Modeliranje encimsko katalizirane biotransformacije z imobiliziranimi encimi na magnetnih nano delcih v mikroreaktorskem sistemu

Grebenc, Andrej (author), Plazl, Igor (mentor), Urbič, Tomaž (comentor)

S simulacijami molekularne dinamike opišemo obnašanje magnetnih nanodelcev v mikrokanalu. Za opis privlačnih sil in navorov uporabimo magnetne interakcije med magnetnimi dipoli. Minimalno razdaljo med nanodelci poskusimo doseči z uporabo Lennard-Jonesovega potenciala. Ta pristop se izkaže kot primeren. Nato poskusimo zadržati nanodelce v celotnem volumnu mikrokanala z uporabo magnetne tuljave. Pri tem pristopu ugotovimo, da imamo majhen pretok skozi mikrokanal. Ker ga želimo povečati, namesto tuljave uporabimo elektromagnet in drugačno usmerjenost magnetnega polja. S tem nam uspe zadržati nanodelce ob steni. Za nastale strukture ob steni izračunamo poroznost. V naslednjem koraku uporabimo simulacije fluidne mehanike. Naredimo jih na osnovi mrežne Boltzmannove metode. Algoritme spišemo v programskem jeziku C++, zato delovanje algoritmov preverimo na problemih, za katere poznamo analitično rešitev. Vpliv strukture iz nanodelcev v simulacijo vključimo z uporabo prej izračunane poroznosti. To se izkaže za dober pristop. Hitrost biotransformacije opišemo z uporabo Michaelis-Mentenove kinetike. Tako narejena simulacija nam poda smiselni rezultat. Poraba substrata se ujema z oceno, ki smo jo naredili z uporabo karakterističnih časov.

• Language: Slovenian
• Keywords: Modeliranje in simulacije, mrežna Boltzmannova metoda, obnašanje magnetnih nanodelcev, LAMMPS
• Work type: Master's thesis/paper
• Typology: 2.09 - Master's Thesis
• Organization: FKKT - Faculty of Chemistry and Chemical Technology
• Year: 2022
• PID: 20.500.12556/RUL-135647
• COBISS.SI-ID: 102151683
• Publication date in RUL: 23.03.2022

Secondary language

• Language: English
• Title: Modeling of enzyme catalyzed biotransformation with immobilized enzymes on magneric nanoparticles in a microreactor system

Abstract

We use simulations of molecular dynamics to describe behavior of magnetic nanoparticles in a microchannel. Magnetic interactions between magnetic dipoles are used to describe attractive forces and torques. We try to achieve the minimum distance between nanoparticles using the Lennard-Jones potential. This approach proves to be appropriate. Then we try to retain nanoparticles in the entire volume of the microchannel using a magnetic coil. We find this approach problematic because of small flow through the microchannel. We use an electromagnet and a different direction of the magnetic field in an attempt to increase it. We successfully retain nanoparticles close to the wall. Then we calculate porosity for the formed structure. In the next step we use fluid mechanics simulations. We base them on the lattice Boltzmann method. Algorithms are written in the C ++ programming language. We have to check the accuracy of algorithms on problems with an analytical solution. The influence of nanoparticle structure is included in the simulation using previously calculated porosity. This turns out to be a good approach. The rate of biotransformation is described using Michaelis-Menten kinetics. The simulation gives us a result that makes sense. Calculated substrate conversion is in agreement with the estimate we made using characteristic times.

• Keywords: Modeling and simulation, lattice Boltzmann method, behavior of magnetic nanoparticles, LAMMPS