Antonio S. Torralba
CVLegacy Pages

CURRICULUM VITÆ

Education

Academic History

1999-2003PhD in ChemistryCum Laude
Temporal aspects and susceptibility of metabolic responses
12 Nov 2003
Dept. Biochemistry and Molecular Biology I, Faculty of Chemistry, Complutense University, Madrid, Spain
Supervisor: Francisco Montero

1999MSc in Biophysics10/10
Intercooperativity in the binding of two ligands to DNA
20 Dec 1999
Dept. Biochemistry and Molecular Biology I, Faculty of Chemistry, Complutense University, Madrid, Spain
Supervisors: Francisco Montero, Guillermo Orellana

1993-1998BSc in Chemistry/Biochemistry8.9/10
June 1998
Faculty of Chemistry, Complutense University, Madrid, Spain

Other Qualifications

Mar 2001Training in Bioinformatics
UCM General Foundation, Madrid, Spain

Sep-Oct 1998Molecular design: Prediction, structure and modelling of proteins and nucleic acids in the computer
UCM General Foundation, Madrid, Spain125h course

Experience

Teaching

2014-Teaching Assistant
Biophysics and Computational Biology
Dept. Biochemistry and Molecular Biology I, Complutense University, Madrid, Spain

Research

2011-2013Research Scientist
Quantum chemical studies of natural and artificial endonucleases
Spanish National Cancer Research Centre (CNIO), Madrid, Spain
Francesco Gervasio's Computational Biophysics Group

2008-2011Independent Scientist
Linear-scaling Density Functional Theory methods with applications to artificial endonucleases
National Institute for Materials Science (NIMS), Tsukuba, Japan
In collaboration with Tsuyoshi Miyazaki

2005-2007Postdoctoral Researcher
Implementation of linear-scaling Density Functional Theory methods for biological systems within the Conquest code
London Centre for Nanotechnology, University College London, London, United Kingdom
Under the supervision of David R. Bowler

May-Sep 2002Visiting Researcher
Experimental identification of chemical network structure by non-equilibrium perturbative methods
Human Genome Technology Center, Stanford University, Palo Alto, CA, United States
Under the supervision of John Ross

May-Nov 2001Visiting Researcher
Theoretical methods for biochemical networks structure identification
Chemistry Dept., Stanford University, Palo Alto, CA, United States
Under the supervision of John Ross

1998-2004Postgraduate Researcher
Network models of cellular metabolism and statistical mechanics of DNA-ligand interactions
Dept. Biochemistry and Molecular Biology I, Complutense University, Madrid, Spain
Under the supervision of Francisco Montero

Supervision

2012-2013Master Thesis9.1/10
Celsa Díaz Tejada
Biocomputational analysis of human dihydroorotase and aspartate transcarbamylase: understanding conformational transitions and specificity in the active sites.
June 2013
Dept. Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain
Work developed at Spanish National Cancer Research Centre (CNIO), Madrid, Spain
Co-supervisor: Santiago Ramón-Maiques

Other Professional Activities

2013-Freelance Programmer
Development of web applications in PHP

2004-2005Junior Programmer
Development of web applications in C, SQL and Java
Bearing Point Software Solutions, Spanish Branch, Madrid, Spain

Awards

Fellowships

2011-2013Marie Curie International Incoming Fellowship
7th Framework Programme, FP7, European Commission

2005-2007Postdoctoral Fellowship
Ramón Areces Foundation

1999-2002PhD Fellowship
Spanish Ministry of Education and Culture

Professional Recognition

2004Extraordinary doctorate prize to the best PhD thesis
Chemistry Faculty, Complutense University, Madrid, Spain

Participation in Projects

External Funding

2018-2020Research project
Emergence, amplification and transference of chirality by spontaneous symmetry breaking
Ministry of Science, Innovation and Universities, Spain
Principal Investigator: David Hochberg

2011-2013Personal research budget
Safer gene repair and targeting based on the monomeric meganuclease I-DmoI
by design of homologous-recombination-inducing nickase activity
Marie Curie Incoming International Fellowship, European Commission
Principal Investigator: Francesco L. Gervasio

2006-2008Research project
Modelling charge transport in conducting polymers and biological systems
Engineering and Physical Sciences Reseach Council (EPSRC), United Kingdom
Principal Investigator: David R. Bowler

2005-2009Research project
Development of a linear-scaling DFT method and applications on nanomaterials
Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan
Principal Investigator: Tsuyoshi Miyazaki

2001-2003Research project
Development of theoretical and informatic techniques for reconstructing metabolic networks
Ministry of Science and Technology, Spain
Principal Investigator: Francisco Montero

1999-2000Research project
Dynamics of metabolic networks and development of molecular probes for detecting final
and intermediate products
Ministry of Science and Technology, Spain
Principal Investigator: Francisco Montero

Other Funding

2008-2010Personal research budget
Artificial endonucleases based on oligonucleotide-ruthenium complexes
National Institute for Materials Science (NIMS), Tsukuba, Japan
Principal Investigator: Antonio S. Torralba

Publications

Papers in Refereed Journals

  1. David Hochberg, Antonio S. Torralba, Federico Morán.
    Chaotic oscillations, dissipation and mirror symmetry breaking in a chiral catalytic network.
    Phys. Chem. Chem. Phys., 22:27214-27223, 2020. DOI: 10.1039/d0cp05109h
  2. Nicole Dölker, Maria W. Górna, Ludovico Sutto, Antonio S. Torralba, Giulio Superti-Furga, and Francesco L. Gervasio.
    The SH2 domain regulates c-Abl kinase activation by a cyclin-like mechanism and remodulation of the hinge motion.
    PLoS Comput. Biol., 10:e1003863, 2014. DOI: 10.1371/journal.pcbi.1003863
  3. Antonio S. Torralba, David R. Bowler, Tsuyoshi Miyazaki, and Michael J. Gillan.
    Non-self-consistent Density-Functional Theory exchange-correlation forces for GGA functionals.
    J. Chem. Theory Comput., 5:1499-1505, 2009. DOI: 10.1021/ct8005425
  4. Antonio S. Torralba, Milica Todorovic, Veronika Brázdová, Rathin Choudhury, Tsuyoshi Miyazaki, Michael J. Gillan, and David R. Bowler.
    Pseudo-atomic orbitals as basis sets for the O(N) DFT code CONQUEST.
    J. Phys.: Condens. Mat., 20:294206, 2008. DOI: 10.1088/0953-8984/20/29/294206
  5. Michael J. Gillan, David R. Bowler, Antonio S. Torralba, and Tsuyoshi Miyazaki.
    Order-N first-principles calculations with the CONQUEST code.
    Comput. Phys. Commun., 177:14-18, 2007. DOI: 10.1016/j.cpc.2007.02.075
  6. Antonio S. Torralba and Yoel Rodríguez.
    Susceptibilities of an irreversible Michaelis-Menten enzyme.
    Bull. Math. Biol., 68:1335-1353, 2006. DOI: 10.1007/s11538-006-9111-y
  7. Antonio S. Torralba.
    Susceptibility of non-linear systems as an approach to metabolic responses.
    Bioinformatics, 19:2428-2435, 2003. DOI: 10.1093/bioinformatics/btg341
  8. Antonio S. Torralba, Yoel Rodríguez, and Francisco Montero.
    Definition of phenomenological response times with application to metabolic reactions.
    J. Theor. Biol., 221:475-489, 2003. DOI: 10.1006/jtbi.2003.3196
  9. Antonio S. Torralba, Kristine Yu, Peidong Shen, Peter J. Oefner, and John Ross.
    Experimental test of a method for determining causal connectivities of species in reactions.
    Proc. Natl. Acad. Sci. USA, 100:1494-1498, 2003. DOI: 10.1073/pnas.262790699
  10. Yoel Rodríguez, Antonio S. Torralba, and Francisco Montero.
    Equivalence of branched and unbranched Michaelian pathways concerning periodic signal transmission.
    Mol. Biol. Rep., 29:63-66, 2002. DOI: 10.1023/A:1020306419098
  11. Yoel Rodríguez, Antonio S. Torralba, and Francisco Montero.
    Periodic signal transmission through metabolic pathways with Michaelian kinetics.
    J. Phys. Chem. B, 106:5536-5542, 2002. DOI: 10.1021/jp013391s
  12. Antonio S. Torralba, Gonzalo Colmenarejo, and Francisco Montero.
    Sequence distribution and intercooperativity detection for two ligands simultaneously binding to DNA.
    Biopolymers, 58:562-576, 2001.
    DOI: 10.1002/1097-0282(200105)58:6<562::AID-BIP1031>3.0.CO;2-8

Chapters in Books

  1. Antonio S. Torralba.
    Structure-dynamics relationships of metabolic networks: The susceptibility-responsivity connection of enzymes, Mathematical Biology Research Trends, pages 55-80.
    Nova Publishers, Hauppauge, 2008.

Conference Communications and Invited Talks

  1. Antonio S. Torralba and Francesco L. Gervasio.
    The allosteric couplings map of the meganuclease I-DmoI reveals long-range anticorrelations between the LAGLIDADG and DNA-binding moieties.
    In Conference of Computational Physics 2012 (CCP2012), Kobe, Japan, 14-18 October 2012.
    Poster presentation.
  2. Antonio S. Torralba and Francesco L. Gervasio.
    Extended DFT models of the I-DmoI active site reveal the presence of a third metallic binding site.
    In International Symposium on Computics: Quantum Simulation and Design (ISC-QSD), Osaka, Japan, 11-13 October 2012.
    Poster presentation.
  3. Antonio S. Torralba, Tsuyoshi Miyazaki, and David R. Bowler.
    Scaling and convergence of all-atom DFT calculations by order-N density-matrix-based methods.
    In CPMD2011: Extending the limits of ab initio molecular dynamics simulations for Chemistry, Materials Science and Biophysics, Barcelona, Spain, 5-9 September 2011.
    Poster presentation.
  4. Antonio S. Torralba and Tsuyoshi Miyazaki.
    DNA-binding mode of and water activation by [Ru(bpy)2(BPG)]2+, a hydrolytic artificial endonuclease:.
    In 14th International Density Functional Theory Conference, Athens, Greece, 29 August-2 September 2011.
    Poster presentation.
  5. Antonio S. Torralba, Tsuyoshi Miyazaki, and David R. Bowler.
    Recent developments in linear-scaling DFT convergence methods using Conquest: Applications to biomolecules in aqueous solution.
    In MANA International Symposium 2011, Tsukuba, Japan, 2-4 March 2011.
    Poster presentation.
  6. Antonio S. Torralba, Takao Otsuka, Milica Todorovic, David R. Bowler, and Tsuyoshi Miyazaki.
    Enzyme-induced polarization calculations of dihydrofolate reductase ligands using linear scaling DFT code CONQUEST.
    In PsiK-2010 Conference, Berlin, Germany, 12-16 September 2010.
    Poster presentation.
  7. Antonio S. Torralba.
    Linear scaling DFT calculations of dihydrofolate reductase: Reassessing polarization effects on the ligands.
    In 71th Colloquium of the Center for Computational Sciences, University of Tsukuba, Japan, 15 April 2010.
    Invited oral communication.
  8. Antonio S. Torralba, and Tsuyoshi Miyazaki.
    Artificial DNA scissors: Recent progress in the theoretical elucidation of the mechanism of the DNA-hydrolytic-cleavage agent [Ru(bpy)2(BPG)]2+ using the linear scaling DFT code CONQUEST.
    In MANA International Symposium 2010, Tsukuba, Japan, 3-5 March 2010.
    Oral communication.
  9. Antonio S. Torralba, Takao Otsuka, Milica Todorovic, David R. Bowler, Michael J. Gillan, and Tsuyoshi Miyazaki.
    Substrate polarization in dihydrofolate reductase: DFT calculations of the complete enzyme with CONQUEST.
    In International Symposium of Electronic Structure Calculations 2009, Tokyo, Japan, 7-9 December 2009.
    Poster presentation.
  10. Antonio S. Torralba, Takahisa Ohno, and Tsuyoshi Miyazaki.
    Hydrolytic cleavage of DNA by the metallic complex [Ru(bpy)2(BPG)]2+: Theoretical study of binding and action.
    In 13th International Congress of Quantum Chemistry, Helsinki, Findland, 22-27 June 2009.
    Poster presentation.
  11. Antonio S. Torralba, Tsuyoshi Miyazaki, and Takahisa Ohno.
    Ruthenium complexes for artificial endonucleases: DFT analysis of ligands and potential binding interactions with DNA.
    In MANA International Symposium 2009, Tsukuba, Japan, 25-27 February 2009.
    Poster presentation.
  12. Antonio S. Torralba, Tsuyoshi Miyazaki, Takahisa Ohno, David R. Bowler, and Michael Gillan.
    Applications of the DFT linear scaling code CONQUEST to biochemical systems.
    In 7th European Conference on Computational Chemistry (CC7), Venice, Italy, 11-15 September 2008.
    Poster presentation.
  13. Antonio S. Torralba, Tsuyoshi Miyazaki, Takahisa Ohno, David R. Bowler, and Michael Gillan.
    Efficient and accurate algorithm for exchange-correlation non-selfconsistent forces with GGA functionals.
    In International Conference on Quantum Simulators and Design 2008, Tokyo, Japan, 31 May-3 June 2008.
    Poster presentation.
  14. Antonio S. Torralba and David R. Bowler.
    Effects of the proteic environment on the electronic density of dihydrofolate reductase substrates.
    In 13th International Workshop on Computational Physics and Material Sciences: Total Energy and Force Methods, Trieste, Italia, 11-13 January 2007.
    Poster presentation.
  15. Antonio S. Torralba and David R. Bowler.
    Polarizability of folate substrates of dihydrofolate reductase in extended models of the active site.
    In VI Ibero-American Congress of Biophysics, Madrid, Spain, 24-27 September 2006.
    Oral communication.
  16. Antonio S. Torralba.
    Role of conformational freedom of tautomers in catalysis.
    In Psi-K 2005 Conference, Schwäbisch Gmünd, Germany, 17-21 September 2005.
    Poster presentation.
  17. Yoel Rodríguez, Antonio S. Torralba, and Francisco Montero.
    Equivalence of branched and unbranched pathways concerning periodic signal transmission.
    In X Biothermokinetics, Arcachon, France, 7-10 September 2002.
    Poster presentation.
  18. Yoel Rodríguez, Antonio S. Torralba, and Francisco Montero.
    Transmission of sinusoidal oscillations through enzyme-catalyzed reactions.
    In VIII Hispanic-Portuguese Congress of Biophysics, Tenerife, Spain, 11-14 July 2002.
    Poster presentation.
  19. Antonio S. Torralba.
    Response time in metabolic systems with time-dependent inputs.
    In Seminars of the Department of Mathematics Applied to Natural Resources, ETSI Montes, Polytechnic University of Madrid (UPM), Madrid, Spain, 26 March 2001.
    Invited oral communication.
  20. Antonio S. Torralba, Yoel Rodríguez, Juan Carlos Nuño, and Francisco Montero.
    Metabolic response times in several-input pathways.
    In IV Iberoamerican Congress of Biophysics, Alicante, Spain, 11-14 October 2000.
    Poster presentation.
  21. Yoel Rodríguez, Antonio S. Torralba, Juan Carlos Nuño, and Francisco Montero.
    Periodic signal transmission through metabolic pathways.
    In Workshop of the Graduate Program. Dynamics and evolution of Cellular and Macromolecular Processes, Berlin, Germany, 27-29 March 2000.
    Oral communication.
  22. Antonio S. Torralba, Yoel Rodríguez, Lloréns Mónica, Juan Carlos Nuño, and Francisco Montero.
    Transition and response times in metabolic pathways: what are the differences?
    In Workshop of the Graduate Program. Dynamics and evolution of Cellular and Macromolecular Processes, Berlin, Germany, 27-29 March 2000.
    Oral communication.

Miscellanea

  1. Antonio S. Torralba, Felix Olasagasti, and Francisco Montero.
    Cycles in nature: from chemical reactions to biological rhythms.
    In V Conference Madrid por la Ciencia, Madrid, Spain, 27-30 March 2004.
    Educational science fair.

Languages

SpanishMother tongue
EnglishFluent, read, written and spoken
FrenchIntermediate, reading; elementary, spoken
JapaneseElementary, written and spoken

Computational Skills

Scientific Codes

QuantumCONQUEST (linear scaling DFT, developer)
VASP
ABINIT
NWCHEM
GAUSSIAN
Classical MDAMBER
GROMACS
DockingAUTODOCK
VisualisationPYMOL (inc. scripting)
VMD

High Performance Computing

SystemsMare Nostrum (IBM PowerPC)
TGCC Curie (Intel Nehalem)
T2K Tsukuba (AMD Opteron)
HECToR (Cray XE6)
SchedulingPBS, SGE
ProgrammingMPI, openMP (rudiments)
Unix OSLinux, IRIX, Solaris, MacOS

Programming Languages

GeneralC/C++, Fortran90, Java
DatabasesSQL
Scriptingbash, awk, sed, python, PHP

Code Development

VersioningCVS, subversion, Git, Safe Source
Buildingmake, ant
IDEEclipse

Miscellanea

Text Editorsvi, emacs
WebHTML, CSS, javascript
MarkupLATEX, docbook
LibrariesOpenGL

Other Skills

Organisational Skills

7-8 Sep 2007Co-organiser
Workshop "Use of the O(N) ab initio code CONQUEST", CECAM
Lyon, France. 7-8 Sep 2007

Referee for professional journals

Bioinformatics

© 2013-2021 Antonio Sánchez Torralba