The Nineteenth International Course & Conference on the Interfaces among Mathematics, Chemistry & Computer Sciences


June 21-26, 2004, Dubrovnik, Croatia

was held under the joint auspices of

Inter-University Center, Dubrovnik, Croatia
Rugjer Boskovic Institute, Zagreb, Croatia
University of Zagreb, Zagreb, Croatia
University of Split, Split, Croatia
International Society for Mathematical Chemistry
International Society for Theoretical Chemical Physics

Scientific Committee

T. Braun (Budapest) R. Ponec (Prague)
J. Brickmann (Darmstadt) M. Randic (Des Moines)
D. Butina (Cambridge) H. Sachs (Ilmenau)
J. Cioslowski (Tallahassee) I. Simon (Budapest)
H. Hosoya (Tokyo) P. F. Stadler (Leipzig)
P. Fowler (Exeter) D. Svrtan (Zagreb)
D. J. Klein (Galveston) N. Trinajstic (Zagreb)
S. McGlynn (Baton Rouge) I. Ugi (Garching)
W. A. Milne (Williston) H. Vancik (Zagreb)
V. A. Ostrovskii (St. Petersburg) D. Veljan (Zagreb)


Organizing Committee

M. V. Diudea (Cluj) D. Plavsic (Zagreb)
A. Graovac (Zagreb), director B. Pokric (Zagreb)
D. Janezic (Ljubljana) V. Smrecki (Zagreb)
E. C. Kirby (Pitlochry), co-dir. N. Stambuk (Zagreb)
I. Lukovits (Budapest) D. Vikic-Topic (Zagreb), co-dir.
T. Pisanski (Ljubljana), co-dir. J. Zerovnik (Maribor)



Scientific Program

The conference covered recent developments in mathematical and computational chemistry and physics with a due respect to applications in materials sciences, drug and vaccine design, genetics and proteins studies, etc. The conference program included invited lectures, contributed oral presentations and posters. The course part coverd the introductory lectures to the topics presented in the conference part.

A series of special sessions were accommodated within the conference: Sessions on Chemoinformatics & Drug Discovery (organized by D. Butina, and Session on Bioinformatics (organized by I. Simon, & P. F. Stadler,











Victor S. Adamchik

Integrals Associated with the Potts Model


Željko Bajzer, Milan Randić

Graph-Theoretic Approach to Characterizaton of Proteome Maps


Matthias Bernt, Daniel Merkle, Martin Middendorf

Solving the Multiple Genome Rearrangement Problem with Common Intervals


Marko Boben, Alen Orbanić, Tomaž Pisanski

Drawing Graphs on Torus


Matevž Bren, Vladimir Batagelj

Mixer Package for Compositional Data Analysis


Urban Bren, Jože Koller, Milan Hodošček

Optimization of Empirical Force Field Parameters for Netropsin


Darko Butina

Use of Chemical Similarity in Drug Discovery


Darko Butina

Performance of Kier-Hall e-States Descriptors in QSAR of Multi‑Functional Molecules


Jerzy Cioslowski, Katarzyna Pernal

Density Matrix Functional Theory


Attila G. Császár, Viktor Szalay, Gábor Czakó

First-Principles Rovibrational Spectroscopy


Tomislav Cvitaš, Leo Klasinc, Nenad Kezele, Sean P. McGlynn, William A. Pryor

How Dangerous is Surfacial Ozone?


Mircea V. Diudea, Istvan Lukovits, Ante Graovac

Perfect Clar Structures by Capra Operation


András Fiser

Protein Structure Modeling and the Protein Structure Initiative


Stanislav Frančišković‑Bilinski

A Mathematical Model Relating Stream Sediment Geochemistry and the Kupa River Drainage Basin Lithology


Jörg Galle, Gernot Schaller

Quantitative Individual Based Models of Multicellular Growth Processes?


Mira Grdiša

Protein Transduction as a Tool for Delivering of Drugs into the Cells


Jürgen Harter

Connecting Biology & Chemistry - Using Ontologies


Davor Juretić, Paško Županović

Enzyme Evolution and Entropy Production


Sandi Klavžar, Petra Žigert

Fibonacci Cubes are the Resonance Graphs of Fibonaccenes


István László

Topological Description of Single-Wall Carbon Nanotube Junctions


Howard M. Lee

Love in van der Waals Equation


Josef Leydold, Türker Biyikoglu

Faber-Krahn Type Inequalities for Trees


Erwin Lijnen, Arnout Ceulemans

Generation and Symmetry Classification of 2‑Cell Embeddings: A Method to Predict New Molecular Structures


István Lukovits

Resonance Energy in Graphite


Daniel Merkle, Martin Middendorf

Combines Phylogenies: Hosts and their Parasites


Milorad Milun

Quantization of Electrons in Ultrathin Metallic Films


Ghorban Ali Moghani, Ali Reza Ashrafi

Symmetry Properies of Some Molecules


Irena Mudri, Slobodan Rendić, Paško Konjevoda

Analysis and Planing of Experiments with Enzyme Inhibitors


Vladimir A. Ostrovskii

New Horizon of Tetrazol Chemistry


Matevž Pompe, Milan Randić

Anti-Connectivity in QSAR Studies


Robert Ponec, Gleb Yuzhakov, David L. Cooper

Electron Reorganization in Chemical Reactions. Strucural Chenges from the Analysis of Bond Order Profiles


Mohammad J. Pourvaghar

The Effect of a Certain Activity on Triglyceride and Cholesterol Blood Serum


Sonja Prohaska

Relative Rate Tests for Conserved non‑Coding Sequences


Milan Randić

Universal Languages of the Past and the Present


Milan Randić

Novel Graphical Representations of DNA Sequences as a Map


Jörg Reichardt, Stefan Bornholdt, Peter Ahnert

Managing the Complexity of Biomedical Information


Gerrit Schüürmann

Quantum Chemical Parameters for Structure‑Activity Relationships – Mechanistic Interpretation and Dependence on the Level of Theory


Peter F. Stadler

Gene Phylogenies of non‑Coding RNAs


Jürgen Sühnel

New Insights into Protein Structure form Structural Bioinformatics Approaches


Alina A. Suzko

Exactly Solvable Models for Investigation of Dynamics


Nikola Štambuk, Paško Konjevoda, Nikola Gotovac

New Binary Algorithm for the Prediction of Protein Folding Types


Dorian Tješić-Drinković, Nikola Štambuk, Duška Tješić-Drinković, Paško Konjevoda, Biserka Pokrić

Met-enkephalin Effects on the Histamine Induced Bronchoconstriction in Guinea-Pigs


Éva Tüdős, István Simon

Redox State of Residue Cys: Which Kind of Information is Stored in the Sequential Vicinity of these Residues?


Donatella Verbanac, Dubravko Jelić, Sanja Koštrun, Višnja Stepanić, Dinko Žiher

Quo Vadis Drug Discovery?


Aleksander Vesel

Characterization of the Resonance Graphs of Catacondensed Hexagonal Graphs


Damir Vukičević, Ante Graovac

Valence Connectivity Versus Randić, Zagreb and Modified Zagreb Index: A Linear Algorithm to Check Discriminative Properties of Indices in Acyclic Molecular Graphs


Damir Vukičević, Ivan Gutman

Almost all Trees and Chemical Trees have Equiseparable Mates


Christina Witwer, Ivo L. Hofacker, Peter F. Stadler

Prediction of Consensus RNA Secondary Structures Including Pseudoknots


Veljko Zlatić

Thermoelectric Properties of Heavy Fermions


Janez Žerovnik

On Modified Wiener Indices


Tomislav P. Živković

Exact Treatment of the Interaction of an Isolated State with the Known Infinite‑Dimensional Quantum System









Yoganand Balagurunathan, Stanislav Frančišković-Bilinski

Granulometric Roundness Parameter Determined on Model and Natural Sediment Grains, Suggested as a Possible Sphericity Index


Carsten Baldauf, Robert Günther, Hans‑Jörg Hofmann

Side Chain Control of Folding into Mixed Peptide Helices


Stephan H. F. Bernhart, Ivo L. Hofacker, Peter F. Stadler

PM_Match - a New Way to Align RNA Structures


Neva Bešker, Claudio Anselmi, Pasquale De Santis

Systematic Search of Possible Compact Nucleosome Structures


Halka Bilinski, Stanislav Frančišković-Bilinski, Darko Hanžel, Gábor Szalontai, László Horvath

Comparative Methods for Characterization of Alumino‑Silicates in Stream Sediments


Tomislav Biljan, Zlatko Meić, Sanda Rončević

Non-Vibrational Features in NIR FT‑Raman Spectra of Lanthanide Sesquioxides


Michael Clausen, Axel Mosig

A Generic Framework for Geometrically Matching Molecular Shapes


Tomislav Cvitaš, Nenad Kezele, Leo Klasinc, Matevž Pompe, Glenda Šorgo, Marjan Veber

Frequency Analysis of Long Term


Marco D'Abramo, Alfredo Di Nola, Massimiliano Aschi , Andrea Amadei

Calculation of the Optical Rotatory Dispersion of Solvated Molecules by Means of the Perturbed Matrix Method


Gergely Dezső, Imre Bálint, Iván Gyémánt

Simultaneous Optimization of Exactly N-Representable Density Matrix and its Geminal Basis


Claudia Fried, Peter Ahnert, Peter F. Stadler

Distribution of SNPs in Genes, Phylogenetic Footprints and Non‑Coding Regions


Ana Jerončić, Davor Juretić

Database of Pore Domain Models from Cationic Channels


Jelena Kašnar-Šamprec, Ljubica Glavaš-Obrovac, Marina Pavlak, Nikola Štambuk, Paško Konjevoda, Biserka Žinić

Synthesis, Spectroscopic Characterization and Biological Activity of N-1-Sulfonylcytosine Derivatives


Saša Kazazić, Leo Klasinc, Bogdan Kralj, Dunja Srzić, Ljerka Tušek‑Božić, Dušan Žigon

Investigation of Liquid and Gas Phase Ligation of Metal Ions with Crown Ethers by Mass Spectrometry


Edward C. Kirby

On Visualizing Carbon Cages


Sandra Kraljević, Nikola Štambuk, Marijeta Kralj, Paško Konjevoda

Met-enkephalin and Naloxone Effects on Head and Neck Squamous Cell Carcinoma Cell Lines


Matthias Kruspe, Dirk Drasdo

Evolution of Artificial Gene Regulation Networks for the Control of Cell-Motion and Cell-Cell-Interaction


Ivana Lojkić, Paško Konjevoda, Zdenko Biđin, Biserka Pokrić

The Differentiation of Virus Strains by Restriction Enzyme Analysis and Determination of Strain Similarities


Bono Lučić, Dragan Amić, Marjana Novič, Damir Nadramija, Ivan Bašic

Improved Structure-Toxicity Relationships for Aquatic Toxicity of Environmental Pollutants


Bono Lučić, Damir Nadramija, Ivan Bašic, Dean Nasteski, Dragan Amić, Nenad Trinajstić

Simplified Structure-Solubility Relationships for Early ADME Evaluation in Drug Discovery


Ante Miličević, Sonja Nikolić, Nenad Trinajstić

Coding and Ordering Kekulé Structures


Svetlana E. Morozova, Andrei V. Komissarov, Kirill A. Esikov, Vladimir A. Ostrovskii

Acidity of Linear Polycyclic Tetrazole Compounds


Ulrike Mückstein, Kurt Grünberger

Shadows and Intersections of RNA Secondary Structure


Stefan Müller, Christoph Flamm, Peter Schuster

A Minimal Model for Gene Regulatory Networks


Sonja Nikolić, Marica Medić-Šarić, Julija Matijević-Sosa, M. Puzović

QSAR Study of Phthalimide Derivatives


Alen Orbanić, Marko Boben, Gašper Jaklič, Tomaz Pisanski

Algorithms for Drawing Polyhedra from 3‑Connected Planar Graphs


Debnath Pal, Manfred S. Weiss, Jürgen Sühnel

The Nest/Egg Motif in Proteins


Igor Pesek, Aleksandar Vesel

Drawing the Resonance Graphs of Catacondensed Benzenoid Graphs


Milan Randić, Nabamita Basak, Dejan Plavšić

Novel Graphical Matrix and Distance‑Based Molecular Descriptors


Nenad Raos

Estimation of Stability of Coordination Compounds by Overlapping Spheres Method


Guillermo Restrepo, José L. Villaveces

From Dendrograms to Topology


Piotr Romiszowski, Andrzej Sikorski

Computer Simulation of Polypeptide Motion


Piotr Romiszowski, Andrzej Sikorski

Static and Dynamic Properties of Branched Polymers


Vilko Smrečki, Norbert Müller

DFT Calculation of NMR CSA Tensors


Camille Stephan‑Otto Attolini, Peter F. Stadler

Evolving towards the Hypercycle


Roman R. Stocsits, Ivo L. Hofacker, Peter F. Stadler

Alignments of Partly Coding Regions: The code2aln – Project


Nikola Štambuk, Duška Tješić-Drinković, Ana Votava-Raić, Paško Konjevoda, Dorian Tješić‑Drinković, Lana Mađerčić

Molecular Modelling of Bioactive Gluten Peptides and Related T-cell Receptors


Andrea Tanzer, Peter Stadler

Statistical Evidence for Specific Expansion of the miRNA Repertoire in Vertebrates


Kurt Varmuza, Wilhelm Demuth, Heinz Scsibrany

Binary Substructure Descriptors for Organic Compounds


Paško Županović, Edita Zenčić, Davor Juretić, Srećko Botrić

Stationary Processes in Dilute Gases and the Maximum Entropy Production Principle









Ivo Hofacker

A Tutorial on RNA Secondary Structure Prediction


Hrvoj Vančik

Course in Philosophy of Chemistry






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