Ran Friedman
ProfessorI am a professor of chemistry with focus on computational chemistry and biochemistry. I teach medicinal and physical chemistry in various courses. I carry out research within the field of computational chemistry, which means that I study chemistry with the help of computer simulations and modelling.
Teaching
I am teaching chemistry mainly to students of nutritional sciences and pharmacy. I teach physical chemistry for the first group and medicinal chemistry for the second. I am also involved at teaching M.Sc and Ph.D students at time.
Research
My research focuses on computational chemistry with specialisation on biomolecules. I want to deepen the understanding of the molecular aspects of diseases through modelling and simulation. In addition, I have interest in protein-ion Interactions. In my research group, we use molecular dynamics simulations, quantum chemistry, and stochastic modelling.
My research groups
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Computational Chemistry and Biochemistry Group We use computer simulations to better understand how biologically-relevant and other interesting molecules behave. By using computer modelling and…
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Linnaeus University Centre for Biomaterials Chemistry Linnaeus University Centre for Biomaterials Chemistry is a principal research environment that deals with the development and the adaptation of…
My ongoing research projects
Publications
Article in journal (Refereed)
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Friedman, R. (2025). Density Functional Theory Calculations Unravel the Structure and Dynamics of NaClO4 and NaPF6 Salts in Sodium-Ion Batteries. The Journal of Physical Chemistry C. 129 (3). 1575-1581.
Status: Published -
Yang, J., Friedman, R. (2025). Resistance to FLT3 inhibitors involves different molecular mechanisms and reduces new DNA synthesis. Biochemistry and Biophysics Reports. 41.
Status: Published -
Lindahl, E., Arvidsson, E., Friedman, R. (2024). Trans vs Cis : A Computational Study of Enasidenib Resistance due to IDH2 Mutations. Physical Chemistry, Chemical Physics - PCCP. 26 (27). 18989-18996.
Status: Published -
Lindström, H.J.G., De Wijn, A.S., Friedman, R. (2024). Interplay of mutations, alternate mechanisms, and treatment breaks in leukaemia : Understanding and implications studied with stochastic models. Computers in Biology and Medicine. 169.
Status: Published -
Freire, T.S., Zukerman-Schpector, J., Friedman, R., Caracelli, I. (2024). Structural and thermodynamic characterization of allosteric transitions in human serum albumin with metadynamics simulations. Physical Chemistry, Chemical Physics - PCCP. 26 (7). 6436-6447.
Status: Published -
Roadnight Sheehan, J., De Wijn, A.S., Freire, T.S., Friedman, R. (2024). Beyond IC50-A computational dynamic model of drug resistance in enzyme inhibition treatment. PloS Computational Biology. 20 (11).
Status: Published -
Lindahl, E., Friedman, R. (2024). Exploring the Impact of Protein Chain Selection in Binding Energy Calculations with DFT. ChemPhysChem. 25 (24).
Status: Published -
Yang, J., Friedman, R. (2024). Synergy and antagonism between azacitidine and FLT3 inhibitors. Computers in Biology and Medicine. 169. 107889-107889.
Status: Published -
Freire, T.S., Caracelli, I., Zukerman-Schpector, J., Friedman, R. (2023). Resistance to a tyrosine kinase inhibitor mediated by changes to the conformation space of the kinase. Physical Chemistry, Chemical Physics - PCCP. 25 (8). 6175-6183.
Status: Published -
Friedman, R. (2023). Estimating the Gibbs Hydration Energies of Actinium and Trans-Plutonium Actinides. ChemPhysChem. 24 (2).
Status: Published -
Meelua, W., Wanjai, T., Thinkumrob, N., Friedman, R., Jitonnom, J. (2023). Multiscale QM/MM Simulations Identify the Roles of Asp239 and 1‑OH···Nucleophile in Transition State Stabilization in Arabidopsis thaliana Cell-Wall Invertase 1. Journal of Chemical Information and Modeling. 63 (15). 4827-4838.
Status: Published -
Månsson, A., Ušaj, M., Moretto, L., Matusovsky, O., Velayuthan, L.P., et al. (2023). New paradigms in actomyosin energy transduction : Critical evaluation of non-traditional models for orthophosphate release. Bioessays. 45 (9).
Status: Published -
Yang, J., Friedman, R. (2023). Combination strategies to overcome drug resistance in FLT+ acute myeloid leukaemia. Cancer Cell International. 23 (1).
Status: Published -
Oruganti, B., Lindahl, E., Yang, J., Amiri, W., Rahimullah, R., et al. (2022). Allosteric enhancement of the BCR-Abl1 kinase inhibition activity of nilotinib by cobinding of asciminib. Journal of Biological Chemistry. 298 (8).
Status: Published -
Lindström, J., Friedman, R. (2022). Rotating between ponatiniband imatinib temporarily increasesthe efficacy of imatinib as shownin a chronic myeloid leukaemiamodel. Scientific Reports. 12.
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Friedman, R. (2022). The molecular mechanisms behind activation of FLT3 in acute myeloid leukemia and resistance to therapy by selective inhibitors. Biochimica et Biophysica Acta. CR. Reviews on Cancer. 1877 (1).
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Moretto, L., Ušaj, M., Matusovsky, O., Rassier, D.E., Friedman, R., et al. (2022). Multistep orthophosphate release tunes actomyosin energy transduction. Nature Communications. 13 (1).
Status: Published -
Xu, Y., Zhang, S., Lindahl, E., Friedman, R., Wu, W., et al. (2022). A general tight-binding based energy decomposition analysis scheme for intermolecular interactions in large molecules. Journal of Chemical Physics. 157 (3).
Status: Published -
Friedman, R. (2022). Computational studies of protein–drug binding affinity changes upon mutations in the drug target. WIREs Computational Molecular Science. 12 (1).
Status: Published -
Xu, Y., Friedman, R., Wu, W., Su, P. (2021). Understanding intermolecular interactions of large systems in ground state and excited state by using density functional based tight binding methods. Journal of Chemical Physics. 154 (19).
Status: Published -
Oruganti, B., Friedman, R. (2021). Activation of Abl1 Kinase Explored Using Well-Tempered Metadynamics Simulations on an Essential Dynamics Sampled Path. Journal of Chemical Theory and Computation. 17 (11). 7260-7270.
Status: Published -
Yang, J., Lindström, J., Friedman, R. (2021). Combating drug resistance in acute myeloid leukaemia by drug rotations : the effects of quizartinib and pexidartinib. Cancer Cell International. 21 (1).
Status: Published -
Friedman, R. (2021). Preferential Binding of Lanthanides to Methanol Dehydrogenase Evaluated with Density Functional Theory. Journal of Physical Chemistry B. 125 (9). 2251-2257.
Status: Published -
Houshmand, F., Friedman, R., Jalili, S., Schofield, J. (2020). Exciton effect in new generation of carbon nanotubes : graphdiyne nanotubes. Journal of Molecular Modeling. 26 (7). 1-10.
Status: Published -
Lindström, J., Friedman, R. (2020). Inferring time-dependent population growth rates in cell cultures undergoing adaptation. BMC Bioinformatics. 21 (1). 1-13.
Status: Published -
Todde, G., Friedman, R. (2020). Pattern and Dynamics of FLT3 Duplications. Journal of Chemical Information and Modeling. 60 (8). 4005-4020.
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Lindström, J., Friedman, R. (2020). The effects of combination treatments on drug resistance in chronic myeloid leukaemia : an evaluation of the tyrosine kinase inhibitors axitinib and asciminib. BMC Cancer. 20 (1).
Status: Published -
Davila-Rodriguez, M.J., Freire, T.S., Lindahl, E., Caracelli, I., Zukerman-Schpector, J., et al. (2020). Is breaking of a hydrogen bond enough to lead to drug resistance?. Chemical Communications. 56 (49). 6727-6730.
Status: Published -
Buetti-Dinh, A., Herold, M., Christel, S., El Hajjami, M., Delogu, F., et al. (2020). Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations. BMC Bioinformatics. 21 (1). 1-15.
Status: Published -
Georgoulia, P.S., Bjelic, S., Friedman, R. (2020). Deciphering the molecular mechanism of FLT3 resistance mutations. The FEBS Journal. 287 (15). 3200-3220.
Status: Published -
Steinz, M.M., Persson, M., Aresh, B., Olsson, K., Cheng, A.J., et al. (2019). Oxidative hotspots on actin promote skeletal muscle weakness in rheumatoid arthritis. JCI Insight. 4 (9). 1-16.
Status: Published -
Lindström, J., De Wijn, A.S., Friedman, R. (2019). Stochastic modelling of tyrosine kinase inhibitor rotation therapy in chronic myeloid leukaemia. BMC Cancer. 19. 1-13.
Status: Published -
Georgoulia, P.S., Todde, G., Bjelic, S., Friedman, R. (2019). The catalytic activity of Abl1 single and compound mutations : Implications for the mechanism of drug resistance mutations in chronic myeloid leukaemia. Biochimica et Biophysica Acta - General Subjects. 1863 (4). 732-741.
Status: Published -
Todde, G., Friedman, R. (2019). Activation and Inactivation of the FLT3 Kinase: Pathway Intermediates and the Free Energy of Transition. Journal of Physical Chemistry B. 123 (26). 5385-5394.
Status: Published -
Friedman, R. (2019). Specific Ion and Concentration Effects in Acetate Solutions with Na+, K+ and Cs+. ChemPhysChem. 20 (8). 1006-1010.
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Todde, G., Friedman, R. (2019). Conformational modifications induced by internal tandem duplications on the FLT3 kinase and juxtamembrane domains. Physical Chemistry, Chemical Physics - PCCP. 21 (34). 18467-18476.
Status: Published -
Gagner, V.A., Lundholm, I., Garcia-Bonete, M., Rodilla, H., Friedman, R., et al. (2019). Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties. Scientific Reports. 9. 1-14.
Status: Published -
Friedman, R. (2019). Simulations of Biomolecules in Electrolyte Solutions. Advanced Theory and Simulations. 2 (4). 1-10.
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Buetti-Dinh, A., Friedman, R. (2018). Computer simulations of the signalling network in FLT3+-acute myeloid leukaemia : indications for an optimal dosage of inhibitors against FLT3 and CDK6. BMC Bioinformatics. 19. 1-13.
Status: Published -
Friedman, R. (2018). Membrane-Ion Interactions. Journal of Membrane Biology. 251 (3). 453-460.
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Buetti-Dinh, A., Jensen, R., Friedman, R. (2018). A computational study of hedgehog signalling involved in basal cell carcinoma reveals the potential and limitation of combination therapy. BMC Cancer. 18 (1). 1-8.
Status: Published -
Ahlstrand, E., Buetti-Dinh, A., Friedman, R. (2018). An interactive computer lab of the galvanic cell for students in biochemistry. Biochemistry and molecular biology education. 46 (1). 58-65.
Status: Published -
Friedman, R. (2017). The molecular mechanism behind resistance of the kinase FLT3 to the inhibitor quizartinib. Proteins : Structure, Function, and Bioinformatics. 85 (11). 2143-2152.
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Ahlstrand, E., Hermansson, K., Friedman, R. (2017). Interaction Energies in Complexes of Zn and Amino Acids : A Comparison of Ab Initio and Force Field Based Calculations. Journal of Physical Chemistry A. 121 (13). 2643-2654.
Status: Published -
Karlsson, B.C.G., Friedman, R. (2017). Dilution of whisky - the molecular perspective. Scientific Reports. 7 (6489).
Status: Published -
Ahlstrand, E., Zukerman Schpector, J., Friedman, R. (2017). Computer simulations of alkali-acetate solutions : Accuracy of the forcefields in difference concentrations. Journal of Chemical Physics. 147. 1-10.
Status: Published -
Becconi, O., Ahlstrand, E., Salis, A., Friedman, R. (2017). Protein-ion Interactions : Simulations of Bovine Serum Albumin in Physiological Solutions of NaCl, KCl and LiCl. Israel Journal of Chemistry. 57 (5). 403-412.
Status: Published -
Maganhi, S.H., Jensen, P., Caracelli, I., Schpector, J.Z., Froehling, S., et al. (2017). Palbociclib can overcome mutations in cyclin dependent kinase 6 that break hydrogen bonds between the drug and the protein. Protein Science. 26 (4). 870-879.
Status: Published -
Buetti-Dinh, A., O'hare, T., Friedman, R. (2016). Sensitivity Analysis of the NPM-ALK Signalling Network Reveals Important Pathways for Anaplastic Large Cell Lymphoma Combination Therapy. PLOS ONE. 11 (9).
Status: Published -
Pineda De Castro, L.F., Dopson, M., Friedman, R. (2016). Biological Membranes in Extreme Conditions : Anionic Tetraether Lipid Membranes and Their Interactions with Sodium and Potassium. Journal of Physical Chemistry B. 120 (41). 10628-10634.
Status: Published -
Friedman, R. (2016). Drug resistance in cancer : molecular evolution and compensatory proliferation. Oncotarget. 7 (11). 11746-11755.
Status: Published -
Buetti-Dinh, A., Dethlefsen, O., Friedman, R., Dopson, M. (2016). Transcriptomic analysis reveals how a lack of potassium ions increases Sulfolobus acidocaldarius sensitivity to pH changes. Microbiology. 162 (8). 1422-1434.
Status: Published -
Pineda De Castro, L.F., Dopson, M., Friedman, R. (2016). Biological Membranes in Extreme Conditions : Simulations of Anionic Archaeal Tetraether Lipid Membranes. PLOS ONE. 11 (5).
Status: Published -
Lundholm, I.V., Rodilla, H., Wahlgren, W.Y., Duelli, A., Bourenkov, G., et al. (2015). Terahertz radiation induces non-thermal structural changes associated with Fröhlich condensation in a protein crystal. Structural Dynamics. 2 (5).
Status: Published -
Cournia, Z., Allen, T.W., Andricioaei, I., Antonny, B., Baum, D., et al. (2015). Membrane Protein Structure, Function, and Dynamics : a Perspective from Experiments and Theory. Journal of Membrane Biology. 248 (4). 611-640.
Status: Published -
Buetti-Dinh, A., Pivkin, I., Friedman, R. (2015). S100A4 and its role in metastasis – computational integration of data on biological networks. Molecular Biosystems. 11. 2238-2246.
Status: Published -
Buetti-Dinh, A., Pivkin, I.V., Friedman, R. (2015). S100A4 and its role in metastasis : simulations of knockout and amplification of epithelial growth factor receptor and matrix metalloproteinases. Molecular Biosystems. 11 (8). 2247-2254.
Status: Published -
Chavan, S., Friedman, R., Nicholls, I.A. (2015). Acute Toxicity-Supported Chronic Toxicity Prediction: A k-Nearest Neighbor Coupled Read-Across Strategy. International Journal of Molecular Sciences. 16 (5). 11659-11677.
Status: Published -
Friedman, R. (2014). Structural and computational insights into the versatility of cadmium binding to proteins. Dalton Transactions. 43 (7). 2878-2887.
Status: Published -
Friedman, R., Caflisch, A. (2014). Wild type and mutants of the HET-s(218-289) prion show different flexibility at fibrillar ends : A simulation study. Proteins : Structure, Function, and Bioinformatics. 82 (3). 399-404.
Status: Published -
Zabriskie, M.S., Eide, C.A., Tantravahi, S.K., Vellore, N.A., Estrada, J., et al. (2014). BCR-ABL1 Compound Mutations Combining Key Kinase Domain Positions Confer Clinical Resistance to Ponatinib in Ph Chromosome-Positive Leukemia. Cancer Cell. 26 (3). 428-442.
Status: Published -
Friedman, R. (2013). Electrolyte Solutions and Specific Ion Effects on Interfaces. Journal of Chemical Education. 90 (8). 1018-1023.
Status: Published -
Friedman, R. (2013). Drug Resistance Missense Mutations in Cancer Are Subject to Evolutionary Constraints. PLOS ONE. 8 (12).
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Karlsson, B.C.G., Olsson, G.D., Friedman, R., Rosengren, A.M., Henschel, H., et al. (2013). How warfarin’s structural diversity influences its phospholipid bilayer membrane permeation. Journal of Physical Chemistry B. 117 (8). 2384-2395.
Status: Published -
Ahlstrand, E., Spångberg, D., Hermansson, K., Friedman, R. (2013). Interaction energies between metal ions (Zn2+ and Cd2+) and biologically relevant ligands. International Journal of Quantum Chemistry. 113 (23). 2554-2562.
Status: Published -
Friedman, R. (2011). Aggregation of amyloids in a cellular context : modelling and experiment. Biochemical Journal. 438. 415-426.
Status: Published -
Friedman, R., Caflisch, A. (2011). Surfactant Effects on Amyloid Aggregation Kinetics. Journal of Molecular Biology. 414. 303-312.
Status: Published -
Friedman, R. (2011). Ions and the protein surface revisited : extensive molecular dynamics simulations and analysis of protein structures in alkali-chloride solutions. Journal of Physical Chemistry B. 115. 9213-9223.
Status: Published -
Seeber, M., Felline, A., Raimondi, F., Muff, S., Friedman, R., et al. (2011). Wordom : a user-friendly program for the analysis of molecular conformations, trajectories, and free energy surfaces. Journal of Computational Chemistry. 32 (6). 1183-1194.
Status: Published -
Friedman, R., Pellarin, R., Caflisch, A. (2010). Soluble Protofibrils as Metastable Intermediates in Simulations of Amyloid Fibril Degradation Induced by Lipid Vesicles. The Journal of Physical Chemistry Letters. 1 (2). 471-474.
Status: Published -
Friedman, R., Caflisch, A. (2010). On the orientation of the catalytic dyad in aspartic proteases. Proteins : Structure, Function, and Bioinformatics. 78 (6). 1575-1582.
Status: Published -
Friedman, R., Caflisch, A. (2009). Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring. ChemMedChem. 4 (8). 1317-1326.
Status: Published -
Friedman, R., Pellarin, R., Caflisch, A. (2009). Amyloid aggregation on lipid bilayers and its impact on membrane permeability. Journal of Molecular Biology. 387 (2). 407-415.
Status: Published -
Friedman, R. (2009). Proton Transfer on the Molecular Surface of Proteins and Model Systems. Israel Journal of Chemistry. 49 (2). 149-153.
Status: Published -
Dashevskaya, S., Kopito, R.B., Friedman, R., Elbaum, M., Epel, B.L. (2008). Diffusion of anionic and neutral GFP derivatives through plasmodesmata in epidermal cells of Nicotiana benthamiana. Protoplasma.
Status: Published -
Friedman, R., Caflisch, A. (2008). Pepsinogen-like activation intermediate of plasmepsin II revealed by molecular dynamics analysis. Proteins : Structure, Function, and Bioinformatics. 73 (4). 814-827.
Status: Published -
Friedman, R., Fischer, S., Nachliel, E., Scheiner, S., Gutman, M. (2007). Minimum energy pathways for proton transfer between adjacent sites exposed to water. Journal of Physical Chemistry B. 111 (21). 6059-6070.
Status: Published -
Tsfadia, Y., Friedman, R., Kadmon, J., Selzer, A., Nachliel, E., et al. (2007). Molecular dynamics simulations of palmitate entry into the hydrophobic pocket of the fatty acid binding protein. FEBS Letters. 581. 1243-1247.
Status: Published -
Friedman, R. (2007). Myosin V movement : Lessons from molecular dynamics studies of IQ peptides in the lever arm. Biochemistry. 46 (50). 14524-14536.
Status: Published -
Friedman, R., Caflisch, A. (2007). The Protonation State of the Catalytic Aspartates in Plasmepsin II. FEBS Letters. 581. 4120-4124.
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Friedman, R., Nachliel, E., Gutman, M. (2006). Fatty Acid Binding Proteins - Same Structure but Different Binding Mechanisms? : Molecular Dynamics Simulations of Intestinal Fatty Acid Binding Protein. Biophysical Journal. 90. 1535-45.
Status: Published -
Gutman, M., Nachliel, E., Friedman, R. (2006). The dynamics of proton transfer between adjacent sites. Photochemical and Photobiological Sciences. 5. 531-537.
Status: Published -
Ganoth, A., Friedman, R., Nachliel, E., Gutman, M. (2006). A molecular dynamics study and free energy analysis of complexes between the Mlc1p protein and two IQ motif peptides. Biophysical Journal. 91 (7). 2436-2450.
Status: Published -
Project, E., Friedman, R., Nachliel, E., Gutman, M. (2006). A Molecular Dynamics Study of the Effect of Ca2+ Removal on Calmodulin Structure. Biophys. J.. 90. 3842-3850.
Status: Published -
Gutman, M., Nachliel, E., Friedman, R. (2006). The mechanism of proton transfer between adjacent sites on the molecular surface. Biochimica et Biophysica Acta. 1757. 931-941.
Status: Published -
Ganoth, A., Nachliel, E., Friedman, R., Gutman, M. (2006). Molecular dynamics study of a calmodulin-like protein with an IQ peptide : spontaneous refolding of the protein around the peptide. Proteins : Structure, Function, and Bioinformatics. 64 (1). 133-146.
Status: Published -
Friedman, R., Nachliel, E., Gutman, M. (2005). Molecular Dynamics of a Protein Surface : Ion-Residues Interactions. Biophysical Journal. 89 (2). 768-781.
Status: Published -
Mezer, A., Friedman, R., Noivirt, O., Nachliel, E., Gutman, M. (2005). The mechanism of proton transfer between adjacent sites exposed to water. J. Chem. Phys. B. 109. 11379-11388.
Status: Published -
Friedman, R., Nachliel, E., Gutman, M. (2005). Protein surface dynamics : Interaction with water and small solutes. Journal of biological physics (Print). 31 (3). 433-452.
Status: Published -
Friedman, R., Nachliel, E., Gutman, M. (2005). Application of Classical Molecular Dynamics for Evaluation of Proton Transfer Mechanism on a Protein. Bioch. Bioph. Acta.. 1710. 67-77.
Status: Published -
Friedman, R., Nachliel, E., Gutman, M. (2005). Molecular Dynamics Simulations of the Adipocyte Lipid Binding Protein Reveal a Novel Entry Site for the Ligand. Biochemistry. 44. 4275-4283.
Status: Published -
Friedman, R., Nachliel, E., Gutman, M. (2005). Protein Surface - the Dynamics of the Interactions between Protein, Water and Small Solutes. Journal of biological physics (Print). 31 (3-4). 433-452.
Status: Published -
Friedman, R., Nachliel, E., Gutman, M. (2003). The role of small intraprotein cavities in the catalytic cycle of bacteriorhodopsin. Biophysical Journal. 85 (2). 886-896.
Status: Published
Conference paper (Refereed)
- Steinz, M., Malin, P., Bejan, A., Cheng, A., Ahlstrand, E., et al. (2018). Identification of oxidative hotspots on actin which promote skeletal muscle weakness in rheumatoid arthritis. Free Radical Biology and Medicine. S106.
- Katona, G., Lundholm, I., Rodilla, H., Garcia-Bonete, M., Duelli, A., et al. (2016). Bayesian analysis of non-thermal structural changes induced by terahertz radiation in protein crystals. 2016 41ST INTERNATIONAL CONFERENCE ON INFRARED, MILLIMETER, AND TERAHERTZ WAVES (IRMMW-THZ).
Chapter in book (Refereed)
- Friedman, R. (2024). The Emerging Role of Molecular Dynamics Simulations in Cancer Research. Comprehensive Computational Chemistry : Molecular Dynamics Simulations and Reaction Rates. Oxford. UK, Elsevier. 910-920.
Article, review/survey (Refereed)
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Friedman, R., Bjelic, S. (2020). Simulations Studies of Protein Kinases that are Molecular Targets in Cancer. Israel Journal of Chemistry. John Wiley & Sons. 60 (7). 667-680.
Status: Published -
Friedman, R., Khalid, S., Aponte-Santamaria, C., Arutyunova, E., Becker, M., et al. (2018). Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology. Journal of Membrane Biology. Springer. 251 (5-6). 609-631.
Status: Published -
Friedman, R., Boye, K., Flatmark, K. (2013). Molecular modelling and simulations in cancer research. Biochimica et Biophysica Acta. CR. Reviews on Cancer. 1836 (1). 1-14.
Status: Published
Article in journal (Other academic)
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Friedman, R., Agmon, N. (2017). Charge Transfer in Proteins : In Celebration of Hemi Gutman's 80th Birthday. Israel Journal of Chemistry. 57 (5). 355-356.
Status: Published