Eric Jakobsson
Description
- Title: Professor Emeritus
- Group: Computational Multiscale Nanosystems
- Status: Beckman Part-time Faculty
- Home: National Center for Supercomputing Applications (NCSA)
Address
- 3261 Beckman Institute
- 405 North Mathews Avenue
- Urbana, Illinois 61801
Contact
Honors
Elected Fellow of the American Physical Society (1994); U of I Advising Award; Tau Beta Pi Engineering Academic Honorary Society.
Research
Jakobsson's Beckman Institute research areas include: Computer-aided design of components for nanodevices, structure of biological membranes, structure-function relationships in biological and synthetic ion channels, computer-aided drug research, comparative genomics of microbes, use of technology to introduce quantitative approaches to biology education.
Publications
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2016
- Barati-Farimani, A.; Tajkhorshid, E.; Aluru, N.; Jakobsson, E., Behavior of Water in 3-D Confinement: Implications for Macromolecular Function. Biophysical Journal 2016, 110, (3), 341a-341a.
- Farimani, A. B.; Aluru, N. R.; Tajkhorshid, E.; Jakobsson, E., Computational Approach to Designing Antibody for Ebola Virus. Biophysical Journal 2016, 110, (3), 537a-537a.
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2015
Sun, J.; Jakobsson, E.; Wang, Y.; Jeffrey Brinker, C. J., Nanoporous Silica-Based Protocells at Multiple Scales for Designs of Life and Nanomedicine. Life 2015, 5, (1), 214-229.
Kim, T. J.; Joo, C.; Seong, J.; Vafabakhsh, R.; Botvinick, E. L.; Berns, M. W.; Palmer, A. E.; Wang, N.; Ha, T.; Jakobsson, E.; Sun, J.; Wang, Y., Distinct Mechanisms Regulating Mechanical Force-Induced Ca2+ Signals at the Plasma Membrane and the ER in Human MSCs. Elife 2015, 4, DOI:ARTN e04876 DOI:10.7554/eLife.04876.
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2014
Fogarty, J. C.; Chiu, S. W.; Kirby, P.; Jakobsson, E.; Pandit, S. A., Automated Optimization of Water-Water Interaction Parameters for a Coarse-Grained Model. Journal of Physical Chemistry B 2014, 118, (6), 1603-1611, DOI: 10.1021/jp409545x.
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2013
Li, Y. H.; Liu, H.; Rata, I.; Jakobsson, E., Building a Knowledge-Based Statistical Potential by Capturing High-Order Inter-Residue Interactions and Its Applications in Protein Secondary Structure Assessment. Journal of Chemical Information and Modeling 2013, 53, (2), 500-508.
Zhou, H.; Jakobsson, E., Predicting Protein-Protein Interaction by the Mirrortree Method: Possibilities and Limitations. Plos One 2013, 8, (12), DOI: 10.1371/journal.pone.0081100.
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2011
Zhao, G. J.; Subbaiah, P. V.; Chiu, S. W.; Jakobsson, E.; Scott, H. L., Conjugated double bonds in lipid bilayers: A molecular dynamics simulation study. Chemistry and Physics of Lipids 2011, 164, (3), 251-257.
Li, Y. H.; Rata, I.; Jakobsson, E., Sampling Multiple Scoring Functions Can Improve Protein Loop Structure Prediction Accuracy. Journal of Chemical Information and Modeling 2011, 51, (7), 1656-1666.
Rendon, G.; Kantorovitz, M. R.; Tilson, J. L.; Jakobsson, E., Identifying Bacterial and Archaeal Homologs of Pentameric Ligand-Gated Ion Channel (pLGIC) Family Using Domain-Based and Alignment-Based Approaches. Channels 2011, 5, (4), 325-344.
Zhao, G. J.; Subbaiah, P. V.; Mintzer, E.; Chiu, S. W.; Jakobsson, E.; Scott, H. L., Molecular Dynamic Simulation Study of Cholesterol and Conjugated Double Bonds in Lipid Bilayers. Chemistry and Physics of Lipids 2011, 164, (8), 811-818.
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2010
Rendon, G.; Ger, M. F.; Kantorovitz, R.; Natarajan, S.; Tilson, J.; Jakobsson, E., Understanding the "Horizontal Dimension" of Molecular Evolution to Annotate, Classify, and Discover Proteins with Functional Domains. Journal of Computer Science and Technology 2010, 25, (1), 82-94.
Rata, I. A.; Li, Y. H.; Jakobsson, E., Backbone Statistical Potential from Local Sequence-Structure Interactions in Protein Loops. Journal of Physical Chemistry B 2010, 114, (5), 1859-1869.
Ger, M. F.; Rendon, G.; Tilson, J. L.; Jakobsson, E., Domain-Based Identification and Analysis of Glutamate Receptor Ion Channels and Their Relatives in Prokaryotes. PLOS One 2010, 5, (10).
Lee, K. I.; Toghraee, R.; Jakobsson, E.; Ravaioli, U., A Study of Brownian Dynamics Simulation for Ion Transport Through a Transmembrane Pore with a Molecular Adapter. Journal of Computational and Theoretical Nanoscience 2010, 7, (12), 2547-2554.
Li, Y. H.; Rata, I.; Chiu, S. W.; Jakobsson, E., Improving predicted protein loop structure ranking using a Pareto-optimality consensus method. BMC Structural Biology 2010, 10.
Natarajan, S.; Mashl, J.; Jakobsson, E., Evolutionary coupling in the K(V)1.2-beta(2) complex. Channels 2010, 4, (5), 355-374.
Toghraee, R.; Lee, K. I.; Papke, D.; Chiu, S. W.; Jakobsson, E.; Ravaioli, U., Simulation of Ion Conduction in alpha-Hemolysin Nanopores with Covalently Attached beta-Cyclodextrin Based on Boltzmann Transport Monte Carlo Model. Journal of Computational and Theoretical Nanoscience 2010, 7, (12), 2555-2567.
Chiu, S. W.; Scott, H. L.; Jakobsson, E., A Coarse-Grained Model Based on Morse Potential for Water and n-Alkanes. Journal of Chemical Theory and Computation 2010, 6, (3), 851-863.
Falkenberg, C. V.; Jakobsson, E., A Biophysical Model for Integration of Electrical, Osmotic, and pH Regulation in the Human Bronchial Epithelium. Biophysical Journal 2010, 98, (8), 1476-1485.
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2009
Jakobsson, E., Biology: Using a Ubiquitous Knowledge Environment to Integrate Teaching, Learning, and Research in Biology and Chemistry. In Ubiquitous Learning, Cope, B.; Kalantzis, M., Eds. University of Illinois Press: Champaign, IL, 2009; pp 216-229
Jakobsson, E., Biology: Using a Ubiquitous Knowledge Environment to Integrate Teaching, Learning, and Research in Biology and Chemistry. In Ubiquitous Learning, Cope, B.; Kalantzis, M., Eds. University of Illinois Press: Champaign, IL, 2009; pp 216-229
Chiu, S. W.; Pandit, S. A.; Scott, H. L.; Jakobsson, E., An Improved United Atom Force Field for Simulation of Mixed Lipid Bilayers. Journal of Physical Chemistry B 2009, 113, (9), 2748-2763.
Natarajan, S.; Jakobsson, E., Functional equivalency inferred from "authoritative sources" in networks of homologous proteins. Public Library of Science 2009, 4, (6), e5898.
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2008
Pandit, S. A.; Chin, S. W.; Jakobsson, E.; Scott, H. L., Atomistic and mean field simulations of lateral organization in membranes. In Computational Modeling of Membrane Bilayers, Elsevier Academic Press Inc: San Diego, 2008; Vol. 60, pp 281-312.
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, (13), 6858-6865.
Sendlinger, S. C.; DeCoste, D. J.; Dunning, T. H.; Dummitt, D. A.; Jakobsson, E.; Mattson, D. R.; Wiziecki, E. N., Transforming chemistry education through computational science. Computing in Science & Engineering 2008, 10, (5), 34-39.
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.
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2007
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.
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.
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.
Mashl, R. J.; Jakobsson, E., Protonation states in potassium channels. Biophysical Journal 2007, 267A-267A.
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2006
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.
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2004
Varma S.; Jakobsson E., Ionization States of Residues in OmpF and Mutants: Effects of Dielectric Constant and Interactions Between Residue. Biophysics Journal 2004, 86, (2), 690-704.
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2003
Chiu S.W., Vasudevan S., Jakobsson E., Mashl R.J., and Scott H.L. (2003), "Structure of Sphingomyelin Bilayers: A Simulation Study," Biophysics Journal 85/6, pp. 3624-3635.
Shealy, R.T., Murphy, A.D., Ramarathnam, R., Jakobsson, E., and Subramaniam, S. (2003), "Sequence-function Analysis of the K+-selective Family of Ion Channels Using a Comprehensive Alignment and the KcsA Channel Structure," Biophysics Journal, 84/5, pp. 2929-2942.
Joseph, S., Mashl, R.J., Jakobsson, E., and Aluru, N.R. (2003), "Electrolytic Transport in Modified Carbon Nanotubes," Nano Lettters (Communication), 3/10, pp. 1399-1403.
Mashl, R.J., Joseph, S., Aluru, N.R., and Jakobsson, E. (2003), "Anomalously Immobilized Water: A New Water Phase Induced by Confinement in Nanotubes," Nano Letters (Communication), 3/5, pp. 589-592.
Press
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