Siegfried Höfinger's HOMEPAGE

last update October 10, 2010

Publications

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

PhD 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, September 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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) → see comments by the Faculty of 1000

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, 19, No.1, 1-13, (2008)

42. Hydrophobicity --- its Origin and an Important Example,
S. Höfinger, M. Calvaresi, F. Lugli, F. Zerbetto, Science and Supercomputing in Europe, HPC-EUROPA++ Report 2008, edited by P. Alberigo, G. Erbacci, & F. Garofalo, 230-236, (2008)

43. Signaling of IL4-R, a typical class I cytokine receptor: what defines the quiescent state ?,
T. Weidemann, S. Höfinger, M. Auer, Handbook of Cell Signaling, 2nd edition, edited by Ralph A. Bradshaw & Edward A. Dennis, chapter 47, 323-328, (2009)

44. Current Performance Gains from Utilizing the GPU or the ASIC MDGRAPE-3 within an Enhanced Poisson Boltzmann Approach,
T. Narumi, K. Yasuoka, K. Taiji, S. Höfinger, J. Comput. Chem., 30, No.14, 2351-2357, (2009)

45. Theoretical mimicry of biomembranes,
P. Kar, M. Seel, T. Weidemann, S. Höfinger, FEBS Lett., 583, No.12, 1909-1915, (2009)

46. Introducing Temperature Dependence in an Enhanced Poisson-Boltzmann Approach,
S. Höfinger, F. Zerbetto, Chem. Phys. Lett., 480, 313-317, (2009)

47. Hydrophobic Hydration at Critical Length Scale - A HPC Endeavour,
S. Höfinger, F. Zerbetto, Proceedings, TAM 2009, Montpellier, (2010) in press

48. Split Impressions from Large Scale Computational Analysis of Hydrophobic Phenomena Carried out on two Different HPC Architectures,
S. Höfinger, F. Zerbetto, HPC-EUROPA-2 Report 2009, edited by P. Alberigo, G. Erbacci, & F. Garofalo, (2010) in press

49. A RNA-based nanodevice recording temperature over time,
S. Höfinger, F. Zerbetto, Chem. Phys., 369, 91-95, (2010)

50. Fast Calculation of Electrostatic Potentials on the GPU or the ASIC MD-GRAPE-3,
T. Narumi, K. Yasuoka, M. Taiji, F. Zerbetto, S. Höfinger, Comput. J., (2010) in press

51. Focus on composition and interaction potential of single-pass transmembrane domains,
R. Worch , C. Bökel, S. Höfinger, P. Schwille, T. Weidemann, Proteomics, (2010) in press

__
5 confidential Novartis internal reports,
several more articles in preparation

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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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) → see comments by the Faculty of 1000
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, 19, No.1, 1-13, (2008)
42.	Hydrophobicity --- its Origin and an Important Example, S. Höfinger, M. Calvaresi, F. Lugli, F. Zerbetto, Science and Supercomputing in Europe, HPC-EUROPA++ Report 2008, edited by P. Alberigo, G. Erbacci, & F. Garofalo, 230-236, (2008)
43.	Signaling of IL4-R, a typical class I cytokine receptor: what defines the quiescent state ?, T. Weidemann, S. Höfinger, M. Auer, Handbook of Cell Signaling, 2nd edition, edited by Ralph A. Bradshaw & Edward A. Dennis, chapter 47, 323-328, (2009)
44.	Current Performance Gains from Utilizing the GPU or the ASIC MDGRAPE-3 within an Enhanced Poisson Boltzmann Approach, T. Narumi, K. Yasuoka, K. Taiji, S. Höfinger, J. Comput. Chem., 30, No.14, 2351-2357, (2009)
45.	Theoretical mimicry of biomembranes, P. Kar, M. Seel, T. Weidemann, S. Höfinger, FEBS Lett., 583, No.12, 1909-1915, (2009)
46.	Introducing Temperature Dependence in an Enhanced Poisson-Boltzmann Approach, S. Höfinger, F. Zerbetto, Chem. Phys. Lett., 480, 313-317, (2009)
47.	Hydrophobic Hydration at Critical Length Scale - A HPC Endeavour, S. Höfinger, F. Zerbetto, Proceedings, TAM 2009, Montpellier, (2010) in press
48.	Split Impressions from Large Scale Computational Analysis of Hydrophobic Phenomena Carried out on two Different HPC Architectures, S. Höfinger, F. Zerbetto, HPC-EUROPA-2 Report 2009, edited by P. Alberigo, G. Erbacci, & F. Garofalo, (2010) in press
49.	A RNA-based nanodevice recording temperature over time, S. Höfinger, F. Zerbetto, Chem. Phys., 369, 91-95, (2010)
50.	Fast Calculation of Electrostatic Potentials on the GPU or the ASIC MD-GRAPE-3, T. Narumi, K. Yasuoka, M. Taiji, F. Zerbetto, S. Höfinger, Comput. J., (2010) in press
51.	Focus on composition and interaction potential of single-pass transmembrane domains, R. Worch , C. Bökel, S. Höfinger, P. Schwille, T. Weidemann, Proteomics, (2010) in press