Prof. Dr. Kay Hamacher
Mathematical modeling, data analytics, and simulation

We analyze and simulate:
- statistically sound
- cryptographically secure
- parallelized and efficient


Refereed Publications


M. Schmidt, K. Hamacher. hoDCA: higher order direct-coupling analysis, BMC Bioinformatics, 19:546, 2018.
Abstract & PDF-Version

Ann-C. Groher, S. Jager: C. Schneider, F. Groher K. Hamacher, B. Suess. Tuning the Performance of Synthetic Riboswitches using Machine Learning, ACS Synthetic Biology, accepted,2018.

K. Hamacher. Hybridization of Stochastic Tunneling with (Quasi)-Infinite Time-Horizon Tabu Search, 11th International Workshop on Hybrid Metaheuristics (HM2019), accepted, 2018.

P. Kunzmann, K. Hamacher. Biotite: A unifying open source computational biology framework in Python, BMC Bioinformatics, 19:346, 2018.
Abstract & PDF-Version

C. Marini, A. Porro, A. Rastetter, C. Dalle, I. Rivolta, D. Bauer, R Oegema, C Nava, E. Parrini, D. Mei, C. Mercer, R. Dhamija, C. Chambers, C. Coubes, J. Thevenon, P. Kuentz, S. Julia, L. Pasquier, C. Dubourg, W. Carre, A. Rosati, F. Melani, T. Pisano, M. Giardino, A.M. Innes, Y. Alembik, S. Scheidecker, M. Santos, S. Figueiroa, C. Garrido, C. Fusco, D. Frattini, C. Spagnoli, A. Binda, T. Granata, F. Ragona, E. Freri, S. Franceschetti, L. Canafoglia, B. Castellotti, C. Gellera, R. Milanesi, M.M. Mancardi, D.R. Clark, F. Kok, K.L. Helbig, S. Ichikawa, L. Sadler, J. Neupauerova, P. Lasuthova, K. Sterbova, A. Laridon, E. Brilstra, B. Koeleman, J.R. Lemke, F. Zara, P. Striano, A. Barbuti, D. DiFrancesco, E. LeGuern, R. Guerrini, B. Santoro, K. Hamacher, G. Thiel, A. Moroni, J.C. DiFrancesco, C. Depienne. HCN1 mutation spectrum: from neonatal epileptic encephalopathy to benign generalized epilepsy and beyond, Brain 141(11):3160-3178, 2018.
Abstract & PDF-Version
Editor's Choice

C. Gross, A. Saponaro, B. Santoro, A. Moroni, G. Thiel, K. Hamacher. Mechanical transduction of cytoplasmic-to-transmembrane-domain movements in a hyperpolarization-activated cyclic nucleotide-gated cation channel, J. Biol. Chem. 293(33)12908-12918, 2018.
Abstract & PDF-Version

O. Tkachenko, C. Weinert, T. Schneider, K. Hamacher. Large-Scale Privacy-Preserving Statistical Computations for Distributed Genome-Wide Association Studies ACM Asia Conference on Computer and Communications Security (ASIACCS), 2018.

M. Dombrowsky, S. Jager, B. Schiller, B. Mayer, S. Stammler, K. Hamacher, StreaMD: Advanced analysis of Molecular Dynamics using R, J. Comp. Chem., 39:1666-1674, 2018.
Abstract & PDF-Version
Cover Page

F. Groher, C. Bofill-Bosch, C. Schneider, J. Braun, S. Jager K. Geißler, K. Hamacher, B. Suess. Riboswitching with ciprofloxacin-development and characterization of a novel RNA regulator, Nucleic Acids Research, 46:2121-2132, 2018.
Abstract & PDF-Version


D. Demmler, K. Hamacher, T. Schneider, S. Stammler. Privacy-Preserving Whole-Genome Variant Queries, 16th International Conference on Cryptology And Network Security (CANS) , accepted, 2017.

M. Schmidt, K. Hamacher. Three body interactions improve contact prediction within direct-coupling-analysis, Phys. Rev. E, 96(5):052405, 2017.
Abstract & PDF-Version
Editor's Suggestion

J. Buchmann, M. Geihs, K. Hamacher, S. Katzenbeisser, S. Stammler. Long-Term Integrity Protection of Genomic Data, 4th Int. Workshop on Genome Privacy and Security (GenoPri'17), 2017, accepted

P. Boba, K. Hamacher, TransferEntropyPT: An R package to assess transfer entropies via permutation tests, 15th Int. Conf. on Comp. Methods in Systems Biology (CMSB2017), Lecture Notes in Bioinformatics (LNBI 10545) 285-290, 2017.
Abstract & PDF-Version
Web-Site with Code and Tutorial

F. Keul, M. Hess, M. Goesele, K. Hamacher. PFASUM: A substitution matrix from Pfam structural alignments, BMC Bioinformatics, 18:293, 2017.
Abstract & PDF-Version

S. Jager, B. Schiller, P. Babel, M. Blumenroth, T. Strufe, K. Hamacher. StreAM-Tg: Algorithms for Analyzing Coarse Grained RNA Dynamics Based on Markov Models of Connectivity-Graphs, Algorithms for Molecular Biology, 12:15 , 2017.
Abstract & PDF-Version

C. Groß, K. Hamacher, K. Schmitz, S. Jager. Cleavage Product Accumulation Decreases the Activity of Cutinase during PET Hydrolysis J. Chem. Inf. Mod. 57(2):243-255, 2017.
Abstract & PDF-Version


S. Weissgraeber, A. Saponaro, G. Thiel, K. Hamacher. A reduced mechanical model for cAMP-modulated gating in HCN channels, Scientific Reports, 7:40168, 2016.
Abstract & PDF-Version

T. Greiner, S. Bolduan, B. Hertel, C. Gross, K. Hamacher, U. Schubert, A. Moroni, G. Thiel. Ion channel activity of Vpu proteins is conserved throughout evolution of HIV-1 and SIV, Viruses 8(12)325, 2016. Abstract & PDF-Version

M. Hess, D. Jente, J. Wiemeyer, K. Hamacher, M. Goesele. Visual Analysis and Comparison of Multiple Sequence Alignments, Eurographics Workshop on Visual Computing for Biology and Medicine, ISBN 978-3-03868-010-9, The Eurographics Association, 2016.
Abstract & PDF-Version

S. Stammler, S. Katzenbeisser, K. Hamacher. Correcting finite sampling issues in Entropy l-diversity, Privacy in Statistical Databases (PSD 2016), Lecture Notes in Computer Science (LNCS 9867), pp. 135-146, 2016.
Abstract & PDF-Version

S. Jager, B. Schiller, T. Strufe, K. Hamacher. StreAM-Tg : Algorithms for Analyzing Coarse Grained RNA Dynamics based on Markov Models of Connectivity-Graphs, Workshop on Algorithms in Bioinformatics (WABI 2016), Lecture Notes in Computer Science (LNCS 9838), pp. 197-209, 2016.
Abstract & PDF-Version

D. Bensinger, T. Neumann, C. Scholz, C. Voss, S. Knorr, U. Kuckelkorn, K. Hamacher, P. Kloetzel, B. Schmidt. Elastase-like activity is dominant to Chymotrypsin-like activity in 20S Proteasome's β5 catalytic subunit, ACS Chemical Biology 11(7):1800-1804, 2016.
Abstract & PDF-Version

M. Hess, F. Keul, M. Goesele, K. Hamacher. Addressing inaccuracies in BLOSUM computation improves homology search performance, BMC Bioinformatics, 17:189, 2016.
Abstract & PDF-Version

K. Hamacher. Using Lisp Macro-Facilities for Transferable Statistical Tests, 9th European Lisp Symposium, ISBN 978-2-9557474-0-7, pp. 31-38, 2016.

P. Manns, K. Hamacher. Evolving Smoothing Kernels for Global Optimization, 19th European Conference on the Applications of Evolutionary Computation (EvoApplications), Lecture Notes in Computer Science (LNCS 9598), pp. 56-72, 2016.
Abstract & PDF-Version

O. Buss, S. Jager, S.M. Dold, S. Zimmermann K. Hamacher, K. Schmitz, J. Rudat. Statistical evaluation of HTS assays for enzymatic hydrolysis of β-keto esters, PLoS One, 11(1): e0146104, 2016.
Abstract & PDF-Version

K. Hamacher. Online Presences of Traditional Media vs. Blogs - Redundancy and Unique News Coverage, Media Convergence Handbook Vol.1. Journalism, Broadcasting, and Social Media Aspects of Convergence, ISBN 978-3-642-54484-2, A. Lugmayr,C. Dal Zotto (eds.) Springer-Verlag, pp. 117-130, 2016.
Abstract & PDF-Version


F. Hoffgaard, S.M. Kast, A. Moroni, G. Thiel, K. Hamacher. Tectonics of a K+ channel: the importance of the N-terminus for channel gating, Biochimica et Biophysica Acta - Biomembranes, 1848(12):3197-3204, 2015.
Abstract & PDF-Version
PDB-Structure used as a homology model

B. Schiller, S. Jager, K. Hamacher; T. Strufe. StreaM - a Stream-based Algorithm for Counting Motifs in Dynamic Graphs, 2nd International Conference on Algorithms for Computational Biology, Lecture Notes in Bioinformatics (LNBI 9119), 53-67, 2015.
Abstract & PDF-Version

P. Boba, D. Bollmann, D. Schoepe, N. Wester, J. Wiesel, K. Hamacher. Efficient computation and statistical assessment of transfer entropy. Frontiers in Physics 3(2015)10
Abstract & PDF-Version

C. Scholz, S. Knorr, K. Hamacher, B. Schmidt. DOCKTITE - A Highly Versatile Step-by-Step Workflow for Covalent Docking and Virtual Screening in MOE. J. Chem. Inf. Model. 55(2):398-406, 2015.
Abstract & PDF-Version


N.P. Karvelas, A. Peter, S. Katzenbeisser, E. Tews, K. Hamacher. Privacy Preserving Whole Genome Sequence Processing through Proxy-Aided ORAM, Workshop on Privacy in the Electronic Society (WPES 2014), p.1-10, 2014.
Abstract & PDF-Version

O. Lenz, F. Keul, S. Bremm, K. Hamacher, T. von Landesberger. Visual Analysis of Patterns in Multiple Amino Acid Mutation Graphs Visual Analytics Science and Technology (VAST), 2014 IEEE Conference on pp.93-102, 2014.
Abstract & PDF-Version

C. Voss, C. Scholz, S. Knorr, P. Beck, M.L. Stein, A. Zall, U. Kuckelkorn, P.-M. Kloetzel, M. Groll, K. Hamacher, B. Schmidt. α-Keto phenylamides provide a link between the primed and non-primed substrate binding site in the 20S proteasome. ChemMedChem, 9(11):1860-7187, 2014.
Abstract & PDF-Version

P.  Boba, S. Gries, K. Hamacher. R as an Integration Tool in High Performance Computing - Lessons Learned, Workshop on Simulation Technology at Informatik2014, Lecture Notes in Informatics 232:138-148, 2014.

K. Hamacher. A Taxonomy of Genomic Privacy and Beyond, PETS Genome Privacy Workshop, Online-Proceedings, 2014.

R. Bose, G. Thiel, K. Hamacher. Clustering of Giant Virus-DNA Based on Variations in Local Entropy, Viruses, 6(6), 2259-2267, 2014.
Abstract & PDF-Version

K. Hamacher. Online Performance Measures for Metaheuristic Optimization, 9th International Workshop on Hybrid Metaheuristics (HM2014), Lecture Notes in Computer Science (LNCS 8457), pp. 169-182, 2014.
Abstract & PDF-Version

B. Mayer, K. Hamacher. Stochastic Tunneling Transformation during Selection in Genetic Algorithms, Genetic and Evolutionary Computation Conference (GECCO2014), 801-806, 2014.
Abstract & PDF-Version

M. Hess, S. Bremm, S. Weissgraeber, K. Hamacher, M. Goesele, J. Wiemeyer, T. von Landesberger. Visual Exploration of Parameter Influence on Phylogenetic Trees, IEEE Computer Graphics & Applications, 34(2): 48-56, 2014.
DOI: 10.1109/MCG.2014.2
Abstract & PDF-Version

M. Hess, J. Wiemeyer, K. Hamacher, M. Goesele. Serious Games for Solving Protein Sequence Alignments - Combining Citizen Science and Gaming, Proc. of GameDays 2014, Lecture Notes in Computer Science (LNCS 8395), pp. 175-185, 2014.
Abstract & PDF-Version

M. Waechter, K. Jaeger, D. Thuerck, S. Weissgraeber, S. Widmer, M. Goesele, K. Hamacher. Using Graphics Processing Units to Investigate Molecular Coevolution, Concurrency and Computation: Practice and Experience, 26(6):1278-1296, 2014.
Abstract & PDF-Version


G. Lauss, C. Schröder, P. Dabrock, J. Eder, K. Hamacher, K.A. Kuhn, H. Gottweis. Towards Biobank Privacy Regimes in Responsible Innovation Societies, Biopreservation and Biobanking, 11:319-323, 2013.
Abstract & PDF-Version

K. Hamacher. Grand challenges in computational physics, Frontiers in Computational Physics, 1:4, 2013.
Abstract & PDF-Version

M. Ober, S. Katzenbeisser, K. Hamacher. Structure and Anonymity of the Bitcoin Transaction Graph, Future Internet, 5(2):237-250, 2013.
Abstract & PDF-Version

K. Hamacher, Information Theoretic Dissection of the Holobiont - Host-Virus Interaction as an Example, Nova Acta Leopoldina, NF 114, No. 391, 307-315, 2013.

K. Hamacher. A New Hybrid Metaheuristic - Combining Stochastic Tunneling and Energy Landscape Paving, 8th International Workshop on Hybrid Metaheuristics (HM2013), Lecture Notes in Computer Science (LNCS 7919), pp. 107-117, 2013.
Abstract & PDF-Version

M. Franz, K. Hamacher, S. Jha, S. Katzenbeisser, H. Schröder. Secure Computations on Non-Integer Values with Applications to Privacy-Preserving Sequence Analysis, Information Security Technical Report 17(3):117-128, 2013.
Abstract & PDF-Version

S. Pape, F. Hoffgaard, M. Dür, K. Hamacher, Distance Dependency And Minimum Amino Acid Alphabets for Decoy Scoring Potentials, J. Comp. Chem., 34: 10-20, 2013.
Abstract & PDF-Version


K. Hamacher, R. Bose. Alternate entropy measure for assessing volatility in financial markets. Phys. Rev. E, 86(5):056112, 2012.
Abstract & PDF-Version

K. Hamacher, Resilience to Leaking - Dynamic Systems Modeling of Information Security, PLoS One, 7(12): e49804, 2012.
Online- & PDF-Version

K. Hamacher, Dynamical regimes due to technological change in a microeconomical model of production, Chaos 22: 033149, 2012.
Abstract & PDF-Version

S. Weißgraeber, K. Hamacher, Generalized Correlations in Molecular Evolution: A Critical Assessment, Proceedings of CBSB12 (From Computational Biophysics to Systems Biology), P. Carloni et al. (eds.), (ISBN 978-3-89336-748-1), pp. 231-234
available in the PDF-Version of the Proceedings

K. Hamacher, T. Greiner, J.L. Van Etten, M. Gebhardt, L.P. Villarreal, A. Moroni, G. Thiel, Phycodnavirus Potassium Ion Channel Proteins Question the Virus Molecular Piracy Hypothesis, PLoS One, 7(6): e38826, 2012
Abstract & PDF

M. Waechter, K. Jaeger, S. Weissgraeber, S. Widmer, M. Goesele, K. Hamacher, Information-Theoretic Analysis of Molecular (Co)Evolution using Graphics-Processing Units, 3rd International Emerging Computational Methods for the Life Sciences Workshop (ECMLS 2012) , 49-58, 2012.
Abstract & PDF-Version
Code (licensed under GPLv3)
Reprint (PDF)

T. Wulfmeyer, C. Polzer, G. Hiepler, K. Hamacher, R. Shoeman, D. Dunigan, J.L. Van Etten, M. Lolicato, A. Moroni, G. Thiel, T. Meckel. Structural organization of DNA in Chlorella viruses, PLoS One, 7(2): e30133, 2012

M. Waechter, K. Hamacher, F. Hoffgaard, S. Widmer, M. Goesele, Is Your Permutation Algorithm Unbiased for n≠2**m ? 9th Int. Conf. on Parallel Processing & Appl.Mathematics (PPAM2011), Lecture Notes in Computer Science (LNCS Volume 7203), pp. 297-306, 2012.
Authors' electronic version (PDF)
Paper at LCNS - SpringerLink (PDF)


S. Weißgraeber, F. Hoffgaard, K. Hamacher, Structure-Based, Biophysical Annotation of Molecular Coevolution of Acetylcholinesterase, Proteins: Structure, Function, and Bioinformatics, 79(11):3144-3154, 2011.
Abstract & PDF

S. Bremm, T. von Landesberger, M. Hess, T. Schreck, P. Weil, K. Hamacher, Interactive Visual Comparison of Multiple Trees, IEEE Conference on Visual Analytics Science and Technology (VAST2011), 31-40, 2011.
Abstract & PDF

E. Gehrmann, C. Glässer, Y. Jin, B. Sendhoff, B. Drossel, K. Hamacher, The robustness of glycolysis in yeast to internal and external noise. Phys. Rev. E 84:021913, 2011.
Abstract & PDF
This paper was discussed in a viewpoint article in Physics(APS) 4, 63 (2011)
(also selected for publication in the Virtual Journal of Biological Physics Research)

K. Hamacher, S. Katzenbeisser. Public Security: simulations need to replace conventional wisdom., Proceedings of the New Security Paradigms Workshop (NSPW11), ISBN 978-1-4503-1078-9, ACM, pp. 115-124, 2011.
Paper (PDF) at Conference Website

K. Hamacher. Free Energy of Contact Formation in Proteins - Efficient Computation in the Elastic Network Approximation. Phys. Rev. E, 84:016703, 2011. (selected for publication in the Virtual Journal of Biological Physics Research)
Abstract & PDF

T. Strunk, K. Hamacher, F. Hoffgaard, H. Engelhardt, M.D. Zillig, K. Faist, W. Wenzel, F. Pfeifer. Structural Model of the Gas Vesicle Protein GvpA and Analysis of GvpA Mutants in vivo, Molecular Microbiology, 81(1):56-68, 2011
Abstract & PDF-Version

M. Gebhardt, F. Hoffgaard, K. Hamacher, S.M. Kast, A. Moroni, G. Thiel. Membrane anchoring and interaction between transmembrane domains is cruical for K+ channel function, J. Biol. Chem., 286(13):11299-11306, 2011
PubMed entry

B. Deiseroth, M. Franz, K. Hamacher, S. Jha, S. Katzenbeisser, H. Schröder. Towards Secure Bioinformatics Services, Financial Cryptography and Data Security (FC2011), Springer Lecture Notes in Computer Sciences (LNCS 7035), pp. 276-283, 2011
PDF in LNCS volume

K. Hamacher. Efficient quantification of the importance of contacts for the dynamical stability of proteins, J. Comp. Chem., 32(5):810-815, 2011
Abstract & PDF-Version

P. Boba, P. Weil, F. Hoffgaard, K. Hamacher. Intra- and Inter-Molecular Co-Evolution: The Case of of HIV1 Protease and Reverse Transcriptase, Proc. of BIOINFORMATICS 2010 (11% acceptance ratio, Best Paper Award), Springer Communications in Computer and Information Science 127:356-366, 2011
PDF-Version of Preproceedings-Paper,    Supplemental Material


D. Reker, S. Katzenbeisser, K. Hamacher. Computation of Mutual Information From Hidden Markov Models, Computational Biology and Chemistry, 34:328-333, 2010
Abstract & PDF-Version

B. Deiseroth, M. Franz, K. Hamacher, S. Jha, S. Katzenbeisser, H. Schröder. Secure Computation on Non-Integer Values, 2010 IEEE International Workshop on Information Forensics and Security (WIFS-2010), IEEE Press (ISBN 978-1-4244-9078-3) p. 1-6, 2010
PDF via IEEE-Xplore
IACR preprint

S. Bremm, T. Schreck, P. Boba, S. Held, K. Hamacher. Computing and Visually Analyzing Mutual Information in Molecular Co-Evolution, BMC Bioinformatics, 11:330, 2010
    Abstract & PDF-Version

K. Hamacher. Efficient Perturbation Analysis of Elastic Network Models - Application to Acetylcholinesterase of T. californica, J. Comp. Phys., 229:7309-7316, 2010
Abstract & PDF-Version

K. Hamacher. Temperature dependence of fluctuations in HIV1-Protease, Eur. Biophys. J., 39:1051, 2010
Abstract & PDF-Version

F. Hoffgaard, P. Weil, K. Hamacher. BioPhysConnectoR: Connecting Sequence Information and Biophysical Models, BMC Bioinformatics, 11:199, 2010.
Abstract & PDF-Version

S. Pape, F. Hoffgaard, K. Hamacher. Distance-Dependent Classification of Amino Acids by Information Theory, Proteins: Structure, Function, and Bioinformatics, 78(10):2322-2328, 2010.
Abstract & Preprint

K. Hamacher. Protein Domain Phylogenies - Information Theory and Evolutionary Dynamics, Proc. of BIOINFORMATICS 2010 (11% acceptance ratio), p. 114-122, A. Fred, J. Filipe, H. Gamboa (eds.), ISBN 978-989-674-019-1


P. Weil, F. Hoffgaard, K. Hamacher. Estimating Sufficient Statistics in Co-Evolutionary Analysis by Mutual Information, Computational Biology and Chemistry 33(6):440-444, 2009.
Abstract & PDF-Version

J. Ackermann, P. Baecher, T. Franzel, M. Goesele, K. Hamacher. Massively-Parallel Simulation of Biochemical Systems, Lecture Notes in Informatics, 154, 739-750, 2009, Proceedings of Massively Parallel Computational Biology on GPUs (BioGPU2009)
Entry at CUDA-Zone


K. Hamacher. Relating Sequence Evolution of HIV1-Protease to Its Underlying Molecular Mechanics , Gene, 422:30-36, 2008.
Abstract & PDF-Version
Erratum (PDF) to correct wrong table headings

K. Hamacher. Coarse-grained molecular models for high-throughput and multi-scale functional investigations, Chem.Cent.J., 2:S14, 2008.
Abstract & PDF-Version

K. Hamacher. Coarse-Grained Molecular Models for High-Throughput and Multi-Scale Functional Investigations, Proceedings of CBSB08 (From Computational Biophysics to Systems Biology), U.H.E. Hansmann, et al. (eds.), (ISBN 978-3-9810843-6-8), NIC Series Volume 40, 97-100, 2008.


K. Hamacher. Adaptive Extremal Optimization by Detrended Fluctuation Analysis, J.Comp.Phys., 227(2):1500-1509, 2007.
Abstract & PDF-Version

K. Hamacher. Information Theoretical Measures to Analyze Trajectories in Rational Molecular Design, J.Comp.Chem., 28(16):2576-2580, 2007.
Abstract & PDF-Version

K. Hamacher. Energy landscape paving as a perfect optimization approach under detrended fluctuation analysis, Physica A 378(2):307-314, 2007.
Abstract & PDF-Version


K. Hamacher. Adaptation in Stochastic Tunneling Global Optimization of Complex Potential Energy Landscapes, Europhys.Lett. 74(6):944, 2006.
Abstract & PDF-Version

K. Hamacher, A. Hübsch, J.A. McCammon. A Minimal Model for Stabilization of Biomolecules by Hydrocarbon Cross-Linking, J.Chem.Phys. 124:164907, 2006. (selected for publication in the Virtual Journal of Biological Physics Research)
Abstract & PDF-Version

K. Hamacher, J.A. McCammon. Computing the amino acid specificity of fluctuations in biomolecular systems, J.Chem.Theo.Comp. 2:873, 2006.
Abstract & PDF-Version

K. Hamacher, J. Trylska, J.A. McCammon. Dependency Map of Proteins in the Small Ribosomal Subunit. PLoS Comput. Biol. 2(2): e10, 2006.
Online- & PDF-Version


K. Hamacher. On Stochastic Global Optimization of one-dimensional functions. Physica A 354:547-557, 2005.
Abstract & PDF-Version

C. Gros, K. Hamacher, W. Wenzel. Breakdown of the Luttinger sum-rule at the Mott-Hubbard transition in the one-dimensional t1-t2 Hubbard model. Europhys. Lett. 69(4):616, 2005.
Abstract & PDF


K. Hamacher, C. Gros, W. Wenzel. Interaction-induced collapse of a section of the Fermi sea in the zig-zag Hubbard ladder. Phys. Rev. Lett 88:217203, 2002. (selected for publication in the Virtual Journal of Nanoscale Science & Technology)
Reprint: PDF-Version

K. Hamacher, J. Stolze, W. Wenzel. Disorder Induced Quantum Phase Transition in Random-Exchange Spin-1/2 Chains. Phys. Rev. Lett. 89:127202, 2002. (selected for publication in the Virtual Journal of Nanoscale Science & Technology)
Abstract & PDF

J. Sirker, A. Klümper, K. Hamacher. Groundstate properties of two-dimensional dimerized Heisenberg models. Phys. Rev. B, 65:134409, 2002.
Abstract & PDF


K. Hamacher, "Untersuchung quantenmechanischer Korrelationen mit der Dichtematrix-Renormierungsgruppe", PhD-Thesis, Dortmund University, 2001.


C. Gros, R. Valenti, J.V. Alvarez, K. Hamacher and W. Wenzel. Test of the frustrated spin-cluster model to describe the low-temperature physics of NaV2O5.    Phys. Rev. B (Rapid Comm.), 62(22):R14617-R14620, 2000.
Reprint: Postscript-Version,   PDF-Version

P. Stampfuß, K. Hamacher, and W. Wenzel. A massively parallel configuration-selecting multi-reference configuration interaction implementation. J. Mol.Struc.(THEOCHEM), 506:99-106, 2000.
Reprint: Postscript-Version,   PDF-Version


W. Wenzel and K. Hamacher. A Stochastic tunneling approach for global minimization. Phys. Rev. Lett., 82(15):3003-3007, 1999.
Abstract & PDF

W. Wenzel and K. Hamacher. Scaling Laws for Protein Folding. In D. Reguera, J.M.G. Vilar, and J.M. Rubi, editors, Statistical Mechanics of Biocomplexity, Springer Lecture Notes in Physics, New York, p. 62-71, 1999. Springer.

K. Hamacher and W. Wenzel. The Scaling Behaviour of Stochastic Minimization Algorithms in a Perfect Funnel Landscape. Phys. Rev. E, 59(1):938-941, 1999.
Abstract & PDF


K. Hamacher. "Optimierung Hochdimensionaler Funktionen im Hinblick auf die Strukturvorhersage von Proteinen" , 1998. Diploma Thesis. Available on request.

K. Hamacher and W. Wenzel. Scaling behaviour of Minimization Algorithms in a Simple Model of Protein Folding. In Proceedings of the HLRZ-Workshop ``Monte Carlo Approach to Biopolymers and Protein Folding'', Singapore, 1998. World Scientific.
Reprint: PostScript-Version,   PDF-Version

Invited Talks

"Coarse-Grained Models of Ion Channels to Elucidate Mechanics and Function", International Symposium on Ion channel design using experimental and computational inputs, 10-12/09/18, Gargnano (Brescia), Italy, Link

"Getting Real: Merging Bioinformatics Standards and Crypto-State-of-the-Art", TMF Workshop - Omics in Medical Research, 12/05/17, Berlin

"Cryptographic Protocols for Data Sharing in Chemo- and Bioinformatics", 13. GCC - German Conference on Chemoinformatics 2017, Mainz, 05.11.2017

"Computational Methods for Biostatistics and (Biological) Meaning", Leibniz-Institute for analytical Sciences ISAS e.V. and TU Dortmund, 05.05.2017

"Computational Biology: Challenges in Discrete Mathematics and Optimization", Colloquium Dept. of Mathematics and Computer Science, Fernuniversität Hagen, Germany 07.03.2016

"Entropy concepts in genomics, biophysics, and other fields", NeuroBioTheory Lecture Series, Max Planck for Brain Research, Frankfurt, Germany 07.07.2015

"Genomic Privacy", Cyber Security Group, TU Delft, The Netherlands, 14.07.2014

"Datenschutz und Genomik", Thüringer Landesbeauftragte für Datenschutz und die Informationsfreiheit, 20-Jahr-Feier, 02.07.2014

"Privacy and IT-Security as Enabling Technologies for Personalized Medicine", Alumni-Treffen of the Boehringer Ingelheim Fonds, Schloss Gracht, 28.06.2014

"Stochastic Tunneling and Time Series Analysis for Global Optimization Techniques", Theorie-Kolloquium, Institut für Physik, Universität Oldenburg, 08.05.2014

"2014 ist später als 1984", 9. Eichstätter Fachtagung zur Sozialinformatik, Katholische Universität Eichstätt-Ingolstadt, 02/27/2014

"The Bitcoin Transaction Network", Gesellschaft für Informatik, Regionalgruppe Heidelberg, 01/23/2014

"Alternate entropy measure for assessing volatility in financial markets", Annual Meeting of the German Physical Society (DPG), Regensburg, Germany; March 2013

"Stochastic Tunneling Optimization and Self-Adaptation in Stochastic Optimization Procedures", Berlin Center for Studies of Complex Chemical Systems, Fritz-Haber-Institute of the Max-Planck-Society, Berlin, 01/18/2013

"Converting Biospecimens into Secure Information: Cryptographic Assurance for Biobank-Derived Data", Biobanks - Advancing Science and Serving Society in the 21st Century of the European, Middle Eastern and African Society for Biopreservation and Biobanking (ESBB), Spain, 11/09/2012

"Fluctuations in Metabolic Systems - from Stability to Metabolic Engineering", at the Conference Complex Network Analysis: From Graph Theory to Systems Biology, Hall in Typrol, Austria, 10/03/2012

"Correlations Everywhere", 05/02/2012, Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Germany

"Computational modeling of intracellular networks beyond flux balance analysis", 1st Annual Meeting PlantEngine I: Current state and vision for the future, 11/18/2011, Murcia, Spain

Talk during Leopoldina-Symposium "Growth and Defence in Plants: Resource Allocation at Multiple Scales", 07/03-05/10, Freising, Germany

"Correlations Everywhere - from GPUs to Visual Analytics", 06/15/2011, Dept. of CS, University of Mainz

"Correlating Evolutionary Dynamics with the Biophysical Realm by Multi-Scale Simulations", 12/15/2010, Kolloquium of the Paul-Ehrlich-Institute des Bundesministeriums für Gesundheit (Federal Ministry of Health)

Talk during "Symposium on Viral Membrane Proteins, Structure, Dynamics and Modulation", Heidelberg University, 11/05-07/10, Germany

"Von der Sequenz zur Systemdynamik und zurück", Dept. of Mathematics, University Potsdam, Germany, 10/15/09

"Molecular Biophysics and Optimization", Groningen Optimization Seminar, Dept. of Mathematics, Rijksuniversiteit Groningen, 09/24/09

"Annotating the molecular phenotype - how to understand HIV1-protease evolution towards drug resistance and a short story about the bacterial ribosome", Institute for Toxicology and Genetics, Research Center Karlsruhe, 06/02/09

"Annotation of the molecular phenotype - connecting information space with the biophysical realm", Theoretical Physics Colloquium, University of Cologne, 04/17/09

"Model Selection for Coevolution in Virology, Drug Resistance Developement, and Biophyiscs", Model Selection Day, joint workshop of the Max-Planck-Institute for molecular Genetics, Magdeburg University and the Max-Planck-Institute for Mathematics in the Natural Sciences, 04/06/09

"Reduced Molecular Models - a Computational Pipeline for Molecular Biophysics and Molecular Biology", CU New York, USA, 03/12/09

"Reduced Molecular Models - a Pipline for in silico Systemsbiology and Bioengineering", Merck KGaA, Darmstadt, Germany, 03/02/09

"Reduced Molecular Models : a Pipeline for in-silico Systemsbiology and Biomolecular Engineering", B-IT Center, Dept. of Computer Science, Bonn University, Germany, 12/23/08

"Reduzierte Molekularmodelle für das Biomolecular Design", FH Giessen-Friedberg, Germany, 12/17/08

"Connecting Physics & Information Theory: models for molecular phenotypes", Dept. of Physics, Technical University Dortmund, Germany, 09/01/08

"Connecting the Physical Realm to Biological Information Acquisition", Max-Planck-Institute for Physics of Complex Systems, Dresden, Germany, 08/28/08

"Global Optimization: a challenge in theoretical physics", Seminar in Optimization, Dept. of Mathematics, TU Darmstadt, 04/07/08

"From the Genome to the Proteome: how phylogenetic relationships can be inferred from genomic data without the need for sequence alignment", Systematics 2008, 04/07-11/08, Göttingen, Germany

"Computational Biophysics at multiple scales" , Theoretical Physics Colloquium, TU Darmstadt, 01/07/08

"Reduzierte Molekulare Modelle in der Biochemie: Ein Brückenschlag zwischen Molekulardynamik und Bioinformatik?", 10. Steinheimer Gespräche des Fonds der chemischen Industrie, Hanau, Germany, 05/10/07-05/12/07

"Reduced Molecular Models - Bridging the Gap between Bioinformatics and Molecular Biophysics", Symposium "Perspectives in Computational Biophysics", Max-Planck-Institute for Biophysics, Frankfurt, Germany, 01/22/07

"A Computational Framework for Bioengineering - Global Optimization and Reduced Molecular Models", Aachen Institute for Advanced Studies in Computational Engineering Science, RWTH Aachen, Germany, 01/12/07

"Reduced Molecular Models - Bridging the Gap between Bioinformatics and Molecular Biophysics", Colloquium Biology Department, Technische Universität Darmstadt, 12/20/06

"Reduced Molecular Models - Increased Systems Knowledge", Gesellschaft für biotechnologische Forschung (GBF), Braunschweig, Germany, 06/01/06

"Assembly of the Small Ribosomal Subunit - Reduced Molecular Model Computations", Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany, 03/14/06

"Reduced Molecular Models", Soft Matter Physics Seminar, Düsseldorf University, Germany, 01/10/06

"Reduced Molecular Models - Going Beyond Bioinformatics", Symposium Biotechnological Center, Technical University Dresden, 12/20/05

"Global Optimization by Tunneling and its Application in Protein Structure Prediction", Biophysics Seminar, Ruhr-Universität Bochum, Germany, 10/10/05

"Amino-Acid specific fluctuations in biomolecular systems -- Application to HIV1-Protease", Interdisciplinary Center for Mathemical and Computational Modelling, Warsaw University, 05/11/05

"Accelerated technological change and the role of time horizons", Symposium on Modeling and Simulation: The future of life, Frankfurt University, 05/05/05

"Molekulare Biophysik der Signal Transduction in B.subtilis", Statistical Physics Group, Wuppertal University, 03/30/05

"Molecular Biophysics of Protein-Protein-Interactions in Signal Transduction", Seminar "Theoretical aspects of the physics of condensed matter", Dortmund University, 01/05/2005

"Molecular Biophysics of Protein-Protein-Interactions in Signal Transduction", Theoretisch Physikalisches Kolloquium, Saarbrücken University, 12/15/2004

"DMRG: von Spins bis zur ab-initio-Rechnung", Frankfurt University, 04/20/2004, slides (German, PDF)

"Correlation effects and DMRG", "Condensed Matter Seminar", Augsburg University, 11/18/2003, slides (English, PDF)

"Computation of correlation effects with the DMRG", "Graduiertenkolleg", Marburg University, 04/23/2001, slides (German, Postscript, Zip-file), slides (German, PDF, Zip-file)

Contributed Talks

"Correlates between Biophysical Dynamics and Sequence Evolution of Proteins", 76. Annual Meeting of the Deutschen Physikalischen Gesellschaft (DPG), Section Condensed Matter Physics (Biophysics Topic Group), Berlin, Germany, 03/28/2012

"Generalized Entropies for Clustering, e.g., in Molecular Evolution", 76. Annual Meeting of the Deutschen Physikalischen Gesellschaft (DPG), Section Condensed Matter Physics (Topic Group on Dynamics and Statistical Physics), Berlin, Germany, 03/26/2012

"Monte-Carlo based Optimization in Computational Biophysics (and beyond)", CCP2010 - Conference on Computational Physics, Trondheim, Norway, 23-26/06/2010
Abstract (PDF)

"Coarse-Grained Parametrization of Protein Structure and Dynamics by Global Optimization", Annual Meeting of the Bunsen Society for Physical Chemistry, Bielefeld, Germany, 05/15/10

"Vom Kreationismus zum Kollektivismus - Fehlende Einsicht in die Leistung komplexer Systeme", 26C3, Berlin, 27-30.12.09
Video (1 of 6)

"Reduced Molecular Models for Functional Annotation of Molecular Phenotypes and Molecular Engineering", DFG/NSC Bilateral Symposium "Viral Membrane Proteins", Heidelberg, Germany, 12/13/08

"Introducing: BioPhysConnectoR", useR! 2008 conference, Dortmund, Germany, 08/13/08

"Coarse-Grained Molecular Models for High-Throughput and Multi-Scale Functional Investigations", Workshop 'From Computational Biophysics to Systems Biology 2008', Jülich, Germany, 05/19-21/08

"From Quantum Chemistry to Go-Models in Biomolecular Design - functional peptides in the BCL2-protein-family in leukaemia", Workshop on Multiscale Methods for the Design of Biofunctional Molecules, University Essen-Duisburg, Germany, 04/02-04/08

"Coarse-Grained Molecular Models for High-Throughput and Mutli-Scale Functional Investigations", 3. German Conference on Chemoinformatics, 21. CIC-Workshop 2007, Goslar, Germany, 11/11-13/07

"Detrended Fluctuation Analysis in Stochastic Global Optimization", 71. Annual Meeting of the Deutschen Physikalischen Gesellschaft (DPG), Section Dynamics and Statistical Physics, Regensburg, Germany, 03/29/07

"Reduced Molecular Models in (Bio)molecular Design", 71. Annual Meeting of the Deutschen Physikalischen Gesellschaft (DPG), Section Biological Physics, Regensburg, Germany, 03/26/07

"Reduced Molecular Models - Increased Systems Knowledge", XX. Sitges Conference on Statistical Mechanics, Sitges, Spain, 06/05/06-06/09/06

"Amino-Acid specific fluctuations in biomolecular systems - Application to HIV1-Protease", Symposium Theoretical Chemistry (STC 2005), Innsbruck, Austria, 09/05/05-09/07/05

"Untersuchung quantenmechanischer Korrelationseffekte mit der Dichtematrix-Renormierungsgruppe", Disputation (German PhD-thesis defense), 12/20/2001, slides (Postscript, Zip-file), slides (PDF)

"Computation of correlation effects with the DMRG", Seminar "Theoretical aspects of the physics of condensed matter", Dortmund University, 01/31/2001, slides (German, Postscript, Zip-file), slides (German, PDF, Zip-file)

"Quantum Mechanics and Game Theory", joined seminar of the computer science and physics department, Dortmund University, 06/27/2000, slides (German, Postscript), slides (German, PDF)

"The Scaling Behaviour of Algorithms for Global Optimization in Protein Folding", Annual Meeting of the German Physical Society (DPG), Bayreuth, 03/11/1998, slides (German, Postscript), slides (German, PDF)

"Protein Folding", Seminar "Theoretical aspects of the physics of condensed matter", Dortmund University, Dec. 1997

Poster Contributions

K. Hamacher, C. Gross, K. Schmitz, S. Jager. "Cleavage Product Accumulation Decreases the Activity of Cutinase during PET Hydrolysis", Annual Meeting of the German Chemical Society (Gesellschaft deutscher Chemiker - GdCh) in Berlin, 2017.

M. Waechter, K. Hamacher, F. Hoffgaard, S. Widmer, M. Goesele, "Random Permutation on a GPU - Is Your Algorithm Unbiased for n ≠ 2**m ?", High-Performance Graphics (HPG 2011), Vancouver, BC, Canada

Poster C. Batram , N.G. Jones, K. Hamacher, M. Günzel, M. Engstler "VSG expression is monitored via a conserved stem-loop in the 3'UTR of VSG genes" at the Kinetoplastid Molecular Cell Biology Meeting 2009, Woodshole, MA, USA, 04/26/09-04/29/09

Poster "Novel approaches to combine information & physics in biomolecular systems" at the Conference "Physical and Chemical Foundations of Bioinformatics Methods", Germany, 06/18/07-06/22/07

Poster "A minimal Model for the Stabilization of Biomolecules by hydrocarbon crosslinkers" at the 367. WE-Heraeus-Seminar: Biomolecular Simulation: From Physical Principles to Biological Function, Bad Honnef, Germany 05/22/06-05/24/06

Poster "Computing amino-acid specific fluctuations in biomolecular systems - Application to HIV1-Protease" at the First European Conference on Chemistry for the Life Sciences, Rimini, Italy, Oct. 05

Poster "Computing amino-acid specific fluctuations in biomolecular systems - Application to HIV1-Protease" at the American Conference on Theoretical Chemistry (ACTC 2005), Los Angeles 07/16/05-07/21/05

Poster "Protein-Protein-Interactions in Signal Transduction" at 91. Bunsen-Kolloquium, Göttingen University, 04/05/05-04/06/05

Poster "Two Aspects of Correlations in Spin-Chains: Breakdown of Universality in Random-Exchange S=1/2 XXZ Chains and Results for dimerized 2D-Heisenberg-Systems" at the Symposium "New Trends in DMRG", Forschungszentrum Jülich, Germany, 07/23/2001
PDF-Version (English)

Poster "Correlations in Random-Exchange S=1/2 XXZ-Chains - Breakdown of Universality" at the conference "Korrelationstage 2001" of the Max-Planck-Institute for complex systems, Dresden, Germany, 02/14-17/2001
Postscript-Version (English), PDF-Version (English)

Talk R.Bundschuh, K.Hamacher, T.Hwa, "RNA secondary structures and phase transitions" , March Meeting of the American Physical Society 1999, Atlanta, GA, USA, 3/21/99-3/26/99
Postscript-Version (English), PDF-Version (English)

Poster "Scaling Behaviour of Minimization Algorithms for a Simple Model of Protein Folding" at the HLRZ-Workshop "Monte Carlo Approach to Biopolymers and Protein Folding", Jülich, 1997
Postscript-Version (English), PDF-Version (English)

Miscellaneous Papers

K. Hamacher. Leistungssschutzrecht: Fragwürdiger Schutz vor der Medienevolution Carta.Info, 2010.

K. Hamacher. Vom Kreationismus zum Kollektivismus - Fehlende Einsicht in die Leistung komplexer Systeme Proc. of 26C3, 2009, 243-247.
(ISBN 978-3-934636-08-8-0)
Paper (PDF)

K.Hamacher, "Probability, Statistics, Science?", ZiF:Mitteilungen, Bielefeld University, 2009(1)52

K.Hamacher, "Accelerated technological change and the role of time horizons", Proceedings of the Symposium on Modeling and Simulation: The Future of Life and the Future of our Civilization, 2006, Springer Series on Biomedicine, pp. 205-215, ISBN 978-1-4020-4968-2
Paper (PDF) at Springer
Paper (PDF) at Z25

K.Hamacher, "Nutzung der Compute-Server in der Computational Physics", ComputerPostille, Hochschulrechenzentrum, Universität Dortmund, 2000 (German)
Postscript-Version,   PDF-Version

K. Hamacher. MINILIB - Documentation for the Minimzation-Objects. Technical report, Theoretical Physics, Dortmund University, 1997.

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