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Research Interest:
→ news, August 2007: POLCH 2.1 released !
The central goal of my scientific efforts is to develop new, and hopefully efficient, algorithms for the quantum chemical calculation of the electron structure of really large molecules - the larger the better. The final goal is to once be able to handle really big molecular structures of biological interest. Although having gained some experience with Density Functional Theory throughout my masters thesis, the current most promising approach is the development of a Direct SCF program operating at the Hartree Fock level with parallel features using PVM as well as MPI (GREMLIN).
The simulation of any biological system will always imply the need for taking into account the effect the environment exerts onto the biomolecule (solvation). The aforementioned Direct SCF Hartree Fock program respects solvation by the inclusion of a solvation potential expanded in multipole moments (SCRF). Alternatively it can be coupled with Connolly's molecular surface program to facilitate a true PCM approach (IDAPCM). A major challenge is the systematic consideration of non-polar contributions in some parameter-free way. Among these are contributions like dispersion and cavitation. The latter effect has its implication also in the related phenomenon of hydrophobic hydration.
An impressive example of how to use specially designed computer hardware for scientific purposes has been given with the development of MD-GRAPE-2. The performance this computer chip offers can hardly be topped by any conventional approach of high performance computing. However, it remains a challenge to get the so called standard methods, e.g. Ewald summation, to fully profit from this special purpose hardware. One possible solution to circumvent these lattice summation methods was to replace them by implicit solvation methods. Recent investigation into this area has identified Poisson Boltzmann models within the Boundary Element Method to be particularly suited for a coupling with MD-GRAPE-2. A first implementation is available as POLCH 2.1.
Most of todays knowledge of biomolecular structure is mainly restricted to water soluble forms of biopolymers. Although comprehensible from a technical point of view the exploration of the structure of membrane bound proteins deserves closer attention because of the important role these membrane complexes play in cell signaling and signal transduction. A related process of particular interest is the exo-transport of cell-internal material into the extracellular space. While of fundamental scientific interest to all biological disciplines this research appears to require a completely revised vision of the physics that takes place in hydrophobic environments such as membranes.
  Publications:

M.S. thesis
DFT-calculations on Zn 2+ within the zinc finger like domain of gag-protein p55, HIV,
University of Vienna, April 1996.

Ph.D. thesis
Development of a Novel Direct SCF Program for the Hartree Fock Treatment of Molecular Systems with Special Emphasis on Biomolecular Ligand Field and Reaction Field Problems,
University of Vienna, Sept. 1998


1.
 MMDCG:Expansion Coefficients of Hermitian-Like Primitive Gaussians,
S. Höfinger, Program QCPE 678, QCPE Bulletin, 18, 3, 27,Quantum Chemistry Program Exchange, 1998
2.
 MMDFMT: Electron Repulsion Integrals,
S. Höfinger, Program QCPE 679, QCPE Bulletin, 18, 3, 27, Quantum Chemistry Program Exchange, 1998
3.
 Performance Analysis and Derived Parallelization Strategy for a SCF Program at the Hartree Fock Level,
S. Höfinger, O. Steinhauser and P. Zinterhof, Lect. Notes Comp. Sci., 1557, 163-172, 1999   
4.
 ERICHK: Check Program for Electron Repulsion Integrals,
S. Höfinger, Program QCPE 685, QCPE Bulletin, 19, 2, Quantum Chemistry Program Exchange, 1999
5.
 ELFCHK: Electric Field Integrals,
S. Höfinger, Program QCPE 686, QCPE Bulletin, 19, 2, Quantum Chemistry Program Exchange, 1999
6.
 Combined Hartree-Fock, Ligand Field and Multipolar Reaction Field Treatment of the Central Zinc Ion in HIV1 Zincfinger Peptide,
S. Höfinger and O. Steinhauser, P.542, Book of Abstracts, 5th World Congress of Theoretically Oriented Chemists, WATOC-99, 1999
7.
 Performance Analysis, PVM and MPI Implementation of a DSCF Hartree Fock Program,
S. Höfinger, O. Steinhauser  and P. Zinterhof,  CIT, Special Issue on Parallel Numerics and Parallel Computing in Image Processing, Video Processing, and Multimedia, 8, 1, 19-30, 2000
8.
 Dielectric Relaxation in Proteins: A Continuum Electrostatics Model Incorporating Dielectric Heterogeneity of the Protein and Time-Dependent Charges,
S. Höfinger  and T. Simonson,  J. Comput. Chem., 22, 3, 290-305,  2001
9.
 Load Balancing for the Electronic Structure Program GREMLIN in a Very Heterogenous SSH-Connected WAN-Cluster of UNIX-Type Hosts,
S. Höfinger, Lect. Notes Comp. Sci., 2074, 801-810, 2001
10.
 POLCH: Polarization Charges,
S. Höfinger, Program QCPE 805, Quantum Chemistry Program Exchange, 2001
11.
 Making Use of Connolly's Molecular Surface Program in the Iso-Density Adapted Polarizable Continuum Model,
S. Höfinger and O. Steinhauser, J. Chem. Phys., 115, 23, 10636-10646, 2001
12.
 Method/Basis Set Dependence of the Traceless Quadrupole Moment Calculation for N2,CO2, SO2, HCl, CO, NH3, PH3, HF and H2O,
S. Höfinger and M.Wendland, Int. J. Quantum Chem., 86, 2, 199-217, 2002
13.
 Dynamic Load Equilibration for Cyclic Applications in Distributed Systems,
S. Höfinger, Lect. Notes Comp. Sci., 2330, 963-971, 2002
14.
 Opportunities and Challenges in Utilizing Application Specific Integrated Circuits in Drug Design,
S. Höfinger, A. Berces, T. Narumi, T. Ebisuzaki, SCI 2002 Proceedings , 7th World Multiconference on Systemics, Cybernetics and Informatics, 16, 2002
15.
 Hardware Accelerated Molecular Dynamics of the Arabinose Binding Protein,
S. Höfinger and A. Berces, PB317, Book of Abstracts, 6th World Congress of Theoretically Oriented Chemists, WATOC-02, 2002
16.
 Automatic Runtime Load Balancing of Dedicated Applications in Heterogeneous Environments,
S. Höfinger, Lect. Notes Comp. Sci., 2474, 62-69, 2002
17.
 Parallel Global Optimization of High-Dimensional Problems,
S. Höfinger, T. Schindler, A. Aszodi, Lect. Notes Comp. Sci., 2474, 148-155, 2002
18.
 On the cavitation energy of water,
S. Höfinger and F. Zerbetto, Chem.-Eur. J., 9, No.2, 566-569, 2003
19. Latency Reduction from Runtime-Interference to the Parallel Quantum Chemistry Program GREMLIN in Heterogeneous and Homogeneous Environments,
S. Höfinger,  Future Gener. Comp. Sy., 19, No.5, 777-788, 2003
20. The Free Energy of Nanobubbles in Organic Liquids,
S. Höfinger and F. Zerbetto,  J. Phys. Chem. A,  107, No.50, 11253-11257, 2003
21. The costly process of creating a cavity in n-octanol,
S. Höfinger and F. Zerbetto,  Theor. Chem. Acc.,  112, No.4, 240-246, 2004
22. What Size Cluster Equals a Dedicated Chip,
S. Höfinger, Lect. Notes Comp. Sci., 3241, 397-404, 2004
23. A Poisson-Boltzmann Solver running on the specialized computer chip MD-GRAPE-2: a case study on the effect of explicit consideration of counter ions,
S. Höfinger, Book of Abstracts, 7th Congress of the World Association of Theoretically Oriented Chemists, WATOC-05, CI1-5, 20, 2005
24. The Collapse of Nanobubbles in Water,
F. Lugli, S. Höfinger, F. Zerbetto, J. Am. Chem. Soc., 127, No.22, 8020-8021, 2005
25. Solving the Poisson Boltzmann Equation with the Specialized Computer Chip MD-GRAPE-2,
S. Höfinger, J. Comput. Chem., 26, No.11, 1148-1154, 2005
26. Probing the Applicability of Polarizable Force-Field Molecular Dynamics for Parallel Architectures: a Comparison of Digital MPI with LAM-MPI and MPICH2,
B. Almeida, R. Mahajan, D. Kranzlmüller, J. Volkert, S. Höfinger, Lect.  Notes Comp. Sci., 3666, 433-440, 2005
27. A new mechanistic model for Interleukin-4 receptor signaling across the lipid bilayer,
T. Weidemann, S. Höfinger, M. Auer, Eur. Biophys. J., 34, No.6, 657, 2005
28. Simple models for hydrophobic hydration,
S. Höfinger, F. Zerbetto, Chem. Soc. Rev., 34, No.12, 1012-1020, 2005
→ inside front cover
29. A Very General Solvation Model for BioMolecular Simulation,
S. Höfinger, Publication Series of the John von Neumann Institute for Computing, 34, 87-90, 2006
30. Large Scale Molecular Dynamics Simulations for the Derivation of Solvation Free Energies of Strongly Hydrophobic Molecules,
R. Mahajan, D. Kranzlmüller, J. Volkert, S. Höfinger, Publication Series of the John von Neumann Institute for Computing, 34, 173-176, 2006
31. The Influence of Molecular Surface Composition on the Outcome of Poisson Boltzmann Calculations Performed to Obtain Solvation Free Energies,
P. Kar, Y. Wei, U.H.E. Hansmann, S. Höfinger, Publication Series of the John von Neumann Institute for Computing, 34, 161-164, 2006
32. A critical β6-β7 loop in the Pleckstrin Homology domain of ceramide kinase,
P. Rovina, M. Jaritz, S. Höfinger, C. Graf, P. Devay, A. Billich, T. Baumruker, F. Bornancin, Biochem. J., 400, 255-265, 2006
33. Assessment and Tuning of a Poisson Boltzmann Program that Utilizes the  Specialized Computer Chip MD-GRAPE-2 and Analysis of the Effect of Counter Ions,
S. Höfinger, Molecular Structure and Reactivity in Biological Systems, RSC Publishing , ISBN 0 85404 668, 151-162, 2006
34. Computational Assessment of the Entropy of Solvation of Small-Sized Hydrophobic Entities,
R. Mahajan, D. Kranzlmüller, J. Volkert, U.H.E. Hansmann, S. Höfinger, Phys. Chem. Chem. Phys., 8, 5515-5521, 2006
35. Beyond dimerization: a membrane-dependent activation model for Interleukin-4 receptor mediated signalling,
T. Weidemann, S. Höfinger, K. Müller, M. Auer, J. Mol. Biol., 366, 1365-1373, 2007
36. Parallel Tempering Molecular Dynamics Folding Simulation of a Signal Peptide in Explicit Water,
S. Höfinger, B. Almeida, U.H.E. Hansmann, Proteins, 68, 662-669, 2007
37. Comparing Semi-Empirical versus Classic Charge Assignments in BioMolecules and their Effect on Electrostatic Potentials,
P. Kar, M. Seel, U.H.E. Hansmann, S. Höfinger, Publication Series of the John von Neumann Institute for Computing, 36, 155-158, 2007
38. Algorithmic Refinements to an Enhanced Poisson-Boltzmann Approach used in BioMolecular Simulation,
P. Kar, M. Seel, U.H.E. Hansmann, S. Höfinger, Publication Series of the John von Neumann Institute for Computing, 36, 173-176, 2007
39. Dispersion Terms and Analysis of Size- and Charge-Dependence in an Enhanced Poisson-Boltzmann Approach,
P. Kar, M. Seel, U.H.E. Hansmann, S. Höfinger, J. Phys. Chem. B, 111, 8910-8911, 2007
40. Systematic Study of the Boundary Composition in Poisson Boltzmann Calculations,
P. Kar, Y. Wei, U.H.E. Hansmann, S. Höfinger, J. Comput. Chem., 28, 2538-2544, 2007
41. Detecting Secondary Bottlenecks in Parallel Quantum Chemistry Applications Using MPI,
R. Mahajan, D. Kranzlmüller, J. Volkert, U.H.E. Hansmann, S. Höfinger, Int. J. Mod. Phys. C, 2007 in press
42. Signaling of IL4-R, a typical class I cytokine receptor: what defines the quiescent state ?
T. Weidemann, S. Höfinger, M. Auer, Handbook of Cell Signalling, edited by Ralph A. Bradshaw & Edward A. Dennis, 2007 in press
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5 confidential Novartis internal reports,
  several more articles currently in progress
Other Interest:
All kinds of sport, especially jogging, biking and climbing.
Contact:
For all comments please send e-mail to siegfried-hoefinger@chello.at