Improving double-ended transition state searches for soft-matter systems

Energy landscapes for a modified repulsive Weeks-Chandler-Andersen potential

The short-range nature of the repulsive Weeks-Chandler-Anderson (WCA) potential can create free particles/rattlers in a condensed system. The presence of rattlers complicates the analysis of the energy landscape due to extra zero-frequency normal modes. By employing a long-range Gaussian tail modification, we remove the rattlers without changing the structure and the dynamics of the system, and successfully describe the potential energy landscape in terms of minima and transition states. This coarse-grained description of the landscape and the dynamical properties of the modified potential exhibit characteristic signatures of glass-forming liquids. However, we show that despite having qualitatively similar behaviour, the modified WCA potential is less frustrated compared to its attractive counterpart.

Energy Landscape for the Membrane Fusion Pathway in Influenza A Hemagglutinin From Discrete Path Sampling

The conformational change associated with membrane fusion for Influenza A Hemagglutinin is investigated with a model based upon pre- and post-fusion structures of the HA2 component. We employ computational methods based on the potential energy landscape framework to obtain an initial path connecting these two end points, which provides the starting point for refinement of a kinetic transition network. Here we employ discrete path sampling, which provides access to the experimental time and length scales via geometry optimization techniques to identify local minima and the transition states that connect them. We then analyse the distinct phases of the predicted pathway in terms of structure and energetics, and compare with available experimental data and previous simulations. Our results provide the foundations for future work, which will address the effect of mutations, changes in pH, and incorporation of additional components, especially the HA1 chain and the fusion peptide.