Nova metoda analize simulacija molekulske dinamike toplinskim mapama

master's thesis

• Title (english): A novel method of molecular dynamics simulation analysis using heatmaps
• Author: Matej Kožić
• Mentor: Branimir Bertoša (mentor)
• Committee member: Branimir Bertoša (predsjednik povjerenstva)
• Committee member: Ivica Đilović (član povjerenstva)
• Committee member: Aleksandra Maršavelski (član povjerenstva)
• Committee member: Tomica Hrenar (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Chemistry); Zagreb
• Defense date and country: 2024-02-29, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Chemistry

Abstract

Simulacije molekulske dinamike generiraju trajektorije koje opisuju evoluciju sustava kroz vrijeme. One se analiziraju vizualno (kvalitativno) te statističkim tehnikama (kvantitativno). Među najčešće korištenim analitičkim metodama spadaju RMSD, RMSF, i Rgyr. Spomenute metode ograničene su svojom striktno statističkom prirodom, te ne reprezentiraju konkluzivno tijek simulacije. Zbog kompleksnosti istraživanih sustava, robusne, brze i intuitivne metode analize od velikog su značaja i istraživačima koji provode istraživanja, kao i korisnicima tih rezultata. Jednoznačne i intuitivne kvantitativne analize pomažu razlučivanju važnih podataka od šuma, umanjuju ljudsku pogrešku, potiču efektivnije prenošenje informacija u svim stadijima istraživanja i pojednostavljuju komunikaciju znanstvenih pronalazaka. U sklopu ovog diplomskog rada razvijena je nova metoda analize simulacija temeljena na prikazivanju trajektorija toplinskim mapama nazvana „Mape trajektorija“ (engl. Trajectory Maps). Ovim pristupom nudi se intuitivna vizualizacija cijelog tijeka simulacije, izravna i konkluzivna usporedba više setova simulacija, intuitivna i efektivna vizualizacija pomicanja regija proteina tijekom simulacije, i dr. Metoda je razvijena sa svrhom da nadopunjuje postojeće kvantitativne i kvalitativne analize i s njima se kombinira, što ju čini posebice korisnom.

Abstract (english)

Molecular dynamics simulations generate trajectories which depict the system's evolution through time. The results are analyzed both visually (qualitatively) and statistically (quantitatively). Among the most common analytical methods are RMSD, RMSF, and Rgyr, which due to their strictly statistical character inconclusively represent simulation courses. Owing to the complexity of analyzed systems, robust, fast, and intuitive analysis methods are invaluable to both researchers conducting the studies and wider audiences using those results. Clear and intuitive quantitative analyses aid in distinguishing important dana from noise, minimize human error, and facilitate the transfer of information in all stages of research, simplifying communication of scientific findings. In this master's thesis a novel method of molecular dynamics simulation analysis was developed, based on representing trajectories with heatmaps called “Trajectory maps”. This approach offers an intuitive visualization of the entire simulation course, a direct and conclusive comparison of multiple simulation sets, an intuitive and an effective visualization of protein region movements during simulation, etc. The method is designed to complement existing quantitative and qualitative analysis approaches and to combine with them, making it particularly useful to both experienced and new researchers.

• Keywords: mapa trajektorija; metodologija analize trajektorija; molekulska dinamika; računalna biokemija; računalne simulacije proteina; toplinska mapa
• Keywords (english): computational biochemistry; computational biophysics; heatmaps; molecular dynamics; protein simulations; trajectory analysis methodology; trajectory map
• Language: croatian
• URN:NBN: urn:nbn:hr:217:320068
• Project: Number: IP-2020-02-3446; Title: Manganovi metalosenzori; Title: Manganese Metallosensors; Acronym: MaMes; Leader: Branimir Bertoša; Jurisdiction: Croatia; Funder: HRZZ; Funding stream: IP
• Study programme: Title: Graduate university studies in chemistry; specializations in: Graduate university studies in chemistry; Course: Graduate university studies in chemistry; Study programme type: university; Study level: graduate; Academic / professional title: sveučilišni/a magistar/magistra kemije (sveučilišni/a magistar/magistra kemije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2024-03-12 12:54:43