ABOUT

We use molecular dynamics (MD) simulations and related theoretical and computational methods to investigate the self-assembly, phase behavior and interaction networks of a range of soft-matter biological systems.

In MD simulations, a complex molecular assembly is modeled by a set of interacting particles, whose evolution in time and space is calculated by numerical integration of Newton’s second law. The method is rigorously based on the laws of statistical mechanics, and allows calculation of bulk thermodynamic properties while simultaneously providing atomic-scale resolution of molecular behavior that cannot directly be obtained from analytical measurements alone.

News

  • We are hiring
    We are looking for a postdoc to work on several aspects of membrane proteins and membranes. Please write to Himanshu Khandelia: hkhandel@sdu.dk

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Research Areas

Accumulation of triolein (red) inside a lipid bilayer (blue): the first steps to lipid droplet biogenesis. See http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0012811
Accumulation of triolein (red) inside a lipid bilayer (blue): the first steps to lipid droplet biogenesis. See http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0012811
Extracts of the Perilla plant inserting into a lipid membrane. http://www.sciencedirect.com/science/article/pii/S0006349510013779 and http://pubs.acs.org/doi/abs/10.1021/jp108675b
Extracts of the Perilla plant inserting into a lipid membrane. http://www.sciencedirect.com/science/article/pii/S0006349510013779 and http://pubs.acs.org/doi/abs/10.1021/jp108675b
The binding of Glutamate and GMP to the Umami receptor, and the subsequent closure of the substrate binding pathway. See http://onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2012.08690.x/abstract
The binding of Glutamate and GMP to the Umami receptor, and the subsequent closure of the substrate binding pathway. See http://onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2012.08690.x/abstract
Coarse-grained simulation of a 25 nm lipid droplet. Triolein (red) and cholesteryl oleate (green) comprise the core, while the phospholipids (blue) form a monolayer. See http://pubs.acs.org/doi/abs/10.1021/jp506693d and http://pubs.acs.org/doi/abs/10.1021/jp503223z
Coarse-grained simulation of a 25 nm lipid droplet. Triolein (red) and cholesteryl oleate (green) comprise the core, while the phospholipids (blue) form a monolayer. See http://pubs.acs.org/doi/abs/10.1021/jp506693d and http://pubs.acs.org/doi/abs/10.1021/jp503223z
The concept of Flexoelectricity. Dipoles pointing in opposite directions in lipid leaflets lead to curvature, when an electrical potential is applied across the membrane. See http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b03439
The concept of Flexoelectricity. Dipoles pointing in opposite directions in lipid leaflets lead to curvature, when an electrical potential is applied across the membrane. See http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b03439

project Examples

Ion Pumps

We investigate the molecular basis of regulation, transport and neurological diseases in Ion Pumps. We work with the Na, K ATPase, the gastric H, K ATPase, and the novel and the unique KdpFABC channel-pump bacterial transport complex. Our simulations are in collaboration with leading experimental groups in Japan, USA, Australia and Europe.

Membrane Repair Mechanisms in Cancer Cells

Annexin proteins repair membranes in cells upon appearance of membrane lesions. Such repair mechanisms are over-expressed in cancer cells. We investigate the molecular mechanisms leading to membrane remodelling and repair in cancer cells, in collaboration with the Danish Cancer Society, the Niels Bohr’s Institute and researchers at SDU.

Method Development

We use a modified Virtual Sites algorithm to run simulations with a time step of 5 fs in MD simulations. Our modified parameters are significantly more accurate that the default parameters available in GROMACS.

Electromechanical Coupling in Lipid Membranes

Lipid membrane are liquid crystals, and therefore, electrical potential is strongly coupled to membrane mechanical properties. We investigate this coupling using molecular simulations. We showed that electrical potentials can bend membranes, and that when the electrical potential across a membrane is released, the membrane does work on the surroundings, resulting in a temperature hike in the surrounding media.