Raziskave strukturnih in termodinamskih lastnosti mešanic nabitih koloidov z nevtralnimi polimeri z računalniškimi simulacijami Monte Carlo

Bercko, Urška (author), Reščič, Jurij (mentor)

S kanoničnimi simulacijami Monte Carlo so bili v tej diplomski nalogi raziskani vplivi privlačnih interakcij med nabitimi proteinskimi molekulami na porazdelitev proteinov. Modelna raztopina je vsebovala nabite koloide, protiione in nevtralne polimere polietilen glikola, ki so bili v raztopini prisotni bodisi kot molekule bodisi kot teoretični privlačni potencial Asakura-Oosawa. Narejena je bila primerjava rezultatov simulacije modela mešanice proteinov in eksplicitnih verig z rezultati simulacije modela, kjer je namesto eksplicitnih verig med proteini deloval teoretični Asakura-Oosawa (AO) potencial. Ugotovljeno je bilo, da AO teorija bistveno premalo upošteva vpliv izključenega volumna monomerov na porazdelitev proteinov, kar je glavni razlog za razkorak med obema modeloma. Podan je bil predlog rešitve tega problema v smislu upoštevanja izključenega volumna monomernih enot preko povečevanja radija sukanja. Ugotovljeno je bilo, da radij sukanja ne nadomesti končne velikosti monomernih enot. Raziskani so bili tudi vplivi koncentracije polimernih verig, radija sukanja, izključenega volumna ter naboja proteinov na porazdelitev protein-protein. Učinkovitost polimerov za destabilizacijo modelne raztopine je bila merjena z radialno porazdelitveno funkcijo protein-protein. Verjetnost destabilizacije modelne raztopine se je povečevala z večanjem koncentracije in radija sukanja polimernih verig.

• Language: Slovenian
• Keywords: privlačna interakcija, simulacija Monte Carlo, protein, polimer, izključeni volumen, radij sukanja
• Work type: Bachelor thesis/paper
• Typology: 2.11 - Undergraduate Thesis
• Organization: FKKT - Faculty of Chemistry and Chemical Technology
• Year: 2021
• PID: 20.500.12556/RUL-133373
• COBISS.SI-ID: 89693955
• Publication date in RUL: 24.11.2021

Secondary language

• Language: English
• Title: Research of structural and thermodynamic characteristics of mixtures of charged colloids with neutral polymers with Monte Carlo computer simulations

Abstract

In this work the effects of depletion interactions between charged protein molecules were studied with canonical Monte Carlo simulations. The model solution contained charged colloids, counterions and neutral polymers of polyethylene glycol, which were present either as molecules or as theoretical Asakura-Oosawa (AO) potential. Simulation results of protein mixture model were compared with simulation results of model which contained theoretical AO potential. It was found that AO theory significantly underestimates the influence of the excluded volume of monomers on protein-protein distribution, which was the main reason for the differences between the models. It was suggested to solve the problem by expanding radius of gyration. It was found that radius of gyration does not effectively replace excluded volume of monomers. Effects of polymer chains concentration, radius of gyration, excluded volume and charge of proteins were also investigated. The ability of polymers to destabilize the model solution was measured by protein-protein radial distribution function. The probability of model solution destabilization increased with polymer chains concentration and with radius of gyration.

• Keywords: depletion interaction, Monte Carlo simulation, protein, polymer, excluded volume, radius of gyration