Curriculum Vitae
Ulf Sigurd Bror Ryde, 631209-3955; Born December 9, 1963 in Lund, Sweden
Married to Anna-Carin Gustafsson, September 12, 1992
At the same time, I removed Pettersson from my surname (first articles published as U. Ryde-Pettersson)
Four children: Martin Wilhelm Sigurd, April 28, 1993 Frej Edvard Bror, September 28, 1995
Embla Anna Kristina, July, 11, 1998 Tor Axel Lennart, December, 6, 1999
Education and titles
Schools: Tunaskolan, Lund 1970–72; Magnus Stenbocksskolan, Helsingborg 1972–79
Science program (Naturvetenskaplig linje) Nicolaiskolan, Helsingborg 1979–82
University and postgraduate courses at Lund University, in total 466 marks (= study weeks):
chemistry (162), biology (78), mathematics (69), physics (49), computer science (35), philosophy
(34), earth science (20), mathematical statistics (20), numerical analysis (19).
Bachelor of Science in Chemistry Lund University, December 12, 1986.
Doctor of Philosophy in Biochemistry, October 9, 1991; Lund University. Supervisors Profs. G.
Pettersson and P.-Å. Albertsson. Thesis: “A theoretical treatment of damped oscillations in
biochemical reaction systems with applications to the photosynthetic oscillations”.
Docent in theoretical chemistry, March 20, 1996; Lund University.
Professor in theoretical chemistry, March 1, 2004.
Positions
Deputy as research assistant (forskningsassistent); Lund, 861001–861231, 870701–871231
Graduate student allowance (utbildningsbidrag); Lund, 870101–870630, 880101–901031
Graduate student position (doktorandtjänst); Lund University, 901101–911101
Postdoctoral scholarship from IBM, 911101–920630
Assistant professor (forskarassistent); Lund University, 920701–000131
Associate professor (lektor); Lund University; 000201–040229
Senior research position (rådsforskare NFR/VR) in bioinorganic chemistry, 2001–2007
Full professor in theoretical chemistry, Lund University; 040301–
Paternal leave: 931011–940721 (50 %) 960513–961011 (100 %)
990406–990818 (80 %) 001101–010108 (100%)
Supervision
Supervisor of 21 PhD students since 1995, including 4 PhD students currently.
Co-supervisor of 13 PhD students since 1995.
Counsellor for 19 post-doctoral scientists since 1996.
Supervised 14 BSc, MSc, diploma, and project works since 1996.
Host of 33 visiting scientist and students since 2006.
Commissions of trust
Faculty opponent for doctoral theses 19 times in Sweden, Finland, Denmark, Norway, Germany,
Romania, Belgium, Italy and France, 2000–
Member of the graduation committee for doctoral theses 29 times in Sweden and Finland, 1998–
External adviser in professor recruitments in Aarhus, Odense, Örebro, Stockholm, Uppsala and
Luisville, 7 times, 2006–.
Referee in international journals typically ~50 manuscripts each year in ~85 different international
journals, including Angew. Chem., ChemBioChem, J. Am. Chem. Soc., JBIC, J. Phys. Chem.,
Nature Chem., Nature Commun., PhysChemChemPhys, Proc. Natl. Ac. Sci. USA, Science.
Expert adviser for applications for the European Research Council, SSF, Nobel Committee, Welcome Trust, PRACE, Swedish Research Council, German Research Council, French Research Council,
Israel Science Foundation, Estonian Research Council, Hungarian Scientific Research Fund,
Polish National Science Centre, and US–Israel binational science foundation.
Lecture invitations
>90 since 1994 (typically ~4 year); the latest was 26th Congress of International Union of
Crystallography, Melbourne.
Organisation of conferences
Member of the programme and local organising committees of EUROBIC-6, Lund, July 2002.
Chairman of the organising committee of QBIC-2, Örenäs, July, 27–29, 2002.
Member of the international organising committee of QBIC-3, Český Krumlov, June 25-28. 2011.
Member of organising committee for the Trends in Inorganic Chemistry meeting, Lund May 22, 2014.
Member of the international organising committee of QBIC-4, Bath, Sept. 3–6. 2018.
Evaluations
My research was graded Excellent in the evaluation of theoretical chemistry in Sweden (VR) 2002 and
Excellent/Outstanding in the evaluation of the chemical centre at Lund University 2007.
Administration merits
Member of the department board, Biochemistry, Lund, 1989–1991.
Safety controller (skyddsombud), Theoretical Chemistry, Lund, 1997–1999.
Fire safety controller (brandskyddsombud), Theoretical Chemistry, Lund, 1999–2013.
Responsible for the teaching (huvudlärare), Theoretical Chemistry, Lund, 2000–2002.
Director (studierektor) of Postgraduate Studies, Chemical Centre, Lund (~150 students), 2000–2001
Evaluator of postgraduate education at the Science Faculty at Lund University, Autumn, 2002.
Responsible for the department seminars, Theoretical Chemistry, Lund, 2010–.
Subject representative, Theoretical Chemistry, Lund, 2012–.
Pedagogic qualifications
Teaching at graduate and postgraduate levels 1987, 1988, and every year since 1995.
I have taken 10 Pedagogic courses at Lund University, in total about 11 weeks (1993–).
Responsible teacher (kursansvarig) for Kem016, 1998.
Design of 3 graduate and 3 postgraduate courses.
Author of one compendium (Theoretical chemistry for novices) and study questions and study material
for 4 courses (1995–).
Author of 14 popular information guides.
Current funding
Swedish Research council: Studies of enzymes with computational chemistry (2023–2026, 3 600 000
SEK).
Swedish Research council and Swedish Agency for Economic and Regional Growth (SREss3), Simple
and reliable neutron crystallography, 2021–2024, 7 850 000 + 1 000 000 SEK (with Esko Oksanen
and Thomas H. Rod, ESS).
Publications
303 published articles in refereed journals, including 22 book chapters or review articles.
The actual status of the manuscripts can be seen in http://www.teokem.lu.se/~ulf/references.html.
22243 citations, h-index 80, i10-index 247 (9432 citations, h-index 31 and i10-index 177 since 2018),
according to Google Scholar, October 2023.
Lecture 32: Ulf Ryde
Recent development in quantum refinement of protein structures
U. Ryde,a K. Lundgren,a E. Oksanenb
a Department of Theoretical Chemistry, Lund University, P.O. Box 124, 221 00 Lund, Sweden, b European Spallation Source ESS ERIC, P. O. Box 176, SE-221 00 Lund, Sweden
Ulf.Ryde@teokem.lu.se
Keywords: X-ray crystallography, cryo-EM, quantum refinement, protein structures, protonation, nitrogenase, pMMO, MnSOD.
In standard crystallographic refinement of biomacromolecules, the experimental data is normally not enough to unambiguously decide the positions of all atoms. Therefore, the crystallographic data are supplemented by a set of empirical restraints that ensure that bond lengths and angles make chemical sense. In order to obtain more accurate results, we have suggested that this potential is replaced by more accurate quantum-mechanical calculations for a small, but interesting part of the protein, giving the method of quantum refinement [1]. We have shown that quantum refinement can locally improve crystal structures [2], decide protonation state of metal-bound ligands [3–6], oxidation state of metal sites [7,8], detect photoreduction of metal ions [7,9] and solve scientific problems regarding what is really is seen in crystal structures [9–11]. Several other groups have implemented this and similar approaches [12]. In this talk, I will describe the method, show some applications and discuss recent developments, e.g. to cryogenic electron microscopy structures. I will also describe the fragment Hirshfeld-atom refinement approach [13] and its application to proteins.
[1] Ryde, U., Olsen, L., Nilsson, K., (2002) J. Comput. Chem. 23, 1058.
[2] Ryde, U., Nilsson, K. (2003) J. Am. Chem. Soc., 125, 14232.
[3] Nilsson, K., Ryde, U. (2004) J. Inorg. Biochem., 98, 1539
[4] Cao, L., Caldararu, O., Ryde, U. (2017) J. Phys. Chem B, 121, 8242.
[5] Cao, L., Caldararu, O., Ryde, U. (2018) J. Chem. Theory Comput., 14, 6653.
[6] Caldararu, O., Feldt, M., Cioloboc, D., van Severen, M.-C., Starke, K., Mata, R. A., Nordlander, E., Ryde, U. (2018) Sci. Rep. 8, 4684
[7] Rulíšek, L., Ryde, U. (2006) J. Phys. Chem. B, 110, 11511
[8] Cao, L., Börner, M. C., Bergmann, J., Caldararu, O. & Ryde, U. (2019) Inorg. Chem., 58, 9672.
[9] Söderhjelm, P., Ryde, U. (2006) J. Mol. Struct. Theochem, 770, 199
[10] Cao, L., Caldararu, O., Rosenzweig, A. C., Ryde, U. (2018) Angew. Chem. Int. Ed., 57, 162.
[11] Bergmann, J., E. Oksanen & Ryde, U. (2021) J. Biol. Inorg. Chem., 26, 341.
[12] Bergmann, J., E. Oksanen, Ryde, U. (2022) Curr. Opin. Struct. Biol., 72, 18
[13] J. Bergmann, M. Davidson, E. Oksanen, U. Ryde, D. Jayatilaka (2020) IUCrJ, 7, 158.