Statistical Physics and Theoretical Biophysics Group

Publications

• Paper
• Books
• Other Articles
• Talks
• Posters
• Patents

Papers 

• The Role of Nucleotide Opening Dynamics in Facilitated Target Search by DNA-Repair Proteins
  Sujeet Kumar Mishra, Sangeeta, Dieter Heermann and Arnab Bhattacherjee
  2024, BBA - Gene Regulatory Mechanisms, accepted
• The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of proVWX in E. coli
  F.Z.M. Rashid, Frederic Cremazy, Andreas Hofmann, D.A., David Grainger, Remus T. Dame and Dieter Heermann
  Nature Communications, 2023-11-17 DOI: 10.1038/s41467-023-43322-y
• Efficient Image Feature Extraction through Simultaneous Training of Nested U-Nets
  Sujeet Kumar Mishra and Dieter Heermann
  9th International Conference on Signal Processing and Communication (ICSC), 2023 accepted
• A chromosomal loop anchor mediates bacterial genome organization
  Gaurav Dugar, Andreas Hofmann, Dieter W. Heermann and Leendert W. Hamoen
  Nat Genet 54, 194–201 (2022)
• Inter-Nucleosomal Potentials from Nucleosomal Positioning Data
  Kunhe Li, Nestor Norio Oiwa, Sujeet Kumar Mishra and Dieter Heermann
  European Physical Journal E 2022, accepted
• Prediction and comparative analysis of CTCF binding sites based on a first principle approach
  Nestor Norio Oiwa, Kunhe Li, Claudette E. Cordeiro and Dieter W. Heermann
  Phys. Biol. 2022 https://doi.org/10.1088/1478-3975/ac5dca
• Robust interaction between insulator-like domains drives genome organization in bacteria
  Gaurav Dugar, Andreas Hofmann, Dieter W. Heermann and Leendert W. Hamoen
  Nature Genetics 2021, accepted
• Topological analysis of γH2AXand MRE11 clusters detected by localization microscopy during X-ray induced DNA double- strand break repair
  Hannes Hahn, Charlotte Neitzel, Olga Kopečná, Dieter W. Heermann, Martin Falk, Michael Hausmann
  preprint 2021
• Elucidation of the clustered nano-architecture of radiation induced DNA damage sites and surrounding chromatin in cancer cells: a single molecule localization microscopy approach
  Michael Hausmann, Martin Falk, Charlotte Neitzel, Andreas Hofmann, Albin Biswas, Theresa Gier, Iva Falkova, Dieter W. Heermann, and Georg Hildenbrand
  preprint 2021
• Telomerase subunit Est2 marks endogenous sites that are prone to accumulate DNA damage
  Satyaprakash Pandey; Mona Hajikazemi; Theresa Zacheja; Stephanie Schalbetter; Jon Baxter; Victor Guryev; Andreas Hofmann; Dieter Heermann; Stefan Juranek; Katrin Paeschke
  preprint 2021
• Single Molecule Localization Microscopy Analyses of DNA-Repair Foci and Clusters Detected along Particle Damage Tracks
  Michael Hausmann, Charlotte Neitzel, Elizaveta Bobkova, David Nagel, Andreas Hofmann, Tatyana Chramko, Elena Smirnova, Olga Kopečná, Eva Pagáčová , Alla Boreyko, Evgeny Krasavin, Iva Falkova, Dieter W. Heermann, Götz Pilarczyk , Georg Hildenbrand, Felix Bestvater, Martin Falk
  Front. Phys. 2020 | doi: 10.3389/fphy.2020.578662
• Space and time in the universe of the cell nucleus after ionizing radiation attacks: a comparison of cancer and non-cancer cell response
  Michael Hausmann, Charlotte Neitzel, Hannes Hahn, Ruth Winter, Iva Falkova, Dieter W. Heermann, Goetz Pilarczyk, Georg Hildenbrand, Martin Falk
  Conference: The 1st International Electronic Conference on Cancers: Exploiting Cancer Vulnerability by Targeting the DNA Damage Response Med. Sci. Forum 2021, 3(1), 15; https://doi.org/10.3390/IECC2021-09219
• Fractality and Topology in the Self-Avoiding Walks
  Jiying Jia and Dieter W. Heermann
  Preprint 2020
• Domain Boundary Detection in Hi-C Maps: A Probabilistic Graphical Model Approach
  Andreas Hofmann, Fatema Zahra Rashid, Fr\'{e}d\'{e}ric Cr\'{e}mazy, Remus T. Dame and Dieter W. Heermann
  Preprint 2020
• Self-organised segregation of bacterial chromosomal origins
  Andreas Hofmann, Jarno Mäkelä, David J Sherratt, Dieter Heermann, Seán M Murray
  eLife 2019;8:e46564
• BEKVAEM: integrative data explorer for HI-C data
  Andreas Hofmann, J. Müggenburg, F. Crémazy and Dieter Heermann
  Journal of Bioinformatics and Genomics 2 (11) 2019
• The Effect of Bending Rigidity on Polymers
  Jiying Jia, Kunhe Li, Andreas Hofmann and Dieter Heermann
  Macromolecular Theory and Simulations Volume28, Issue3 May 2019, 1970005
• Using Persistent Homology as a New Approach for Super-Resolution Localization Microscopy Data Analysis and Classification of γH2AX Foci
  Andreas Hofmann, Matthias Krufczik, Dieter W. Heermann, Michael Hausmann
  Interational Journal of Molecular Biophysics, Volume 19 Issue 8, 2018
  doi.org/10.3390/ijms19082263
• Overview of processing and analyzing Hi-C data on bacteria (chapter)
  Andreas Hofmann and Dieter W. Heermann
  Methods in Molecular Biology, Book edited by Remus Dame, Springer 2018
• Deciphering 3D organization of chromosomes using Hi-C data (chapter)
  Andreas Hofmann and Dieter W. Heermann
  Methods in Molecular Biology, Book edited by Remus Dame, Springer 2018
• Robust detection and quantification of nuclear structures in histopathological images within a computational topology framework
  Rodrigo Rojas-Moraleda, Wei Xiong, Katja Breitkopf-Heinlein, Steven Dooley, Steven Härtel, Luis Salinas, Dieter W. Heermann, Nektarios A. Valous
  Medical Image Analysis 2017 DOI
• A Three-Pronged Attack To Investigate the Electronic Structure of a Family of Ferromagnetic Fe4Ln2 Cyclic Coordination Clusters: A Combined Magnetic Susceptibility, High-Field/High-Frequency Electron Paramagnetic Resonance, and 57Fe Mössbauer Study
  Schmidt, Sebastian F. M. and Koo, Changhyun and Mereacre, Valeriu and Park, Jaena and Heermann, Dieter W. and Kataev, Vladislav and Anson, Christopher E. and Prodius, Denis and Novitchi, Ghenadie and Klingeler, Rüdiger and Powell, Annie K.
  Inorganic Chemistry, 2017 PMID: 28186414
• The Electronic Behavior of Zinc-Finger Protein Binding Sites in the Context of the DNA Extended Ladder Model
  Nestor N. Oiwa, Claudette E. Cordeiro and Dieter W. Heermann
  Front. Phys., 11 May 2016 | http://dx.doi.org/10.3389/fphy.2016.00013
• Computational topology based quantification of hepatocytes nuclei in lipopolysaccharide-induced liver injury in mice
  R. Rojas Moraleda, W. Xiong, N. Valous, L. Salinas, K. Breitkopf-Heinlein, S. Dooley, I. Zoernig, D.W. Heermann, D. Jüger<\br> Proceedings of the 13th EUROPEAN CONGRESS ON DIGITAL PATHOLOGY DOI: 10.13140/RG.2.1.4959.4484 (2016)
• Viral channel forming proteins - how to assemble and depolarize lipid membranes in silico
  Wolfgang Fischer, Monoj Mon Kalita and Dieter Heermann
  BBA - Biomembranes, BBAMEM-15-411R1 2016 accepted
• The role of loops on the order of eukaryotes and prokaryotes
  Andreas Hofmann and Dieter W. Heermann
  FEBS Letters, Volume 589, Issue 20 Part A, pages 2958–2965, October 07, 2015
• Computational Complexity of Agent-based Multi-scale Cancer Modeling
  Fei Xing, Jörg Eisele, Peter Bastian and Dieter W. Heermann
  2015 Summer Simulation Multi-Conference
  Society for Modeling & Simulation International (SCS) July 26-29, 2015, Chicago, IL, USA
• Radiation induced chromatin conformation changes analysed by fluorescent localization microscopy, statistical physics, and graph theory
  Yang Zhang, Gabriell Mate, Patrick Müller, Sabina Hillebrandt, Matthias Krufczik, Margund Bach, Rainer Kaufmann, Michael Hausmann, Dieter W. Heermann
  PLoS One, 2015 DOI: 10.1371/journal.pone.0128555
• A multiscale approach to simulating the conformational properties of unbound multi-C2H2 zinc finger proteins
  Lei Liu Rebecca C. Wade Dieter W. Heermann
  Proteins, DOI: 10.1002/prot.24845 2015
• Phase Transition and Winding properties of a Flexible Polymer adsorbed to a Rigid Perioidic Copolymer
  Lei Liu, David Schubert, Min Chu, and Dieter W. Heermann
  Phys. Rev. E 91, 032601 - Published 11 March 2015
• A generalized Potts model for confocal microscopy images
  Gabriell Mate and Dieter W. Heermann
  Int. J. Mod. Phys. B DOI: 10.1142/S0217979215500484
• The interaction of DNA with multi-Cys2His2 zinc finger proteins
  Lei Liu and Dieter W Heermann
  J Phys Condens Matter. 2015 Feb 18;27(6):064107. doi: 10.1088/0953-8984/27/6/064107. Epub 2015 Jan 7.
• Depletion of the chromatin looping proteins CTCF and cohesin causes chromatin compaction: insight into chromatin folding by polymer modelling
  Mariliis Tark-Dame, Hansjoerg Jerabek, Erik M.M. Manders, Dieter W. Heermann, Roel van Driel
  PLoS Comp Bio, DOI:10.1371/journal.pcbi.1003877 2014
• A three-dimensional distribution model of RNA polymerase II in a yeast nucleus
  Xiao Dong; Chao Li; Wu Wei; Rudong Li; Zhen Wang; Yunqin Chen; Tao Xu; Dieter W Heermann; Xiangyin Kong; Guohui Ding; Yixue Li
  Preprint 2014
• Statistical Analysis of Protein Ensembles
  Gabriell Mate and Dieter W. Heermann
  Frontiers in Physics, Vol. 2, 00020, 2014 (DOI=10.3389/fphy.2014.00020)
• Persistence Intervals of Fractals
  Gabriell Mate and Dieter W. Heermann
  Physica A, 2014 accepted, online since March 2014
• How Chromatin Looping and Nuclear Envelope Attachment Affect Genome Organization in Eukaryotic Cell Nuclei.
  Hansjoerg Jerabek and Dieter W Heermann
  International review of cell and molecular biology 01/2014 307C:351-381.
• A topological similarity measure for proteins
  Gabriell Mate, Andreas Hofmann, Nicolas Wenzel and Dieter W. Heermann
  BBA - Biomembranes, Available online 10 September 2013
• Mechanics of Sister Chromatids studied with a Polymer Model
  Yang Zhang, Sebastian Isbaner and Dieter W. Heermann
  Front. Physics doi: 10.3389/fphy.2013.00016
• Chromosome segregation by the Escherichia coli Min system
  Barbara Di Ventura, Benoit Knecht, Helena Andreas, William J. Godinez, Miriam Fritsche, Karl Rohr, Walter Nickel, Dieter W Heermann, Victor Sourjik
  Molecular Systems Biology 9 Article number: 686 doi:10.1038/msb.2013.44
• DNA Double-Strand Breaks: Linking Gene Expression to Chromosome Morphology and Mobility
  Yang Zhang and Dieter W. Heermann
  Chromosoma 2013 Aug 28. PMID: 23982751
• Transcriptional regulatory network shapes the genome structure of Saccharomyces cerevisiae
  Songling Li and Dieter W. Heermann
  Nucleus, Volume 4, Issue 3 May/June 2013 Pages 216 - 228 http://dx.doi.org/10.4161/nucl.24875
• Variation in structure of a protein (H2AX) with knowledge-based interactions
  Miriam Fritsche, Dieter W. Heermann, Barry Farmer and Ras Pandey
  PLoS ONE 2013
• Expression-Dependent Folding of Interphase Chromatin
  Hansjoerg Jerabek, Dieter W. Heermann
  PLoS One, Published: May 23, 2012, DOI: 10.1371/journal.pone.0037525
• Zinc Finger Proteins and the 3D Organisation of Chromosomes
  Christoph J. Feinauer, Andreas Hofmann, Sebastian Goldt, Lei Liu, Gabriell Mate, Dieter W. Heermann
  Advances in Protein Chemistry and Structural Biology, accepted 2012
• Using Chimeric ESTs as the Reference to Identify 3D Chromosome Contacts
  Songling Li and Dieter W. Heermann
  DNA Research 2012; doi: 10.1093/dnares/dss032
• A model for the 3D chromatin architecture of pro and eukaryotes
  Dieter W. Heermann, Hansjoerg Jerabek, Lei Liu,Yixue Li
  Methods, Available online 4 June 2012
• Mitotic Chromosome Structure
  Dieter W. Heermann
  Experimental Cell Research 318 (2012), pp. 1381-1385
• The Impact of Entropy on the Spatial Organization of Synaptonemal Complexes within the Cell Nucleus
  Miriam Fritsche, Laura G. Reinholdt, Mark Lessard, Mary Ann Handel, Jörg Bewersdorf, Dieter W. Heermann
  PLoS ONE 7(5): e36282. doi:10.1371/journal.pone.0036282
• Enhancing phosphorylation cascades by anomalous diffusion
  M. Hellmann, Dieter W. Heermann and M. Weiss
  EPL (Europhysics Letters), Vol. 97, Number 5, DOI: 10.1209/0295-5075/97/58004
• Conformational Temperature-Dependent Behavior of a Histone H2AX: A Coarse-Grained Monte Carlo Approach Via Knowledge-based Interaction Potentials
  Miriam Fritsche, Dieter W. Heermann, Barry Farmer and Ras Pandey
  PLoS ONE 7(3): e32075. doi:10.1371/journal.pone.0032075
• Using Chimeric ESTs as the Reference to Identify Inter- and Intra-chromosomal Gene Loci Interactions
  Songling Li, Dieter W. Heermann
  DNA Res (2012) doi: 10.1093/dnares/dss032
• Loops determine the mechanical properties of mitotic chromosomes
  Yang Zhang and Dieter W. Heermann
  PLoS ONE 6(12): e29225. doi:10.1371/journal.pone.0029225
• Understanding genome function: quantitative modelling of chromatin folding and chromatin-associated processes
  Mariliis Tark, Martijn S. Luijsterburg, Dieter W. Heermann, Roel van Driel
  book chapter edited by K. Rippe 2011 (see the online version of the book here)
• A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation
  Miriam Fritsche, Songling Li, Dieter W. Heermann, Paul A. Wiggins
  Nucleic Acids Research 2011, doi: 10.1093/nar/gkr779
• Confinement Driven Spatial Organization of Semiflexible Ring Polymers: Implications for Biopolymer Packaging
  Miriam Fritsche and Dieter W. Heermann
  Soft Matter 2011, Advance Article, DOI: 10.1039/C1SM05445G
• Challenges in determining anomalous diffusion in crowded fluids
  Marcel Hellmann, Joseph Klafter, Dieter W. Heermann, and Matthias Weiss
  J. Phys.: Condens. Matter 23 (2011) 234113
• Physical Nuclear Organization: Loops and Entropy
  Dieter W. Heermann
  Current Opinion in Cell Biology, DOI: 10.1016/j.ceb.2011.03.010 2011
• Anomalous reaction kinetics and domain formation on crowded membranes
  Marcel Hellmann, Dieter W. Heermann, and Matthias Weiss
  EPL 2011 accepted
• Repulsive Forces Between Looping Chromosomes Induce Entropy-Driven Segregation
  Manfred Bohn and Dieter W. Heermann
  PLoS ONE 6(1): e14428. doi:10.1371/journal.pone.0014428 (2011)
• Chromatin folding: from biology to polymer models and back
  Mariliis Tark-Dame, Roel van Driel, Dieter W. Heermann
  doi:10.1242/jcs.077628, March 15, 2011 J Cell Sci 124, 839-845
• Histone Depletion facilitates Chromatin Loops on the kbp Scale
  Philipp M. Diesinger, Susanne Kunkel, Jörg Langowski and Dieter W. Heermann
  Biophysical Journal, Volume 99 November 2010 2995-3001
• Monte Carlo Simulations indicate that Chromatin Nanostructure is accessible by Light Microscopy
  Philipp M Diesinger and Dieter W Heermann
  PMC Biophysics 2010, 3:11 doi:10.1186/1757-5036-3-11
• Conformational and Dynamical Properties of the Isolated, Three-Dimensional Single- and Double-Tethered Polymer Chain on an In
  nite Surface
  Miriam Fritsche, Dieter W. Heermann, Mariana Dutra and Claudette E. Cordeiro
  Macro Mol. Theo and Sim. 2010 DOI: 10.1002/mats.201000025
• Localization microscopy reveals expression-dependent parameters of chromatin nanostructures
  Manfred Bohn, Philipp Diesinger, Rainer Kaufmann, Yanina Weiland, Patrick Müller, Manuel Gunkel, Alexa von Ketteler, Paul Lemmer, Michael Hausmann, Dieter W. Heermann and Christoph Cremer
  Biophysical Journal, Biophysical Journal, Volume 99, Issue 5, 1358-1367, 8 September 2010
• Temperature-dependent structural behavior of self-avoiding walks on three-dimensional Sierpinski square lattices
  Miriam Fritsche and Dieter W. Heermann,
  Phys. Rev E. 2010 accepted
• Polymer translocation through a nanopore - the effect of solvent conditions
  Felix Kapahnke, Ulrich Schmidt, Dieter Heermann, and Matthias Weiss
  J. Chem. Phys. 132, 164904 (2010); doi:10.1063/1.3400650
• On the Influence of Topological Catenation and Bonding Constraints on Ring Polymers
  Manfred Bohn, Dieter W. Heermann, Odilon Lourenço, Claudette Cordeiro
  Macromolecules, 2010, 43 (5), pp 25642573 DOI: 10.1021/ma902623u
• Topological interactions between ring polymers: Implications for chromatin loops
  Manfred Bohn and Dieter W. Heermann
  J. Chem. Phys. 132, 044904 (2010); doi:10.1063/1.3302812
• The Relation between the Gene Network and the Physical Structure of Chromosomes
  Dieter Heermann, Manfred Bohn and P.M. Diesinger
  Proceedings HPSC Hanoi 2009
• Hydrophobicity as a possible Reason for Gelation of FG-rich Nucleoporins
  P.M. Diesinger and D.W. Heermann
  European Biophysics Journal: Volume 39, Issue 2 (2010), Page 299
• Brownian Dynamics simulations reveal regulatory properties of higher order chromatin structures
  Jens Odenheimer, Dieter W. Heermann, Gregor Kreth
  European Biophysics Journal Volume 38, Number 6, 749-756, DOI: 10.1007/s00249-009-0486-1
• Depletion Effects Massively Change Chromatin Properties and Influence Genome Folding
  P.M. Diesinger and D.W. Heermann
  Biophysical Journal Volume 97, Issue 8, 21 October 2009, Pages 2146-2153, doi:10.1016/j.bpj.2009.06.057
• Conformational properties of compact polymers
  M. Bohn and D.W. Heermann
  J. Chem. Phys. 130, 174901 (2009); DOI:10.1063/1.3126651
• Phase transition of a two-dimensional, multiplicatively coupled XY-Potts model
  Marcel Hellmann, Youjin Deng, Matthias Weiss, and Dieter W. Heermann
  J. Phys. A: Math. Theor. 2009
• Spatially confined folding of chromatin in the interphase nucleus
  Julio Mateos-Langerak, Manfred Bohn, Wim de Leeuw, Osdilly Giromus, Erik M. M. Manders, Pernette J. Verschure, Mireille H. G. Indemans, Hinco J. Gierman, Dieter W. Heermann, Roel van Driel and Sandra Goetze
  PNAS March 10, 2009 vol. 106 no. 10 3812-3817
• Average crossing number of equilateral and Gaussian chains with and without excluded volume
  P.M. Diesinger and Dieter W. Heermann,
  European Journal of Physics B, Volume 62, Number 2, 209-214 (2008), DOI 10.1140/epjb/e2008-00145-6
• Computational Modelling of the Chromatin Fiber,
  J. Langowski and Dieter W. Heermann,
  Seminars in Cell and Developmental Biology, 2007
• The influence of the cylindrical shape of the nucleosomes and H1 defects on properties of chromatin,
  P.M. Diesinger and Dieter W. Heermann, Biophys. J. doi:10.1529/biophysj.107.113902
• Superdiffusion in a Model for Diffusion in a Molecularly Crowded Environment,
  Dietrich Stauffer, Christian Schulze, Dieter W. Heermann, preprint 2007
• A Random Loop Model for Long Polymers,
  M. Bohn, D.W. Heermann and R. van Driel, Phys. Rev. E 76, 051805 (2007)
• Percolation in a Class of Band Structured Random Matrices,
  D.W. Heermann and M. Bohn, preprint 2007
• Monte Carlo simulations reveal the straightening up of an end-grafted flexible chain with a rigid side chain,
  M. Hellmann, M. Weiss, D.W. Heermann,Phys. Rev. E 76, 021802 (2007)
• Gene Silencing by Structural Inacessibility of 1Mbp Chromatin Domains,
  J. Odenheimner, G. Kreth, D. W. Heermann and Ch. Cremer, preprint 2006
• Structure of Polymer Brushes in Cylindrical Tubes: A Molecular Dynamics Simulation,
  D. I. Dimitrov, A. Milchev, K. Binder, and D. W. Heermann, Macromolecular Theory and Simulation, 7, 523 - 526 (2006)
• Modelling of Polycomb-dependent chromosomal interactions involved in Drosophila gene silencing, Silke Ritter, Jens Odenheimer, Dieter W. Heermann, Frederic Bantignies, Charlotte Grimaud and Giacomo Cavalli
  Biophysical Review and Letters 1, 151-162 (2006)
• Forces by and on a polymer grafted to a repulsive wall, J. Odenheimer, M. Brill and D.W. Heermann, Int. J. Mod. Phys. C, 16, 1577-1586 (2005)
• Modelling and simulation of polycomb-dependent chromosomal interactions in drosophilas, S. Ritter, D.W. Heermann, F. Bantignies, G. Cavalli, Eur. Biophys. J, 34, 604 (2005)
• The two-angle model and the phase diagram of chromatin, P.M. Diesinger and D.W. Heermann, Eur. Biophys. J, 34, 632 (2005)
• Accessibility and diffusion of transcription factor complexes into 1Mbp chromatin domains, J.A. Odenheimer, G. Kreth, D.W. Heermann, R. Martin, C. Cardoso, Eur. Biophys. J, 34, 637 (2005)
• Knots in Macromolecules in constraint space,
  M. Brill, P.M. Diesinger, D.W. Heermann, cond-mat/0507020 2005
• The two-angle model and the phase diagram for Chromatin P.M. Diesinger, D.W. Heermann, cond-mat/0505042 2005
• Dynamic Simulation of Active/Inactive Chromatin Domains J. Odenheimer, G. Kreth, D.W. Heermann, J. Bio. Phys. (2004) accepted
• Mathematical Modeling reveals threshold behaviour of CD95-induced Apoptosis M. Bentele, I. Lavrik, M. Ulrich, S. Stösser, H. Kalthoff, D. W. Heermann, P. H. Krammer, R. Eils, J. Cell. Bio. (2004) accepted
• Computing the compressibility for macromolecular systems, D.W. Heermann, preprint 2004
• Simulation of Scratching in amorphous polymer films, D.W. Heermann and G. Schöppe, preprint 2003
• Reconstruction of the Free Energy in the Metastable Region using the Path Ensemble, A. Ticona, D.W. Heermann, and C. Cordeiro, J. Chem. Phys. (2004) accepted
• Experiments and Modelling of Nulceation in the Hexadecan/CO2-System, E. Hädike, H. Schuch, K. Binder, P. Virnau, M. Müller and L.G. MacDowell, preprint 2003
• Evidence for sharper than expected transition between metastable and unstable states, D.W. Heermann and C. Cordeiro, Int. J. Mod. Phys. 13, 1419 (2003)
• Teaching Science Using a Mobile Phone, D. W. Heermann, Int. J. Mod. Phys. 13, 1393 (2002)
• Nucleation and Metastability in the CO2-System, Dieter W. Heermann, Ting Wang and Wei-Der Lee, Int. J. Mod. Phys. 13, 81 (2002)
• Nucleation in Polymer / CO2-Systems, Internal Report BASF-BMBF Fall 2001
• Nucleation in Polymer / CO2-Systems, Internal Report BASF-BMBF Spring 2001
• Computer simulation of nano-indentation into polymer films, D.W. Heermann, MRS Fall Meeting, Symposium Z: Multiscale Materials Modelling, 2000
• Computer simulation of friction of polymer surfaces, D.W. Heermann, MRS Fall Meeting Symposium Q: Fundamentals of Nanoindentation and Nanotribology II, 2000
• Teaching Physics in the Virtual University: The Mechanics Toolkit D. W. Heermann and T.T. Fuhrmann Comput. Phys. Commun. (Netherlands), Netherlands: Elsevier, vol.127, no.1, May 2000 p.11-15, 5 Refs. / 6616785
• Universal Physics Modeling Environment in Java, T. Fuhrmann and D.W. Heermann, CA Conference paper (C) / 2nd International Conference on New Learning Technologies / Fluckiger, F.; Braun, T.; Ninck, A.. - Berne, Switzerland, Switzerland: NDIT/FPIT, 1999, vii+308 p.112-17, 8 Refs. / 6566080
• Java Teachware  The Java Remote Control Tool and its Applications, S. T. Fuhrmann, C. Kuhmünch, G. Schöppe, G. Pätzold, D.W. Heermann and W. Effelsberg
• Diffusion of Gas Molecules in the Polystyrene Matrix, T.   Wang, D.W. Heermann, J.C. Heilig,
  Macromolecular Theory and Simulations Volume 9, Issue 9 , Pages 687 - 697 (2000)
• Entwicklung eines web-basierten interaktiven Physikbaukastens und mathematischen Vorkurses
  Thomas Fuhrmann, Dieter W. Heermann, Klaus Hefft, and Jörg HüfnerProceedings of the Workshop on Physics and Computer Science, pages 157-161, Kiel, Germany, 1999
• Molecular Dynamics Simulation of Scratching Test on Amorphous Polymer Films, Y. Sasajima, G. Schöppe, T. Hapke, D.W. Heermann, Preprint (1999)
• Alternative off-lattice model with continuous backbone mass for polymers, G. Schöppe and D.W. Heermann, Phys. Rev. E. 59, 636-641 (1999)
• Surface Tension of amorphous polymer films, T. Hapke and D.W. Heermann, J. Chem. Phys. 109, 10075-10081 (1998)
• Description of noble gas diffusion in a polymer matrix by a hopping model, A.K. Hartmann and D.W. Heermann, J.Chem. Phys. 108,  9550-9557 (1998)
• Computer Simulation of Nanoindentation into polymer films, G. Pätzold, A Linke, T. Hapke and D.W. Heermann, Z. Phys. B (1997)
• Simulation of Polymers Using the Ellipsoidal Model, G. Schöppe and D.W. Heermann, Preprint 1997
• Properties of polymer melts and solutions using the ellipsoidal model, K. M. Zimmer, G. Schöppe and D.W. Heermann, preprint 1997
• Evidence of Repation Using the Ellipsoidal Model, G. Schöppe and D.W. Heermann, preprint 1996
• A tool for materials exploration, Ch. Münkel, A. Linke, and D.W. Heermann, Simulation Practice and Theory (1996) accepted
• Deformation of polymer films by bending forces G. Pätzold, Th. Hapke A. Linke and D.W. Heermann, J. Thin Film Solids, accepted
• Modelling of amorphous polymer surfaces in computer simulation, Th. Hapke, A. Linke, G. Pätzold and D.W. Heermann, Surface Science, 1997 (accepted)
• Monte Carlo simulation of film growth, S. Ozawa, Y . Sasajima, and D.W. Heermann, Thin Solid Films 272, 172-183 (1996)
• Scaling solutions and finite-size effects in the Liftshitz-Slyozov theory, D.W. Heermann, Li Yixue and K. Binder, Physica A 230, 132-148 (1996)
• Ellipsoidal Potential Parameterization for BPA-PC polymer systems, K. Zimmer, A. Linke, J. Batoulis and D.W. Heermann, Macromol. Theory Simul. 5, (1996)
• A New General Model with non-spherical interactions for dense polymer systems  and a potential parameterization for BPA-PC, K. Zimmer, A. Linke and D.W. Heermann, Anual Meeting of the American Chemical Engineering Society, Miami, Florida, (1995)
• Parallelization of Physics Problems, D.W. Heermann, Proceedings of  the Summer School on Computer Simulation Methods, Como, 1995
• Large-Scale Simulation of the  Two-dimensional Kinetic Ising Model, A. Linke, D.W. Heermann, P. Altevogt and M. Siegert,  Physica A. (1995)
• The Crumbling Transition of Dynamically Triangulated Random Surfaces, Ch. Münkel and D.W. Heermann, J. Phys. I France 3, 1359-1370 (1994)
• A new model with non-sperherical intercations for dense polymer systems, D.W. Heermann, K. Zimmer, preprint (1994)
• Phase Diagram of Polyethylene in the Canonical Ensemble, D.W. Heermann, S. Ozawa, K. Zimmer and Ch. Münkel,  preprint (1994)
• A Monte Carlo Study of the Ising Model with Uniaxial Anisotropy, N. Wilding and D.W. Heermann, J. Mag. and Mag. Mat. 135, 51-56 (1994)
• Domain growth and finite-size-scaling in the kinetic Ising model, N.B. Wilding, Ch. Münkel and D.W. Heermann Z. Phys. B (1994)
• Large Scale Simulations of the Kinetic Ising Model, Ch. Münkel and D.W. Heermann, Int. J. Mod. Phys. C  x, xx (1993)
• Structural properties of two-dimensional polymers, Ch. Münkel and D.W. Heermann, Physica A (1993)
• A Global-Update Simulation Method for Polymer Systems, D.W. Heermann and Li Yixue   Makroml Chemie: Theory and Sim. 2, 299-308 (1993)
• Metastability and Dynamics, D.W. Heermann, Int. J. Mod. Phys. C  3, 49-52 (1992)
• The Dynamical Critical Exponent of the Two-, Three- and Five-Dimensional Kinetic Ising Model, Ch. Münkel, D.W. Heermann, J. Adler, M. Gofman, and D. Stauffer, Physica A, (1992)
• Critcal Dynamics of the Hybrid Monte Carlo Algorithm, B. Mehlig, A. Ferreira, and D.W. Heermann  Phys. Lett B., (1992)
• Visualization of Polymer Systems, Ch. Münkel and D.W. Heermann,   J. of Visualization and Comp. Animation 3 175-181 (1992)
• Spinodal Decomposition of Polymer Blends, D.W. Heermann and B.M. Forrest  Polymer Preprints 1992
• A Global Simulation Algorithm, B. Mehlig, D.W. Heermann and B. Forrest  Theoretica Chimica Acta, (1992)
• Exact Langevin Algorithms, B. Mehlig, D.W. Heermann, and B. Forrest, Mol. Phys.  76 1347-1357 (1992)
• Fractal Dimensions of Dynamically Triangulated Random Surfaces, Ch. Münkel and D.W. Heermann   J. de Physique,  2, 2181-2190 (1992)
• Computer Simulation of the glass Transition of polymer melts, K. Binder, W. Paul, H.-P Wittmann, J. Baschnagel, K.Kremer and D.W. Heermann, Progr. Colloid Polym Sci.  91,5-7 (1993)
• Computer Simulation of the glass Transition of polymer melts, K. Binder, W. Paul, H.-P Wittmann, J. Baschnagel, K.Kremer and D.W. Heermann, EPS Conference, Crete (1991)
• Theoretical and Experimental Correlation between primary Chemical Structure and Property Phenomena of Polycondensates, J. Batoulis, K. Binder, F.T. Gentile, D.W.Heermann, W. Jilge, K. Kremer, M. Laso, P.J. Ludovice, L. Morbitzer, W. Paul, B. Pittel, R. Plaetschke, K. Reuter, K. Sommer, U.W. Suter, R. Timmermann and G. Weymans  Advanced Materials,  3, 590-599 (1991)
• Self-Diffusion in Polymer Solutions using the Bond-Fluctuation Monte Carlo  Algorithm, W. Paul, K. Binder, D.W. Heermann and K. Kremer, J. Non-Crystal. Solids 131-133, 650-653(1991)
• Dynamics of Polymer Solutions and Melts: Reptation Predictions and Scaling of Relaxation Times, W. Paul, K. Binder, D.W. Heermann and K. Kremer  J. Chem. Phys., 95 7726-7740 (1991)
• Kinetics of Domain Growth in finite Ising Strips, E.V. Albano, K. Binder, D.W. Heermann, and W. Paul  Physica A, 183, 130 (1992)
• Structure Property Correlation of Polymers, a Monte Carlo Approach, W. Paul, K. Binder, K. Kremer and D.W. Heermann, Macromol.,  24, 6332-6334 (1991)
• The Size of a Random Surface, D.W. Heermann  Int. J. Modern Phys. C, 2, 613-621 (1991)
• Hybrid Monte Carlo Method for Condensed Matter Systemes, B. Mehlig, D.W. Heermann, and B. Forrest  Phys. Rev. B, 45, 679 (1991)
• Spinodal Decomposition of Polymer Films, B.M. Forrest and D.W. Heermann, J. Phys II France  1, 909-919 (1991)
• Crossover Scaling in Semidilute Polymer Solutions: A Monte Carlo Test, W. Paul, K. Binder, D.W. Heermann and K. Kremer  J. Phys. II  1, 37-60 (1991)
• Parallel Simulation of Dense Two-Dimensional Polymer Systems, B.M. Forrest, A. Baumgärtner, and D.W. Heermann  Comp. Phys. Commun., 59, 455-462 (1990)
• Dynamical Block Analysis in a Non-Equilibrium System, P. Nielaba and D.W. Heermann  Physica A, 170, 471-487 (1990)
• Hybrid Molecular Dynamcis, D.W. Heermann, P. Nielaba, and M. Rovere  Comp. Phys. Commun., 60, 311-318 (1990)
• Finite-Size Scaling Study of Non-Equilibrium Percolation, G. Lironis, D.W. Heermann, and K. Binder  J. Phys. A: Math. Gen., 23 L329-L334 (1990)
• Critical Wetting in the Square Ising Model with a Boundary Field, E.V. Albano, K. Binder, D.W. Heermann, and W. Paul  preprint, (1989)
• System Size Dependence of the Autocorrelation Time for the Swendsen-Wang Ising Model, D.W. Heermann and A.N. Burkitt  Physica A,  162 210-214 (1990)
• Gas-Liquid Transition of the Two-Dimensional Lennard-Jones Fluid, M. Rovere, D.W. Heermann, and K. Binder,  J. Phys.: Condens. Matter, 2 7009-7032 (1989)
• Simulation of Three-Dimensional Boostrap Percolation, S.S. Manna, J. Adler, D. Stauffer, and D.W. Heermann  Physica A, 162, 20 (1990)
• Parallel Computing, D.W. Heermann and A.N. Burkitt, in  Proceeedings of the Workshop: Physics at the HRLZ, ed M. Kremer, 71-84, KFA Press, Jülich 1990
• Parallel Algorithms in Statistical Mechanics, D.W. Heermann and A.N. Burkitt  to appear in The Monte Carlo Method in Statistical Physics, ed K. Binder, Springer Verlag, Heidelberg 1999
• Parallelization of Computational Physics Algorithms, D.W. Heermann and A.N. Burkitt, in "Simulation Studies in Condensed Matter Physics: Recent  Developments", ed. D.P Landau, K.K. Mon, and H.B. Schüttler, Springer Proc. Phys., Springer Verlag, Heidelberg, 1989
• Monte Carlo Study of the Ising Model Phase Transition in Terms of the Percolation Transition of ``Physical Clusters'', M. De Meo, D.W. Heermann, and K. Binder  J. Stat. Phys., (1989)
• Shift of First-Order Transitions in Thin Films due to boundary fields: A Computer Simulation, E.V. Albano, K. Binder, D.W. Heermann, and W. Paul  J. Chem. Phys.,  91, 3700 (1989)
• Adsorption on Stepped Surfaces: A Monte Carlo Simulation, E.V. Albano, K. Binder, D.W. Heermann, and W. Paul  Surf. Science, 223, 151-178 (1989)
• The Ising Square Lattice in a L x M Geometry: A Model for the Effect of Surface Steps on Phase Transitions in Adsorbed Monolayers, E.V. Albano, K. Binder, D.W. Heermann, and W. Paul  Z. Phys. B, 77, 445-460 (1989)
• Exponential Growth out of Non-equilibrium, A.N. Burkitt and D.W. Heermann  Euro. Phys. Lett., 10, 207-211 (1989)
• Parallelization of the Ising model and its performance evaluation, D.W. Heermann and A.N. Burkitt,  Parallel Computing, 13, 345-357 (1990)
• Relaxation of Metastable States in Finite Mean Field Kinetic Systems, W. Paul, D.W. Heermann and K. Binder,  J. Phys. A: Math. Gen., 22 3325-3337 (1989)
• Parallelization of a Cluster Algorithm, A. N. Burkitt, D.W. Heermann,  Commupt. Phys. Commun., 54, 201-209 (1989)
• Block Density Distribution Function Analysis of Two-Dimensional Lennard-Jones Fluids, M. Rovere, D.W. Heermann, and K. Binder,  Euro. Phys. Lett., 6, 585-590 (1988)
• Finte Size Scaling of the Microcanonical Ising Model, R.C. Desai, D.W. Heermann, and K. Binder,  J. Stat. Phys., 53, 795 (1988)
• Ising Model, Transputer and Dynamic Correlations using a Microcanonical  Ensemble Method, D.W. Heermann and R.C. Desai,  Comput. Phys. Commun., 50, 297 (1988)
• Implementation of a Random Number Generator in OCCAM, W. Paul, D.W. Heermann and R.C. Desai,  J. Comput. Phys., 82, 487 (1989)
• Metastable States studied by Relaxation Paths, W. Paul and D.W. Heermann,  Euro.Phys. Lett. 6, 701 (1988)
• Dynamic Percolation Transition Induced by Phase Separation: A Monte Carlo  Analysis, S. Hayward, D.W. Heermann and K. Binder,  J. Statis. Phys. 49, 1053 (1987)
• Monte Carlo Simulation of the Cahn-Hilliard Model of Spinodal Decomposition, A. Milchev, D.W. Heermann, and K. Binder,  Acta Metal 36, 377 (1988)
• Parallel Processing of Statistical Mechanical Models, D.W. Heermann, in SPEEDUP, ed. P. Henzi, Bern (1988)
• Phase Separation and Percolation, D.W. Heermann, in Proceedings: Phenomenes Non Lineaires en Sience des Materiaux, ed. G. Martin, Aussois (1987)
• Transient Reversible Growth and Percolation during Phase Separation, D.W. Heermann, in  Proceedings: Dynamics of Ordering Processes in Condensed Matter, ed. K. Kawasaki, Kyoto (1987)
• Pathwise Approach to Non-Equilibrium, D.W. Heermann, W. Paul, and B. Schmittmann, in Proceedings of the 32nd Scottish Universities Summer School  on Computational Physics, eds. R. Kenway and S. Pawley,  (1987)
• From Random Percolation to Dynamical Percolation, D.W. Heermann, in Proceedings of the 32nd Scottish Universities Summer School on Computational Physics, eds. R. Kenway and S. Pawley,  (1987)
• Domain Growth, Overlap and Random Numbers, D.W. Heermann and M. Rovere, in Proceedings of the 32nd Scottish Universities Summer School on Computational Physics, eds. R. Kenway and S. Pawley,  (1987)
• Self-Averaging Properties of Quantities in the Study of First Order Transitions, D.W. Heermann, in Proceedings of the 32nd Scottish Universities Summer School on Computational Physics, eds. R. Kenway and S. Pawley,  (1987)
• The Monte Carlo Method in the Study of First Order Phase Transitions, D.W. Heermann, in Proceedings of the 32nd Scottish Universities Summer Schoolon Computational Physics, eds. R. Kenway and S. Pawley,  (1987)
• Non-Equilibrium Percolation, D.W. Heermann, K. Binder, and S. Hayward, in Proceedings of the 2nd Bar-Ilan  Conference, ed. C. Domb,  Phil. Mag./  56 843 (1987-9
• Formation of Ordered Structures in Quenching Experiments: Scaling Theory and Simulations, D.W. Heermann and K. Binder, in  Proceedings of the International Conference on: The Physics of Structure Formation, Theory and Simulation, ed. W. Güttinger, Springer Series in Synergetics/, Springer Verlag, Heidelberg, 1987
• Dynamics of Formation of Ordered Domains out of Disordred Configurations, K. Binder, D.W. Heermann, A. Milchev, and A. Sadiq, in  Heidelberg Colloquium on Glassy Dynamics and Optimization, eds J.L. van Hemmen and I. Morgenstern, Springer, Berlin, 1987
• Critical Phenomena in Polymer Mixtures: Monte Carlo Simulation on a Lattice Model, A. Sariban, K. Binder, and D.W. Heermann,  Colloid & Polymer Sci. 265, 424 (1987)
• A Monte Carlo Test of the Flory-Huggins Theory for Polymer Mixtures, A. Sariban, K. Binder, and D.W. Heermann,  Phys. Rev. B 35, 6873 (1987)
• Influence of a Continuous Quenching Procedure on the Initial Stages of Spinodal Decomposition, H.-O. Carmesin, D.W. Heermann, and K. Binder,  Z. Phys. B 65, 89 (1986)
• Fluctuations and Lack of Self-Averaging in the Kinetics of Domain Growth, A. Milchev, K. Binder, and D.W. Heermann,  Z. Phys. B 63, 521 (1986)
• Spinodal Decomposition of Polymer Films, A. Baumgärtner and D.W. Heermann,  Polymer 27, 1777 (1986)
• Finite Size Scaling Analysis of the $phi^4$ Field Theory off the Square Lattice, A. Milchev, D.W. Heermann, and K. Binder,  J. Statis. Phys. 44, 749 (1986)
• Growth of Domains and Scaling in the Late Stages of Phase Separation, K. Binder and D.W. Heermann, in  Scaling Phenomena in Disordered Systems/, eds P. Pynn and A. Skjeltrop, Plenum, 1985
• Scaling and Mean-Field-Like Behaviour in Phase Separation Processes, D.W. Heermann,  Z. Phys. B 61, 311 (1985)
• Computer Simulations of First Order Phase Transformations, Part II:  Spinodal  Decomposition, D.W. Heermann, in Computer Simulations in Physical Metallurgy/, ed. G. Jaccuci,  Riedel Publ. Co, Dordrecht (1984)
• Computer Simulations of First Order Phase Transformations, Part I: Metastability, D.W. Heermann, in Computer Simulations in Physical Metallurgy/, ed. G. Jaccuci,  Riedel Publ. Co, Dordrecht (1984)
• Metastability and Spinodal Nucleation, D.W. Heermann, Proceedings of the International Conference on Early Stages of Decomposition/, ed. M.F. Ashby,  Acta Metal/ (1984)
• Dynamical Spinodal: The Transition from Nucleation to Spinodal Decomposition,  D.W. Heermann,  Z. Phys. B 55, 309 (1984)
• Test of the Validity of the Classical Theory of Spinodal Decomposition,  D.W. Heermann,  Phys. Rev. Lett. 55, 1126 (1984)
• Nucleation and Metastability in Three-Dimensional Ising Models, D.W. Heermann, W. Klein, A. Coniglio, and D. Stauffer, J. Statis. Phys.  36, 447 (1984)
• Nucleation and Growth of Non-Classical Droplets,  D.W. Heermann and W. Klein,  Phys. Rev. Lett. 50, 1062 (1983)
• Percolation and Droplets in a Medium-Range Three Dimensional Ising Model,  D.W. Heermann and W. Klein,  Phys. Rev. B 27, 1732 (1983)
• Spinodals in a Long-Range Interaction System, D.W. Heermann, W. Klein, and D. Stauffer, Phys. Rev. Lett. 49, 1292 (1982)
• Monte Carlo Experiment for Nucleation Rate in the Three-Dimensional Ising Model,  D. Stauffer, A. Coniglio, and D.W. Heermann,  Phys. Rev. Lett. 49, 1299 (1982)
• Classical Nucleation Theory with a Tolman Correction,  D.W. Heermann,  J. Statis. Phys. 29, 631 (1982)
• Phase Diagram for the Three Dimensional Correlated Site-Bond Percolation,  D.W. Heermann and D. Stauffer,  Z. Phys. B 44, 339 (1981)
• Influence of Boundary Conditions on Square Bond Percolation near p_c ,D.W. Heermann and D. Stauffer,  Z. Phys. B 40, 133 (1980)