Jan Halborg Jensen – University of Copenhagen

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Center for Synthetic Biology > Meet the Researchers > Jan Halborg Jensen

Jan Halborg Jensen


Scientific Computing Group
Department of Chemistry
Faculty of Science

More information about Jan's research here.

Jan Jensen's research is primarily in the area of biocomputational chemistry - at the intersection between quantum chemistry and structural biology/ bioinformatics. The work involves, in roughly equal parts, software development and applications to biochemistry.

Computational methods aid in the rational design of objects at the nano-scale: complex experimental data can be rationalized and the outcome of expensive or time-consuming experiments can be predicted.

More specifically our research program has three main foci:
(1) Development and application of the PROPKA program to the rational design of more stable proteins. Enzymes are increasingly used as industrial catalysts, such as in the production of bioethanol, but may need to be modified to work better at industrial conditions such as extreme pH values. The project uses modeling programs developed in house to help guide these modifications by predicting at what pH values the enzymes are most stable and work best.

(2) Development of quantum chemical and QM/MM methods and application to enzyme catalysis. The description of chemical bonding requires quantum mechanics, which is computationally expensive, and difficult to apply to molecules as large as proteins. The project is aimed at the development of quantum mechanical methods that are fast enough to be applied to proteins.

(3) Extension of PROPKA to protein-ligand binding and drug design. This program can rapidly and accurately predict the pH-dependent physicochemical properties of a protein, such as stability and activity.


2011-present Deputy Head of Department in charge of teaching 
2009-present Professor of Bio-Computational Chemistry, Department of Chemistry, University of Copenhagen 
2006-2009 Associate Research Professor/Skou Fellow, Department of Chemistry, University of Copenhagen
2003-2006 Associate Professor of Chemistry and Applied Mathematical & Computational Sciences, University of Iowa
2002-2003 Assistant Professor, Interdisciplinary Graduate Degree Program in Applied Mathematical and Computational Sciences, University of Iowa.
1997-2003 Assistant Professor, Department of Chemistry, University of Iowa
1996-1997 Postdoctoral Associate, Iowa State University
1995 Ph.D. in Theoretical Chemistry from Iowa State University, Ames, Iowa.

Collaborations within the Center for Synthetic Biology
Karen Martinez
Jesper Nygård

Selected Scientific Publications
Upadhyay, S., Frederiksen, R., Lloret, N., De Vico, L., Krogstrup, P., Jensen, J.H., Martinez, K.L., and Nygard, J.Indium arsenide nanowire field-effect transistors for pH and biological sensing. Applied Physics Letters 104, 5, doi:10.1063/1.4878659 (2014).

Lloret, N., Frederiksen, R.S., Møller, T.C., Rieben, N.I., Upadhyay, S., De Vico, L., Jensen, J.H., Nygard, J., and Martinez, K.L. Effects of buffer composition and dilution on nanowire field-effect biosensors. Nanotechnology 24, doi:10.1088/0957-4484/24/3/035501(2013).

De Vico, L., Iversen, L., Sorensen, M.H., Brandbyge, M., Nygard, J., Martinez, K.L., and Jensen, J.H. Predicting and rationalizing the effect of surface charge distribution and orientation on nano-wire based FET bio-sensors. Nanoscale 3, 3635-3640, doi:10.1039/c1nr10316d (2011).

De Vico, L., Sorensen, M.H., Iversen, L., Rogers, D.M., Sorensen, B.S., Brandbyge, M., Nygard, J., Martinez, K.L., and Jensen, J.H. Quantifying signal changes in nano-wire based biosensors.Nanoscale 3, 706-717, doi:10.1039/c0nr00442a (2011).

Jensen, J.H. Molecular modeling basics. London: CRC Press LLC (2010).

Bas, D.C., Rogers, D.M., Jensen, J.H. Very fast prediction and rationalization of pKa values for protein–ligand complexes. Proteins: Structure, Function, and Bioinformatics 73(3), 765-783, doi:10.1002/prot.22102 (2008).

Li, H., Robertson, A.D., Jensen, J.H. Very fast empirical prediction and rationalization of protein pKa values. Proteins: Structure, Function, and Bioinformatics 61(4), 704-721, doi:10.1002/prot.20660 (2005).

Schmidt, M.W., Baldridge, K.K., Boatz, J.A., Elbert, S.T., Gordon, M.S., Jensen, J.H., Koseki, S., Matsunaga, N., Nguyen, K.A., Su, S., Windus, T.L., Dupuis, M., Montgomery, J.A. General atomic and molecular electronic structure system. Journal of Computational Chemistry 14(11), 1347-1363 doi:10.1002/jcc.540141112 (1993).