List of Biophysics PhD Students at University of Split, Croatia

 

Marijana Mijaković

 

MSc. Physics

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Mentor: Franjo Sokolić

 

Research Interest: Microheterogenity of Multi-component Liquid Mixtures Using Molecular Dynamics

Publications: 

• M. Mijaković, B. Kežić, L. Zoranić, F. Sokolić, A. Asenbaum, C. Pruner, E. Wilhelm, A. Perera: Ethanol-Water mixtures: Ultrasonic, Brillouin scattering and Molecular Dynamics study. Journal of Molecular Liquids 164, Issues 1-2, Pages 66-73 (doi:10.1016/j.molliq.2011.06.009)
• A. Asenbaum,  C. Pruner, Emmerich Wilhelm, M. Mijakovic, L. Zoranic, F. Sokolic, B. Kezic, A. Perera: Structural changes in ethanol–water mixtures: Ultrasonics, Brillouin scattering and molecular dynamics studies. Vibrational Spectroscopy (in press but already available online) (doi:10.1016/j.vibspec.2011.10.015)

 

 

 

 

Mario Hlevnjak

 

MSc. Molecular Biology

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Mentor: Bojan Žagrović

 

Research Interest: Structural and Computational Biophysics 

 

Publications:

• Hlevnjak M, Zitkovic G, Zagrovic B (2010) Hydrophilicity matching – a potential prerequisite for the formation of protein-protein complexes in the cell. PLoS ONE 5(6): e11169.
• Munic V, Hlevnjak M, Erakovic Haber V (2011) Characterization of rhodamine-123, calcein and 5(6)-carboxy-2',7'-dichlorofluorescein (CDCF) export via MRP2 (ABCC2) in MES-SA and A549 cells. Eur J Pharm Sci  43.359-369.
• Stepanic V, Kostrun S, Malnar I, Hlevnjak M, Butkovic K, Caleta I, Duksi M, Kragol G, Makaruha-Stegic O, Mikac L, Ralic J, Tatic I, Tavcar B, Valko K, Zulfikari S, Munic V (2011) Modelling cellular pharmacokinetics of 14- and 15-membered macolides with physicochemical properties. J med Chem 54:719-733
• Munic V, Banjanac M, Kostrun S, Nujic K, Bosnar M, Marjanovic N, Ralic J, Matijasic M, Hlevnjak M, Erakovic Haber V (2011) Intensity of macrolide anti-inflammatory activity in J774A.l cells positively correlates with cellular accumulation and phospholipidosis. Pharmacol Res 64:298-307
• Strelec I, Ugarcic-Hardi Z, Hlevnjak M (2008) Accumulation of Amadori and Maillard products in wheat seeds aged under different storage conditions. Croat Chem Acta 81:131-137.

 

 

 

 

Antonija Kuzmanić

 

MSc. Molecular Biology

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Mentor: Bojan Žagrović

 

Research Interest: Computational Biophysics 

 

Publications:

• Kuzmanic A. & Zagrovic B. (2010). Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors. Biophysical Journal  98(5): 861-871.
• Kuzmanic A., Kruschel D., van Gunsteren W.F., Pannu N.S. & Zagrovic B. (2011). Dynamics may significantly influence the estimation of interatomic distances in biomolecular X-ray structures. Journal of Molecular Biology 2011:  doi:10.1016/j.jmb.2011.05.033.

 

 

Nada Ilić

 

MSc. Biology and Chemistry

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Mentor: Davor Juretić

 

Research Interest: Synthesis, Design and Testing of Novel Peptide Antibiotics with High Therapeutic Index

Publications:

• Juretić, D., Vukičević, D., Ilić, N., Antcheva, N., Tossi, A., Computational Design of Highly Selective Antimicrobial Peptides, J. Chem. Inf. Model. 2009, 49, 2873–2882
• Juretić, D., Vukičević, D., Petrov, D., Novković, M., Bojović, V., Lučić, B., Ilić, N., Tossi, A., Knowledge-based computational methods for identifying or designing novel, non-homologous antimicrobial peptides, Eur. Biophys. J. 2011, 40, 371–385, DOI 10.1007/s00249-011-0674-7

Poster award:

• Ilić, N., Novković, M., Guida, F., Antcheva, N., Tossi, A., Copić, T., Puizina, J., Juretić, D., Adepantins a new class of ab-initio designed antimicrobial peptides // AMP2010, Australia-Croatia Workshop on Antimicrobial Peptides / http://split4.pmfst.hr/konferencija/ Faculty of Science, University of Split, August 9-13 2010. Organisers: Davor Juretić and Frances Separovic. Conference proceedings, 2010, 41-41.

 

 

 

 

Jadranko Batista

 

MSc. Mathematics and Physics

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Mentor: Bono Lučić

 

Research Interest: Protein structure

 

Jadranko Batista has been working since April 2009 on validation of statistical significance, and possibility of simplification and improvement of some structure-property models related to bioactive molecules and proteins. All analysed models were taken from literature. Jadranko Batista also worked on comparison between product-connectivity index and new version of connectivity index (sum-connectivity), and obtained interesting results that will be published.

Performed researches are introductory research related to the field of his doctoral thesis (development and application of models in structural bioinformatics of proteins).  We will strictly define the subject of his doctoral thesis soon.

Publications:

• Lučić, Bono; Sović, Ivan; Batista, Jadranko; Skala, Karolj; Plavšić, Dejan; Vikić-Topić, Dražen; Nikolić, Sonja; Trinajstić, Nenad. The Additive Variant of the Randić Connectivity index. Accepted for Current Computer-Aided Drug Design.

 

 

 

Sofia Pinto

 

graduated in biomedical engineering, bioinformatics and clinical informatics branch

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Mentor: Kristian Vlahoviček

 

Research Interest: Bioinformatics 

 

Publications:

• Pučić, M., Pinto, S., Novokmet, M., Knežević, A., Gornik, O., Polašek, O., Vlahoviček, K., Wei, W., Rudd, P. M., Wright, A. F., Campbell, H., Rudan, I., and Lauc, G. (2010) Common aberrations from normal human N‐glycan plasma profile. Glycobiology 20, 970-975.
• Pinto, S., Vlahoviček, K. and Buratti, E. (2011), PRO-MINE: A Bioinformatics Repository and Analytical Tool for TARDBP Mutations. Human Mutation, 32: E1948–E1958. (doi: 10.1002/humu.21393)

 

 

 

 

Bernarda Kežić

 

MSc. Physics and Mathematics

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in joint PhD program (Cotutelle) with Université Pierre et Marie Curie, Paris, France

Mentors: Franjo Sokolić and Aurélien Perera

 

 

Research Interest: Structure of One-component Liquid and their Mixture with Water Using Statistical Theory of Liquids and Molecular Dynamics.

 

Publications:

• P. Stipanović, L. Vranješ-Markić, J. Boronat, B. Kežić: Ground state of small mixed helium and spin-polarized tritium clusters: a quantum Monte Carlo study, J. Chem. Phys. 134, 054509 (2011); (doi:10.1063/1.3530837)
• M. Mijaković, B. Kežić, L. Zoranić, F. Sokolić, A. Asenbaum, C. Pruner, E. Wilhelm, A. Perera: Ethanol-Water mixtures: Ultrasonic, Brillouin scattering and Molecular Dynamics study, Journal of Molecular Liquids 164, Issues 1-2, Pages 66-73 (doi:10.1016/j.molliq.2011.06.009)
• A. Asenbaum,  C. Pruner, Emmerich Wilhelm, M. Mijakovic, L. Zoranic, F. Sokolic, B. Kezic, A. Perera: Structural changes in ethanol–water mixtures: Ultrasonics, Brillouin scattering and molecular dynamics studies. Vibrational Spectroscopy (in press but already available online) (doi:10.1016/j.vibspec.2011.10.015)
• B. Kežić, A. Perera: Towards a more accurate reference interaction site model integral equation theory for molecular liquids, J. Chem. Phys. 135, 234104 (2011); (doi:10.1063/1.3666006)

 

 

 

 

Dražen Petrov

 

MSc. Physics

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Mentor: Bojan Žagrović

Research interest: Structural and Computational Biophysics

 

 

Publications:

• Županović P, Kuić D, Lošić Z B., Petrov D, Juretić D, Brumen M (2010) The Maximum Entropy Production Principle and Linear Irreversible Processes. Entropy 12(5):996-1005.
• Juretić D, Vukičević D, Petrov D, Novković M, Bojović V, Lučić B, Ilić N, Tossi A. (2011) Knowledge-based computational methods for identifying or designing novel, nonhomologous antimicrobial peptides. Eur Biophys J. 40(4):371-85.
• Petrov D, Zagrovic B. (2011) Microscopic analysis of protein oxidative damage: effect of carbonylation on structure, dynamics, and aggregability of villin headpiece J Am Chem Soc. 133(18):7016-24.

 

 

 

 

Marija Borozan

 

MSc. Physics and Informatics

 

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Mentor: Sanja Tomić

 

 

Research Interest:

• Computational Simulations of Protein Structure
• Molecular Dynamics Simulations
• Subsets of Signal Peptides from Amphibians and Mammals.
  

 

 

 

 

Margita Nimac-Kalcina

 

MSc. Medical Biochemistry

 

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Mentor: Vedrana Čikeš-Čulić

 

Research Interest: Biochemistry and Medical Biochemistry

 

 

 

 

 

Mario Novković

 

MSc. Physics  with Biophysics Orientation

 

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Mentor: Davor Juretić

 

 

Research Interest:

• Computational Methods in Identifying Novel Antimicrobial Peptides
• Database of Amphibian Skin Bioactive Peptides
• Subsets of Signal Peptides from Amphibians and Mammals
• Antimicrobial Cryptides Hidden in Sequences of Highly Conserved Proteins

Publications:

• Davor Juretić, Damir Vukičević, Dražen Petrov, Mario Novković, Viktor Bojović, Bono Lučić, Nada Ilić, Alessandro Tossi (2011) Knowledge-based computational methods for identifying or designing novel, non-homologous antimicrobial peptides. Eur Biophys J 40:371-385 (http://www.ncbi.nlm.nih.gov/pubmed/21274708)

Conference posters:

• Ilić, N., Novković, M., Guida, F., Antcheva, N., Tossi, A., Copić, T., Puizina, J., Juretić, D., Adepantins a new class of ab-initio designed antimicrobial peptides // AMP2010, Australia-Croatia Workshop on Antimicrobial Peptides / http://split4.pmfst.hr/konferencija/ Faculty of Science, University of Split, August 9-13 2010. Organisers: Davor Juretić and Frances Separovic. Conference proceedings, 2010, 41-41.

 

 

 

 

Marjan Krstić

 

MSc. PhysicsPhysics with Engineer Physics Orientation

 

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Mentor: Vlasta Bonačić-Koutecky

 

 

Research Interest:

• Optical properties of protected noble metal particles for biosensing application
• New materials design
• Molecular dynamics

 

 

Željka Sanader

 

MSc. Physics with Biophysics Orientation

 

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Mentor: Vlasta Bonacic-Koutecky

 

 

Research Interest:

• Optical properties and optimal control of hybrid metal-biomolecule systems
• Hybrid metal-protein systems in the context of biological aging
• Physical properties of peptides