In many complex molecular systems, including proteins and lipid membranes, diffusion processes do not follow the simple linear law that we all know from physics and chemistry textbooks. Such diffusion processes are called anomalous. The most frequent form is subdiffusion, in which the average displacement grows more slowly than any linear function of time. We are working on various models for subdiffusion in biological systems and calibrate them using experimental data and atomic-scale simulations.
Most of today’s theoretical work on proteins is focused on empirical models at the atomic or near-atomic scale. We are pursuing an alternative approach of developing minimal models that describe specific important phenomena, such as the secondary structure of proteins or the wide spread of time scales in protein dynamics. The main advantage of these minimal models is to provide more insight into the behavior of proteins.
Elastic Network Models are coarse-grained models that describe the flexibility of a protein as a function of its structure. They have found numerous applications in structural biology due to their simplicity and low computational cost. We have been developing, evaluating, and applying ENMs for many years, with applications including in particular the interpretation of low-resolution protein structures and the analysis of conformational transitions.
The complexity of computing technology has made most of computer-aided research irreproducible: since nobody, not even the authors, knows exactly which software was used to prepare a published figure or dataset, it is impossible to re-do the computations exactly and therefore impossible to check if mistakes were made. We are participating in the world-wide efforts to make computer-aided research reproducible, focusing on the specific needs of biomolecular simulation.
A major technical challenge in publishing biomolecular simulation data is the lack of suitable file formats for many data types. It is difficult to publish anything other than molecular structures and simulation trajectories in a form that other scientists can use easily. We are developing data models and data formats for all aspects of molecular simulation.