Functional Sampling Tool: A Novel Method to Enhance Sampling in Molecular Dynamics Simulations : with applications to NMDAR dynamics

Show full item record



Permalink

http://urn.fi/URN:NBN:fi:hulib-202206282961
Title: Functional Sampling Tool: A Novel Method to Enhance Sampling in Molecular Dynamics Simulations : with applications to NMDAR dynamics
Author: Paajanen, Santeri
Other contributor: Helsingin yliopisto, Matemaattis-luonnontieteellinen tiedekunta
University of Helsinki, Faculty of Science
Helsingfors universitet, Matematisk-naturvetenskapliga fakulteten
Publisher: Helsingin yliopisto
Date: 2022
Language: eng
URI: http://urn.fi/URN:NBN:fi:hulib-202206282961
http://hdl.handle.net/10138/345537
Thesis level: master's thesis
Degree program: Materiaalitutkimuksen maisteriohjelma (Materials Research)
Master 's Programme in Materials Research
Magisterprogrammet i materialforskning
Specialisation: Laskennallinen materiaalifysiikka
Computational Materials Physics
Beräkningsmaterialfysik
Abstract: NMDA receptors are ionotropic glutamate receptors (iGluRs), tetrameric proteins, mediating synaptic transmission in the brain and the whole nervous system. Together with another type of iGluRs, AMPA receptors, they are considered essential for neuronal plasticity and memory. Understanding their dynamics and different kinetics is vital for studying various neurological diseases. The relatively slow dynamics, where the time scales of related processes range up to hundreds of milliseconds, make studying them with Molecular Dynamics (MD) simulations challenging. We developed the Functional Sampling Tool (FST), a novel method for enhancing the sampling of a function of interest. Compared to existing enhanced sampling schemes it strikes a balance between generality and simplicity, minimising the need of user input, while allowing for maximal customisability. Using FST, we studied two processes of the NMDA receptor. By keeping all four ligands bound we simulated a desensitisation pathway, and by removing all four we simulated an inactivation pathway. The tool sampled both, giving a good distribution between open and closed states. The tool also allowed us to change the function in the middle of sampling. With the new function we were able to produce more data, focusing on a certain value range.
Subject: Molecular Dynamics
MD simulations
Functional sampling
Enhanced sampling
iGluR
NMDAR


Files in this item

Total number of downloads: Loading...

Files Size Format View
santeri_paajanen_gradu.pdf 6.218Mb PDF View/Open

This item appears in the following Collection(s)

Show full item record