Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

Equipment

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Memetic algorithms for the excited ligand diffusion in condensed biological matter

2015/19/N/ST3/02171

Keywords:

molecular dynamics nanophysics computer modeling optogenetics ligand-protein complexes non-adiabatic dynamics diffusion

Descriptors:

  • NZ1_3: Biophysics
  • ST4_7: Electrochemistry, microfluidics in chemistry, sensors
  • ST3_4: Electronic properties of materials, surfaces, interfaces, nanostructures, etc.

Panel:

ST3 - Condensed matter physics: structure, electronic properties, fluids, nanosciences, biological physics

Host institution :

Uniwersytet Mikołaja Kopernika, Wydział Fizyki, Astronomii i Informatyki Stosowanej

woj. kujawsko-pomorskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

Jakub Rydzewski 

Number of co-investigators in the project: 2

Call: PRELUDIUM 10 - announced on 2015-09-15

Amount awarded: 100 000 PLN

Project start date (Y-m-d): 2016-08-23

Project end date (Y-m-d): 2019-08-22

Project duration:: 36 months (the same as in the proposal)

Project status: Project settled

Project description

Download the project description in a pdf file

Note - project descriptions were prepared by the authors of the applications themselves and placed in the system in an unchanged form.

Equipment purchased [PL]

  1. Przenośny komputer osobisty (5 000 PLN)
  2. Licencja oprogramowania GLIDE firmy Schoedinger (12 560 PLN)

Information in the final report

  • Publication in academic press/journals (5)
  1. Thermodynamics of camphor migration in cytochrome P450cam by atomistic simulations
    Authors:
    J. Rydzewski, W. Nowak
    Academic press:
    Scientific Reports (rok: 2017, tom: 7, strony: 7736), Wydawca: Nature
    Status:
    Published
    DOI:
    10.1038/s41598-017-07993-0 - link to the publication
  2. Ligand diffusion in proteins via enhanced sampling in molecular dynamics
    Authors:
    J. Rydzewski, W. Nowak
    Academic press:
    Physics of Life Reviews (rok: 2017, tom: 22--23, strony: 58--74), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.plrev.2017.03.003 - link to the publication
  3. Rare-Event Sampling in Ligand Diffusion
    Authors:
    J. Rydzewski, W. Nowak
    Academic press:
    Physics of Life Reviews (rok: 2017, tom: 22--23, strony: 85--87), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.plrev.2017.08.011 - link to the publication
  4. Photoinduced Transport in an H64Q Neuroglobin Antidote for Carbon Monoxide Poisoning
    Authors:
    J. Rydzewski, W. Nowak
    Academic press:
    Journal of Chemical Physics (rok: 2018, tom: 148, strony: 115101), Wydawca: AIP
    Status:
    Published
    DOI:
    10.1063/1.5013659 - link to the publication
  5. maze: Heterogeneous Ligand Unbinding along Transient Protein Tunnels
    Authors:
    J. Rydzewski
    Academic press:
    Computer Physics Communications (rok: 2020, tom: 247, strony: 106865), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.cpc.2019.106865 - link to the publication

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