103/PhysRevLett.121.140602
Physical Review Letters 121/14 2019-08-30
2018 Pablo M. Piaggi, Michele Parrinello
Predicting polymorphism in molecular crystals using orientational entropy
published pages: 10251-10256, ISSN: 0027-8424, DOI: 10.1073/pnas.1811056115
Proceedings of the National Academy of Sciences 115/41 2019-08-30

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