Research

Current interests and peer-reviewed publications

Research Interests

Origins of Life & Prebiotic Chemistry

Investigation of glycine formation mechanisms in condensed phase conditions using ab initio molecular dynamics (AIMD). Study of prebiotic reactions on montmorillonite nanoclay surfaces through Car-Parrinello molecular dynamics simulations. Exploring how simple molecules like carbon monoxide, formaldimine, and water can lead to amino acid formation.

Structural Biology & Bioinformatics

Quality assessment of RNA 3D structure predictions in the RNA-Puzzles initiative. Computational analysis of protein secondary structure elements, including Ramachandran plot studies. Investigation of beta-sheet structures in oligopeptides and fibroin.

Metalloprotein Dynamics & Drug Mechanisms

QM/MM dynamics studies of bleomycin-DNA interactions and anti-cancer drug mechanisms. Molecular dynamics of hemoglobin-haptoglobin complexes and their relevance to oxidative stress. Studies on hemerythrin and spin-labeled derivatives.

Computational Methods

Quantum molecular dynamics, ab initio molecular dynamics (AIMD), Car-Parrinello molecular dynamics (CPMD), classical molecular dynamics, QM/MM hybrid methods, DFT calculations, and semi-empirical methods. Software expertise: AMBER, GROMACS, Gaussian, MOPAC, Autodock, VMD, SYBYL, and Quantum Espresso.

Peer-Reviewed Publications

Total publications: 10  |  First-author: 8  |  ORCID: 0000-0003-4311-5951  |  Download full list (PDF)

  1. Carrascoza, F., Lukasiak, P., Nowak, W., & Blazewicz, J.
    Ab Initio Study of Glycine Formation in the Condensed Phase: Carbon Monoxide, Formaldimine, and Water Are Enough.
    Life, 13(10), 2023.
  2. Carrascoza, F., & Silaghi-Dumitrescu, R.
    The dynamics of hemoglobin-haptoglobin complexes: Relevance for oxidative stress.
    Journal of Molecular Structure, 1250(1), 131829, 2022.
  3. Carrascoza, F., Antczak, M., Miao, Z., Westhof, E., & Szachniuk, M.
    Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions.
    RNA, 28(3), 250–262, 2022.
    doi:10.1261/rna.078685.121
  4. Carrascoza, F., Branzanic, A.M.V., & Silaghi-Dumitrescu, R.
    The dynamics of hemerythrin and hemerythrin derivatives.
    Studia Universitatis Babes-Bolyai Chemia, 66(4), 77–88, 2021.
  5. Carrascoza Mayen, J.F., & Blazewicz, J.
    Recent Results on Computational Molecular Modeling of The Origins of Life.
    Foundations of Computing and Decision Sciences, 45(1), 21–40, 2020.
  6. Carrascoza, F., Surducan, M., Eriksson, L.A., & Silaghi-Dumitrescu, R.
    Interaction of cobalt and iron hydroperoxo bleomycin with deoxyribonucleic acid (DNA): Dynamic vs. electronic structure considerations.
    Inorganica Chimica Acta, 509, 119682, 2020.
    doi:10.1016/j.ica.2020.119682
  7. Carrascoza Mayen, J.F., Rydzewski, J., Szostak, N., Blazewicz, J., & Nowak, W.
    Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations.
    Life, 9(2), 46, 2019.
    doi:10.3390/life9020046
  8. Carrascoza Mayen, J.F., Lupan, A., Cosar, C., Kun, A.-Z., & Silaghi-Dumitrescu, R.
    On the roles of the alanine and serine in the beta-sheet structure of fibroin.
    Biophysical Chemistry, 197, 10–17, 2015.
    doi:10.1016/j.bpc.2014.11.001
  9. Carrascoza, F., Zaric, S.D., & Silaghi-Dumitrescu, R.
    Computational study of protein secondary structure elements: Ramachandran plots revisited.
    Journal of Molecular Graphics and Modelling, 50, 125–133, 2014.
    doi:10.1016/j.jmgm.2014.04.001
  10. Lupan, A., Kun, A.-Z., Carrascoza, F., & Silaghi-Dumitrescu, R.
    Performance comparison of computational methods for modeling alpha-helical structures.
    Journal of Molecular Modeling, 19(1), 193–203, 2013.
    doi:10.1007/s00894-012-1531-z