Leonor Saiz, PhD
| Assistant Professor & Lab Head, Department of Biomedical Engineering, University of California, Davis |  |
Department of Biomedical Engineering
College of Engineering
University of California
451 East Health Sciences Drive
Davis, CA 95616
Office: 2315 GBSF
Lab: 3402 GBSF
Phone: +1 530-752-6700 (Office)
Phone: +1 530-754-0325 (Lab)
Fax: +1 530-752-7156
E-mail: lsaiz@ucdavis.edu
Join the lab: There are great opportunities for talented undergraduate, graduate students and postdocs to join the group. To apply for a postdoctoral position send an e-mail with a summary of research interests and experience, a complete CV including list of publications, and the names and contact information of 2-3 references to lsaiz@ucdavis.edu. Undergraduate and graduate students can contact me at lsaiz@ucdavis.edu. See below: Openings. New Courses: I will be teaching an interdisciplinary graduate course on Molecular and Multiscale Approaches to Systems Biology during the Spring 2008 Quarter (see below: Teaching). Note: advertised as BIM 289C Part 1 in the UC Davis Spring 2008 class schedule and registration guide. October 2007: I have just moved to the Biomedical Engineering Department of the University of California, Davis. The brand new lab for our group is up and running!
Research Interests
Molecular Systems Biology
The research of our laboratory focuses on the integration of the molecular properties of the cellular components into the dynamics of relevant cellular processes, including signal transduction and gene regulation and their combined networks, with special interest in those altered in cancer and other diseases. Integration of the events that follow from the sensing of extracellular signals to the resulting cellular responses is needed to faithfully understand the functioning of the cell as a unit. Our work is highly interdisciplinary, drawing from techniques and tools from chemistry, physics, mathematics, computer science, biomedical sciences, and engineering; a key feature required for successful approaches to molecular systems biology. We combine computational and theoretical approaches together with experimental data to build models for accurately predicting the cellular behavior in terms of molecular properties. This type of models is also used "in reverse" to infer detailed molecular properties, such as the in vivo DNA mechanics, from cellular physiology measurements. In general, we want to understand and follow the impact of molecular perturbations in the cellular components, such as a mutation in a protein or interactions with small molecules or drugs, through the different cellular processes up to the cellular behavior. [read more... Leonor Saiz profile at Biomedical Engineering]
Publications
Articles in journals
25. L. Saiz and J. M. G. Vilar, Protein-protein/DNA interaction networks: versatile macromolecular structures for the control of gene expression,
IET Systems Biology, in press (2008). 24. L. Saiz and J. M. G. Vilar, Ab initio thermodynamic modeling of distal multisite transcription regulation,
Nucleic Acids Research, 30, 726-731 (2008). 23. L. Saiz and J. M. G. Vilar, Multilevel deconstruction of the in vivo behavior of looped DNA-protein complexes,
PLoS One, 2(4): e355. doi:10.1371/journal.pone.0000355 (2007). 22. S. Vemparala, L. Saiz, R. G. Eckenhoff, and M. L. Klein, Partitioning of anesthetics into a lipid bilayer and their interaction with membrane-bound peptide bundles,
Biophys. J., 91, 2815-2825 (2006). 21. J. M. G. Vilar and L. Saiz, Multiprotein DNA looping, Phys. Rev. Lett., 96, 238103 (2006). 20. L. Saiz and J. M. G. Vilar, DNA looping: the consequences and its control, Curr. Opin. Struct. Biol., 16, 344-350 (2006). 19. L. Saiz and J. M. G. Vilar, Stochastic dynamics of macromolecular-assembly networks, Nature/EMBO Molecular Systems Biology, 2, doi:10.1038/msb4100061 (2006). 18. Leonor Saiz, J. Miguel Rubi, and Jose M.G. Vilar, Inferring the in vivo looping properties of DNA,
Proc. Natl. Acad. Sci. USA, 102, 17642-17645 (2005).
17. Jose M.G. Vilar and Leonor Saiz, DNA looping in gene regulation: From
the assembly of macromolecular complexes to the control of
transcriptional noise,
Current Opinion in Genetics & Development, 15, 136-144
(2005).
16. Leonor Saiz and M.L. Klein, The
transmembrane domain of the
acetylcholine receptor: Insights from simulations on synthetic peptide models,
Biophys. J., 88, 959-970 (2005).
15. M. Pickholz, Leonor Saiz, and M.L.
Klein, Concentration
effects of volatile anesthetics on the properties of model membranes: A
coarse-grain approach,
Biophys. J., 88, 1524-1534 (2005).
14. Leonor Saiz, S. Bandyopadhyay, and
M.L. Klein, Effect
of the pore region of a transmembrane ion-channel on the physical
properties of a simple membrane,
J. Phys. Chem. B, 108, 2608-2613 (2004).
13. L. Koubi, Leonor Saiz, M. Tarek,
D. Scharf, and M.L. Klein, Influence
of anesthetic and nonimmobilizer molecules on the physical properties
of a polyunsaturated lipid bilayer,
J. Phys. Chem. B 107, 14500-14508 (2003). (Abstract)
12. Leonor Saiz, S. Bandyopadhyay, and
M.L. Klein, Towards
an understanding of complex biological membranes from atomistic
molecular dynamics simulations,
Bioscience Reports 22, 151-173 (2002). (Abstract)
11. Leonor Saiz and M.L. Klein, Computer
simulation studies of model biological membranes,
Accounts of Chemical Research 35, 482-489 (2002). (Abstract)
10. E. Guardia, J. Marti, J.A. Padro,
Leonor Saiz, and A.V. Komolkin, Dynamics
in hydrogen bonded liquids: water and alcohols,
J. Mol. Liq. 96-97, 3-17 (2002). (Abstract)
9. Leonor Saiz and M.L. Klein, Electrostatic
interactions in a neutral model phospholipid bilayer by molecular
dynamics simulations,
J. Chem. Phys. 116, 3052-3057 (2002). (Abstract)
This work appears also in the Membrane Biophysics section of the
Virtual Journal of Biological Physics Research (Vir.
J. Bio. Phys. Res. 3, 18 (2002)).
8. Leonor Saiz and M.L. Klein, Influence
of highly polyunsaturated lipid acyl chains of biomembranes on the NMR
order parameters,
J. Am. Chem. Soc. 123, 7381-7387 (2001). (Abstract)
7. Leonor Saiz and M.L. Klein, Structural
properties of a highly polyunsaturated lipid bilayer from molecular
dynamics simulations,
Biophys. J. 81, 204-216 (2001). (Abstract)
This work appears also on the cover
of the July 2001 issue of the Biophys. J.
6. Leonor Saiz, J. M. G. Vilar, and J. Miguel
Rubi, Field-induced
force-suppression in ferromagnetic colloids,
Physica A 293, 51-58 (2001). (Abstract)
5. Leonor Saiz, J.A. Padro, and E.
Guardia, Structure
of liquid ethylene glycol: A molecular dynamics simulation study
with different force fields,
J. Chem. Phys. 114, 3187-3199 (2001). (Abstract)
4. Leonor Saiz, E. Guardia, and J.A.
Padro, Dielectric
properties of liquid ethanol. A computer simulation study,
J. Chem. Phys. 113, 2814-2822 (2000). (Abstract)
3. Leonor Saiz, J.A. Padro, and E.
Guardia, Dynamics
and hydrogen bonding in liquid ethanol,
Mol. Phys. 97, 897-905 (1999). (Abstract)
2. J.A. Padro, Leonor Saiz, and E.
Guardia, Hydrogen
bonding in liquid alcohols: A computer simulation study,
J. Molec. Structure 416, 243-248 (1997). (Abstract)
J. Phys. Chem. B 101, 78-86 (1997). (Abstract)
Other Publications
1. L.
Saiz, Computer simulation study of the structure and dynamical properties of liquid alcohols.
Ph.D. Thesis (Physics). Publisher: University of Barcelona, Spain
(1998).
Upcoming Invited Talks
Multiscale modeling of biological networks
XI International Workshop on Complex Systems. Andalo, Trento (Italy); March 17-20,
2008.
Stochastic dynamics of macromolecular-assembly networks
PepCon 2008: From concept to market. Shenzhen (China); April 22-24,
2008.
Selected Invited Talks
Multilevel modeling of biological processes,
Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY; May,
2007.
Stochastic dynamics of macromolecular-assembly networks,
X International Workshop on Disordered Systems. Molveno, Trento (Italy); March 18-21,
2006.
Modeling of biological membranes,
International Summer School "Modeling
of
Biomolecular Systems". Helsinki, Finland; May 30-June 1,
2005.
Computational studies of lipid interactions with
peptides and small molecules in
phopholipid bilayers,
Meeting on "Biological
Membranes: Emerging Challenges at the Interface between Theory,
Computer
Simulation, and Experiment". Sun Valley, Idaho; 20-25 June,
2004.
Modeling of biological membranes,
2nd European School on
Computational Chemistry, Reaction, and Molecular Dynamics.
Barcelona, Spain; 23-28 June, 2003.
Stucture of the pore forming region of
the nicotinic acetylcholine receptor ion channel,
Symposium on Structure-Function correlation for Biological Ion channels,
225th ACS National Meeting, New Orleans, LA, March 23-27, 2003.
Computer simulation studies of polyunsaturated
model membranes,
ISSFAL 2002 "Dietary Fats and Health" Fifth Congress of the
International Society for the Study of Fatty Acids and Lipids.
Montreal, May 2002.
Videoconference Series: Laboratory for Research on the Structure of Matter (Univ. of Pennsylvania) and University of Puerto Rico-Humacao, as part of the Outreach Program at the Laboratory for the Research on the Structure of Matter, University of Pennsylvania, Philadelphia, April 2002.
Graduate students
Students with with backgrounds in any of the broad fields of physics, biophysics, mathematics, chemistry, biochemistry, biology, computer science or engineering, that want to join the lab for their Ph.D. are encouraged to contact me (e-mail: lsaiz@ucdavis.edu).
First year and incoming students in the Biomedical Engineering Graduate Program (or any other Graduate Program) at UC Davis interested in joining the lab for their Ph.D. thesis can contact me (e-mail: lsaiz@ucdavis.edu). Current projects focus mainly on biological networks and processes relevant to cancer and other diseases.
PostdocsThere are postdoctoral positions currently available in the group. To apply: send a summary of research interests and experience, a complete CV including list of publications, and the name and contact information of three references to lsaiz@ucdavis.edu.
Undergraduate CoursesBIM 105: Probability, Random Processes, and Statistics for Biomedical Engineers. Offered during Academic Year 2008-2009 (Spring 2009 Quarter). New upper division course (core course for BME major). Graduate CoursesBIM 289C Part 1 (provisional course number): Molecular and Multiscale Approaches to Systems Biology. Offered during Academic Year 2007-2008 (Spring 2008 Quarter: Tuesdays and Thursdays from 4:10pm to 6:00pm). New interdisciplinary graduate course. More course details available at the course webpage: MSB. Research Opportunities Join the lab: There are great opportunities for talented undergraduate and graduate students to join the group. Interested undergraduate and graduate students are encouraged to contact me at lsaiz@ucdavis.edu (see: Openings).
