Molekulska dinamika solvatacije nepolarnega topljenca v dvodimenzionalnem modelu vode

Andolšek, Katja (author), Urbič, Tomaž (mentor)

Z računalniškimi simulacijami molekulske dinamike smo preučevali lastnosti solvatacije Lennard-Jonesovega (LJ) diska v 2D modelu vode Mercedes-Benz (MB). Simulacije so potekale v NPT ansamblu. Z metodo termodinamične integracije s sklopitvenim parametrom smo računali Gibbsovo prosto energijo solvatacije nepolarnega topljenca v vodi. Preučevali smo tudi odvisnost le-te od temperature, tlaka in velikosti LJ delca. Za modeliranje interakcije med LJ in MB delci smo uporabili tri različne potenciale, od tega dva mehko-jedrna. Analizirali smo ponovljivost rezultatov in učinkovitost simulacij ter predlagali možne izboljšave.

• Language: Slovenian
• Keywords: molekulska dinamika, model Mercedes-Benz, NPT ansambel, termodinamična integracija, mehko-jedrni potencial
• Work type: Bachelor thesis/paper
• Typology: 2.11 - Undergraduate Thesis
• Organization: FKKT - Faculty of Chemistry and Chemical Technology
• Year: 2025
• PID: 20.500.12556/RUL-171763
• COBISS.SI-ID: 251692547
• Publication date in RUL: 02.09.2025

Secondary language

• Language: English
• Title: Molecular Dynamics of Solvation of a Nonpolar Solute in a Two-Dimensional Water Model

Abstract

Using molecular dynamics computer simulations, we studied the solvation properties of a Lennard–Jones (LJ) disk in a 2D Mercedes–Benz (MB) water model. The simulations were carried out in the NPT ensemble. Employing the thermodynamic integration method with a coupling parameter, we calculated the Gibbs free energy of solvation of a nonpolar solute in water. We also investigated its dependence on temperature, pressure, and the size of the LJ particle. To model the interaction between LJ and MB particles, we used three different potentials, two of which were soft-core. We analysed the reproducibility of the results and the efficiency of the simulations, and proposed possible improvements.

• Keywords: molecular dynamics, Mercedes-Benz model, NPT ensemble, thermodynamic integration, soft-core potential