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Modeliranje agregacije proteinov kot efektivnih koloidnih delcev
Markoja, Uroš (Author), Ravnik, Miha (Mentor) More about this mentor... This link opens in a new window

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Abstract
Magistrsko delo obravnavna agregacijo koloidov v vodnih raztopinah pod vplivom različnih interakcijskih parskih potencialov kot efektivnega modela za agregacijo proteinov. Opisan je razvoj numerične metode za modeliranje kinetike in dinamike agregacije na osnovi programske opreme KAPSEL in rezultati simulacij, ki smo jih izvedli s to opremo. Postopek simulacije temelji na numeričnem reševanju Navier-Stokesove enačbe z metodo gladkega profila, ki mu je v vsakem koraku dodan naključen termični šum in vpilv interakcijske sile med delci. Simulirali smo agregacijo koloidov velikosti od 1 nm do 1000 nm, med katerimi deluje privlačna van der Waalsova interakcija ($1/r^{6}$), Londonove disperzijske sile med makroskopskimi telesi ($1/r$) in hidrofobna interakcija ($e^{-r/d}$), za različne številske gostote sistemov in različna razmerja moči interakcij v primerjavi s termičnim šumom. Kot osrednji rezultat študija agregacije ugotovimo, da sta kinetika in dinamika agregacije pogojeni s termodinamskim pogojem za nastanek agregacije, ki ga pogojuje razmerje med močjo interakcije in termičnim šumom ($\epsilon/k_bT$), manj pa s samo obliko potencialov in njihovim dosegom. Ko je razmerje med močjo interakcije in termičnim šumom večje ali enko okvirno 2, opazimo stabilen proces agregacije. Pri zviševanju tega razmerja ostane kinetika agregacije kvalitativno nespremenjena. Prav tako je bila kinetika agregacije efektivno kvalitativno neodvisna od gostote sistema. Kinetia agregacije je tako osrednje odvisna od gibljivosti molekul v raztopini, ki je neposredno povezana s temperaturo in izpolnjenim termodinamskim pogojem za nastanek agregatov.

Language:Slovenian
Keywords:fizikalna kemija, agregacija, koloidne raztopine, CFD simulacije
Work type:Master's thesis/paper (mb22)
Tipology:2.09 - Master's Thesis
Organization:FMF - Faculty of Mathematics and Physics
Year:2018
COBISS.SI-ID:3180132 This link opens in a new window
Views:545
Downloads:585
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Secondary language

Language:English
Title:Modelling of aggregation of proteins as colloidal particles
Abstract:
The master thesis focuses on aggregation of colloidal solutions with different interactional pair potentials, as an effective coarse grain approximation for aggregation of proteins. We use numerical based method for the simulation of kinetics and dynamics of colloidal aggregation based on open-source program KAPSEL. The simulation solves Navier-Stokes equation for fluid flow using smooth profile method with addition of a random thermal noise and influence of interaction forces between the colloidal particles. We simulate aggregation of colloids in size range of 1 nm-1000 nm which interact with either van der Waals ($1/r^{6}$), London dispersion force between macroscopic objects ($1/r$) or hydrophobic interaction ($e^{-r/d}$). Also we explore the role of different particle density and different ratios of interactions strengths against thermal noise. As the main result of the study of aggregation we have observed, that the kinetics and dynamics of colloidal aggregation depend primarily on the ratio between the strength of inter-particle interaction and thermal noise ($\epsilon/k_bT$) and less on the exact form and range of interactional potentials. When the ratio ($\epsilon/k_bT$) is greater or equals roughly 2, stable process of aggregation is observed. By increasing this ration, the kinetics of aggregation qualitatively does not change and is qualitatively similar also for different particle densities of the system tested. Finally we show that aggregation of colloids in solutions depends primarily on their ability to explore space –i.e. effective Brownian motion-being directly connected with the temperature and fulfilment of thermodynamical condition for emergence of aggregates.

Keywords:physical chemistry, aggregation, colloidal solutions, CFD simulations

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