Professor Emeritus of Biochemistry
Professor Emeritus of Molecular and Integrative Physiology
Professor Emeritus of Biophysics and Computational Biology
Professor Emeritus of Bioengineering
Professor Emeritus of Neuroscience
Beckman Institute for Advanced Science and Technology
Director, National Center for Biomimetic Nanoconductors
Senior Research Scientist, National Center for Supercomputing Applications
B.A. 1959 Columbia College
B.S. 1960 Chemical Engineering, Columbia University School of Engineering
Ph.D. 1969 Physics, Dartmouth College
Postdoc. 1969-1971 Department of Physiology, Case Western Reserve University School of Medicine
Computational studies of biological transport: understanding and engineering life at the interface
Two major lines of effort in computational biochemistry are: 1) the use of simulations to understand the physical chemical bases of biomolecular function, and 2) bioinformatics, the use of advanced information technology to extract meaning from databases containing information on sequence, structure, and function. In our laboratory we use both bioinformatics and simulation to understand biological transport.
In one line of work, we are doing simulations of patches of lipid bilayer membranes. The initial phase of this work has involved establishing the basic technology for molecular dynamics simulations of membranes, such as boundary conditions, force fields, and statistical methods for conformational sampling. More recently we have embarked on studies of heterogenous membranes and the development of multiscale methods to.
In a second line of work, we are studying permeation in ion channels. We do sequence- and physics-based structural modeling, simulation studies of permeation, and studies on sequence-function relationships.
Finally, we are working with engineers and materials scientists to transform our understanding into the design of devices that utilize the technology of self-assembly of biological or biomimetic transporters on nanoporous silicon.
Varma, S., and E. Jakobsson. 2004 Ionization states of residues in OmpF and mutants: effects of dielectric constant and interactions between residues. Biophys J. 86:690-704
Pandit, S. A., Vasudevan, S., Chiu, S. W., Mashl, R. J., Jakobsson, E. and L. R. Scott 2004 Sphingomyelin-Cholesterol Domains in Phospholipid Membranes: Atomistic Simulation. Biophys. J. 87:1092-1100
Pandit SA, Jakobsson E, Scott HL. 2004 Simulation of the early stages of nano-domain formation in mixed bilayers of sphingomyelin, cholesterol, and dioleylphosphatidylcholine. Biophys J. (5):3312-22
Malmberg NJ, Varma S, Jakobsson E, Falke JJ 2004 Ca2+ activation of the cPLA2 C2 domain: ordered binding of two Ca2+ ions with positive cooperativity. Biochemistry. (51):16320-8
Tasneem A, Iyer LM, Jakobsson E, 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. 2005;6(1):R4
Varma, S., Chiu, S.W., and E. Jakobsson. 2005 The influence of amino acid protonation states on molecular dynamics simulations of bacterial porin OmpF. Biophys. J. in press