• A computational study of a ionic liquid and its ability to dissolve cellulose 

      Skanke, Tord (Master thesis, 2022)
      Oppløsningsmekanismen til en cellulosebunt solvatisert i blandinger av vann, Na+ og OH ble analysert gjennom molekylær dynamikksimulering og sammenlignet med den første i sitt slag simulerte ionisk væske som løsningsmiddel. ...
    • Alchemical Non-Equilibrium Free Energy Calculations Of CSF-1R Inhibitors 

      Tiller, Julie Lovise (Master thesis, 2022)
      Abstract will be available on 2025-02-01
    • An implicit solvent coarse-grained model for alginate hydrogels crosslinked with chitosan oligomers 

      Baldauf, Lukas (Master thesis, 2022)
      En grovkornet tilnærming er tatt i bruk i dette masterprosjektet for å undersøke hydrogeler i mikroskopisk skala ved bruk av molekylær dynamikksimuleringer. Hydrogelene som er studert er sammensatt av alginater tverrbundet ...
    • Analyse glycol ether and pesticide metabolites in Norwegian children and their potential determinants 

      Selma Tofte Granerud (Master thesis, 2022)
      Ikke-persistente stoffer er mye brukt i forbruksvarer og i miljøet. De finnes i hverdagsprodukter som plastikk, smøremidler, løsningsmidler, og insektsmidler, og eksponering av disse stoffene i lave konsentrasjoner kan ...
    • Analyzing Complex Reaction Mechanisms Using Path Sampling 

      van Erp, Titus Sebastiaan; Moqadam, Mahmoud; Riccardi, Enrico; Lervik, Anders (Journal article; Peer reviewed, 2016)
      We introduce an approach to analyze collective variables regarding their predictive power for a reaction. The method is based on already available path sampling data produced by for instance transition interface sampling ...
    • Computational study of the dissolution of cellulose into single chains: the role of the solvent and agitation 

      Bering, Eivind; Torstensen, Jonathan Økland; Lervik, Anders; de Wijn, Astrid S. (Journal article; Peer reviewed, 2022)
      We investigate the dissolution mechanism of cellulose using molecular dynamics simulations in both water and a mixture solvent consisting of water with Na+, OH− and urea. As a first computational study of its kind, we apply ...
    • De Første Stegene mot en Perturbasjonsteori for Små Systemer 

      Zhang, Daniel Tianhou (Master thesis, 2020)
      Tilstandsligninger (EOS) utviklet gjennom perturbasjonsteori er kjent i litteraturen og kan være et nyttig verktøy for å modellere væskeoppførsel. Selv om populære perturbasjonsteorier av f.eks. Barker-Henderson (BH) ...
    • Energy dissipation in biomolecular machines 

      Lervik, Anders (Doktoravhandlinger ved NTNU, 1503-8181; 2012:231, Doctoral thesis, 2012)
      The operation of a molecular pump, the calcium pump of sarcoplasmic reticulum is studied using mesoscopic non-equilibrium thermodynamics and molecular dynamics. The mesoscopic non-equilibrium thermodynamic description of ...
    • Entropy facilitated active transport 

      Rubi, Miguel; Lervik, Anders; Bedeaux, Dick; Kjelstrup, Signe (Journal article; Peer reviewed, 2017)
      We show how active transport of ions can be interpreted as an entropy facilitated process. In this interpretation, a particular change in the pore geometry through which substrates are transported gives rise to a driving ...
    • Entropy facilitated active transport 

      Rubi, J.M.; Lervik, Anders; Bedeaux, Dick; Kjelstrup, Signe (Journal article; Peer reviewed, 2017)
      We show how active transport of ions can be interpreted as an entropy facilitated process. In this interpretation, a particular change in the pore geometry through which substrates are transported gives rise to a driving ...
    • Forbedring av perturbasjonsteori for Lennard-Jones blandinger med store forskjeller i brønndybder 

      Price, Sebastian Everard Nordby (Master thesis, 2020)
      Statistisk assosierende fluid teori (SAFT) har hatt stor suksess i å beskrive assosierende kjede fluider. Disse SAFT-type-tilstandsligningene er som regel skrevet som en sum av Helmholtz fri energi, bestående av et ideelt ...
    • Gluing Potential Energy Surfaces with Rare Event Simulations 

      Lervik, Anders; van Erp, Titus Sebastiaan (Journal article; Peer reviewed, 2015)
      We develop a new method combining replica exchange transition interface sampling with two distinct potential energy surfaces. The method can be used to combine different levels of theory in a simulation of a molecular ...
    • Identification of a Pivotal Residue for Determining the Block Structure-Forming Properties of Alginate C-5 Epimerases 

      Stanisci, Annalucia; Tøndervik, Anne; Gaardløs, Margrethe; Lervik, Anders; Skjåk-Bræk, Gudmund; Sletta, Håvard; Aachmann, Finn Lillelund (Peer reviewed; Journal article, 2020)
      Alginate is a linear copolymer composed of 1→4 linked β-d-mannuronic acid (M) and its epimer α-l-guluronic acid (G). The polysaccharide is first produced as homopolymeric mannuronan and subsequently, at the polymer level, ...
    • Local initiation conditions for water autoionization 

      Moqadam, Mahmoud; Lervik, Anders; Riccardi, Enrico; Venkatraman, Vishwesh; Alsberg, Bjørn Kåre; van Erp, Titus Sebastiaan (Journal article; Peer reviewed, 2018)
      The pH of liquid water is determined by the infrequent process in which water molecules split into short-lived hydroxide and hydronium ions. This reaction is difficult to probe experimentally and challenging to simulate. ...
    • Molecular dynamics in exited systems; problems and application for photochemical reactions 

      (Bachelor thesis, 2021)
      This thesis aims to illustrate the limitations of quantum chemistry under the Born-Oppenheimer approx-imation, especially related to exited state systems and electronic transitions. Two of the most suitablemethods for ...
    • Non-equilibrium thermodynamics as a tool to compute temperature at the catalyst surface 

      Cruz, Carolina; Barragán, Daniel; Magnanelli, Elisa; Lervik, Anders; Kjelstrup, Signe (Journal article; Peer reviewed, 2019)
      The surface temperature is computed for a heterogeneous catalytic reaction model, namely the oxidation of carbon monoxide on platinum. The surface temperature was found using non-equilibrium thermodynamic theory, a theory ...
    • Protein Folding of Chignolin 

      Selavko, Katrina (Master thesis, 2022)
      Chignolin, et miniprotein med 10 aminosyrer, er et modellsystem for β-tråder. For å bestemme hyppigheten og foldemetoden til chignolin, ble chignolin simulert ved hjelp av RETIS, en simuleringsmetode for sjeldne hendelser, ...
    • PyRETIS: A well-done, medium-sized python library for rare events 

      Lervik, Anders; Riccardi, Enrico; van Erp, Titus Sebastiaan (Journal article, 2017)
      Transition Path Sampling techniques are becoming common approaches in the study of rare events at the molecular scale. More efficient methods, such as transition interface sampling (TIS) and replica exchange transition ...
    • Rare event simulations reveal subtle key steps in aqueous silicate condensation 

      Moqadam, Mahmoud; Riccardi, Enrico; Trinh, Thuat; Lervik, Anders; van Erp, Titus Sebastiaan (Journal article; Peer reviewed, 2017)
      A replica exchange transition interface sampling (RETIS) study combined with Born-Oppenheimer molecular dynamics (BOMD) is used to investigate the dynamics, thermodynamics and mechanism of the early stages of the silicate ...