Browsing NTNU Open by Author "Dahlen, Oda"

Now showing items 1-6 of 6

    • 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, ...

    • 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 ...

    • 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 ...

    • Simulating the unwinding of DNA - Method development, application and didactic dissemination. 

      Dahlen, Oda (Doctoral theses at NTNU;2019:13, Doctoral thesis, 2019)
      Understanding diseases related to DNA requires insight into the nature of DNA dynamics, specifically how the dynamics affects the equilibrium properties. The mesoscopic Peyrard-Bishop-Dauxois model has been able to ...

    • 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 ...

    • The dynamics of DNA denaturation 

      Dahlen, Oda (Master thesis, 2013)
      Gaining knowledge and understanding of the structure and function of DNA, our genetic material, is crucial for dealing with diseases related to DNA. In 2004, the mapping of the complete human genome was accomplished, leading ...