• 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 ...
    • A procedure to find thermodynamic equilibrium constants for CO2 and CH4 adsorption on activated carbon 

      Trinh, Thuat; van Erp, Titus Sebastiaan; Bedeaux, Dick; Kjelstrup, Signe; Grande, Carlos Adolfo (Journal article; Peer reviewed, 2015)
      Thermodynamic equilibrium for adsorption means that the chemical potential of gas and adsorbed phase are equal. A precise knowledge of the chemical potential is, however, often lacking, because the activity coefficient of ...
    • Diffusion of gas mixtures in the sI hydrate structure 

      Waage, Magnus Heskestad; Trinh, Thuat; van Erp, Titus Sebastiaan (Journal article; Peer reviewed, 2018)
      Replacing methane with carbon dioxide in gas hydrates has been suggested as a way of harvesting methane, while at the same time storing carbon dioxide. Experimental evidence suggests that this process is facilitated if gas ...
    • Fast Decorrelating Monte Carlo Moves for Efficient Path Sampling 

      Riccardi, Enrico; Dahlen, Oda; van Erp, Titus Sebastiaan (Journal article; Peer reviewed, 2017)
      Many relevant processes in chemistry, physics, and biology are rare events from a computational perspective as they take place beyond the accessible time scale of molecular dynamics (MD). Examples are chemical reactions, ...
    • Foundations and latest advances in replica exchange transition interface sampling 

      Cabriolu, Raffaela; Skjelbred, Kristin Marie; Bolhuis, Peter G; van Erp, Titus Sebastiaan (Journal article; Peer reviewed, 2017)
      Nearly 20 years ago transition path sampling (TPS) emerged as an alternative method to free energy based approaches for the study of rare events such as nucleation, protein folding, chemical reactions, and phase transitions. ...
    • 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 ...
    • Improving the mesoscopic modeling of DNA denaturation dynamics 

      Marty-Roda, Marta; Dahlen, Oda; van Erp, Titus Sebastiaan; Cuesta-Lopez, Santiago (Journal article; Peer reviewed, 2018)
      Although previously developed mesoscopic DNA models have successfully reproduced thermodynamic denaturation data, recent studies show that these overestimate the rate of denaturation by orders of magnitude. Using adapted ...
    • 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. ...
    • Mesoscopic modeling of DNA denaturation rates: Sequence dependence and experimental comparison 

      Dahlen, Oda; van Erp, Titus Sebastiaan (Journal article; Peer reviewed, 2015)
      Using rare event simulation techniques, we calculated DNA denaturation rate constants for a range of sequences and temperatures for the Peyrard-Bishop-Dauxois (PBD) model with two different parameter sets. We studied a ...
    • Molecular Simulations of Gas Hydrates: Stability and Transport Properties 

      Waage, Magnus Heskestad (Doctoral theses at NTNU;2018:213, Doctoral thesis, 2018)
      At high pressures, mixtures of water and gas can form a crystalline compund called a gas hydrate. A considerable amount of methane hydrate exists at the sea floor and in permafrost regions. It is desirable to harvest this ...
    • Multiscale partial charge estimation on graphene for neutral, doped and charged flakes 

      Maslechko, Anastasiia; Verstraelen, Toon; van Erp, Titus Sebastiaan; Riccardi, Enrico (Journal article; Peer reviewed, 2018)
      The minimal-basis iterative stockholder (MBIS) and restrained electrostatic potential (RESP) methods were applied to examine the effects of edges and of nitrogen and boron dopants on the atomic partial charges of neutral ...
    • On the relation between the Langmuir and thermodynamic flux equations 

      van Erp, Titus Sebastiaan; Trinh, Thuat; Kjelstrup, Signe; Glavatskiy, Kirill (Journal article; Peer reviewed, 2014-01-22)
      Despite its approximative nature, the Langmuir theory has shown to be a very successful approach to describe experimental adsorption isotherms. Langmuir kinetics is based on systems of non-interacting particles that can ...
    • 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 ...