• 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 ...
    • 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 ...
    • 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 ...
    • 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. ...
    • 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 ...
    • 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 ...
    • Teaching complex molecular simulation algorithms: Using self‐evaluation to tailor web‐based exercises at an individual level 

      Dahlen, Oda; Lervik, Anders; Aarøen, Ola; Cabriolu, Raffaela; Lyng, Reidar; van Erp, Titus Sebastiaan (Peer reviewed; Journal article, 2020)
      It is quite challenging to learn complex mathematical algorithms used in molecular simulations, stressing the importance of using the most advantageous teaching methods. Ideally, individuals should learn at their pace and ...
    • Temperature anisotropy at equilibrium reveals nonlocal entropic contributions to interfacial properties 

      Wilhelmsen, Øivind; Trinh, Thuat; Lervik, Anders (Journal article, 2018)
      Density gradient theory for fluids has played a key role in the study of interfacial phenomena for a century. In this work, we revisit its fundamentals by examining the vapor-liquid interface of argon, represented by the ...