Computational biophysics of membranes and ion channels
My lab does theoretical and computational studies on the physics and functional organizational of biological membranes. We use electrodiffusion theory, stochastic dynamics, molecular dynamics, and liquid crystal theory to understand the detailed mechanism of ion and water permeation across membranes. We do simulations of the dynamic behavior of airway epithelia, with the application of understanding the physiology associated with the cystic fibrosis genetic defect, as well as understanding the basic principles of epithelial function. We do simulations of the coding behavior of neurons under realistic synaptic stimulation, to understand the logic of neural coding, at the single neuron level.
Mashl, R. J.; Jakobsson, E., End-point targeted molecular dynamics: Large-scale conformational changes in potassium channels. Biophysical Journal 2008, 94, (11), 4307-4319.
Pandit, S. A.; Chiu, S. W.; Jakobsson, E.; Grama, A.; Scott, H. L., Cholesterol packing around lipids with saturated and unsaturated chains: A simulation study. Langmuir 2008, 24, 6858-6865.
Mashl, R. J.; Jakobsson, E., Protonation states in potassium channels. Biophysical Journal 2007, 267A-267A.
Pandit, S. A.; Chiu, S. W.; Grama, A.; Jakobsson, E.; Scott, H. L., Molecular dynamics simulations of mixtures of cholesterol with POPC, DOPC, and DPPC. Biophysical Journal 2007, 548A-548A.
Pandit, S. A.; Chiu, S. W.; Jakobsson, E.; Grama, A.; Scott, H. L., Cholesterol surrogates: A comparison of cholesterol and 16 : 0 ceramide in POPC Bilayers. Biophysical Journal 2007, 92, (3), 920-927.
Pandit, S. A.; Khelashvili, G.; Jakobsson, E.; Grama, A.; Scott, H. L., Lateral organization in lipid-cholesterol mixed bilayers. Biophysical Journal 2007, 92, (2), 440-447.
Pandit, S.; Chiu, S. W.; Jakobsson, E.; Grama, A.; Scott, H. L., Molecular dynamics simulation of a dioleylphosphatidylserine lipid bilayer. Biophysical Journal 2007, 548A-548A.
Tilson, J. L.; Rendon, G.; Ger, M. F.; Jakobbson, E. MotifNetwork: A grid-enabled workflow for high-throughput domain analysis of biological sequences: Implications for annotation and study of phylogeny, protein interactions, and intraspecies variation, In Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007.
Varma, S.; Jakobsson, E., How does the C2 domain "calcium trigger" work? Insights from molecular dynamics simulations. Biophysical Journal 2007, 595A-595A.
Varma, S.; Jakobsson, E., The cPLA(2) C2 alpha domain in solution: Structure and dynamics of its Ca2+-activated and cation-free states. Biophysical Journal 2007, 92, (3), 966-976.
Tseng, T. T.; McMahon, A. M.; Zahm, R. J.; Pacold, M. E.; Jakobsson, E., Calcium channel auxiliary subunits. Journal of Molecular Microbiology and Biotechnology 2006, 11, (6), 326-344.
Tasneem A, Iyer LM, Jakobsson E, and Aravind L. 2005. Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels. Genome Biol. 6(1):R4.