Where Physics Meets Biology


  • Mario Nicodemi University of Naples Federico II




Technology management, ethical organizations, physics, biology


The frontier between life and physical sciences currently includes the strategic research field where the wealth of data produced by new quantitative technologies in molecular biology naturally meets the advanced analysis and modelling tools of theoretical physics. For its profound scientific implications and huge potential impacts in biomedicine, such an area of investigation is attracting substantial interest. Therefore, in the following contribution, I briefly review some developments in the research field under scrutiny.


Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., Suzuki, T., Ntini, E., Arner, E., Valen, E., Li, K., Schwarzfischer, L., Glatz, D., Raithel, J., Lilje, B., Rapin, N., Bagger, F.O., Jørgensen, M., Andersen, P.R., Bertin, N., Rackham, O., Burroughs, A.M., Baillie, J.K., Ishizu, Y., Shimizu, Y., Furuhata, E., Maeda, S., Negishi, Y., Mungall, C.J., Meehan, T.F., Lassmann, T., Itoh, M., Kawaji, H., Kondo, N., Kawai, J., Lennartsson, A., Daub, C.O., Heutink, P., Hume, D.A., Jensen, T.H., Suzuki, H., Hayashizaki, Y., Müller, F., The FANTOM Consortium, Forrest, A.R.R., Carninci, P., Rehli, M., and Sandelin, A. (2014), “An Atlas of Active Enhancers across Human Cell Types and Tissues”, Nature, 507: 455–461. DOI: 10.1038/nature12787.

Barbieri, M., Chotalia, M., Fraser, J., Lavitas, L.M., Dostie, J., Pombo, A., and Nicodemi, M. (2012), “Complexity of Chromatin Folding Is Captured by the Strings and Binders Switch Model”, Proceedings of the National Academy of Sciences Oct. 2012, 109 (40): 16173–16178. DOI: 10.1073/pnas.1204799109.

Barbieri, M., Xie, S.Q., Triglia, E.T., Chiariello, A.M., Bianco, S., de Santiago, I., Branco, M.R., Rueda, D., Nicodemi, M., and Pombo, A. (2017), “Active and Poised Promoter States Drive Folding of the Extended HoxB Locus in Mouse Embryonic Stem Cells”, Nature Structural & Molecular Biology, 24 (6): 515–524. DOI: 10.1038/nsmb.3402.

Beagrie, R.A., Scialdone, A., Schueler, M., Kraemer, D.C.A., Chotalia, M., Xie, S.Q., Barbieri, M., de Santiago, I., Lavitas, L.M., Branco, M.R., Fraser, J., Dostie, J., Game, L., Dillon, N., Edwards, P.A.W., Nicodemi, M., and Pombo, A. (2017), “Complex Multi-Enhancer Contacts Captured by Genome Architecture Mapping (GAM), a Novel Ligation-Free Approach”, Nature, 543: 519–524. DOI: 10.1038/nature21411.

Bianco, S., Lupiáñez, D.G., Chiariello, A.M., Annunziatella, C., Kraft, K., Schöpflin, R., Wittler, L., Andrey, G., Vingron, M., Pombo, A., Mundlos, S., and Nicodemi, M. (2018), “Polymer Physics Predicts the Effects of Structural Variants on Chromatin Architecture”, Nature Genetics, 50: 662–667. DOI: 10.1038/s41588-018-0098-8.

Conte, M., Fiorillo, L., Bianco, S., Chiariello, A.M., Esposito, A., and Nicodemi, M. (2020), “Polymer Physics Indicates Chromatin Folding Variability across Single-Cells Results from State Degeneracy in Phase-Separation”, Nature Communications, 11 (1): 3289–3295. DOI: 10.1038/s41467-020-17141-4.

de Gennes, P.G. (1979), Scaling Concepts in Polymer Physics, Ithaca/London: Cornell University Press.

Dekker, J., and Mirny, L. (2016), “The 3D Genome as Moderator of Chromosomal Communication”, Cell, 164 (6): 1110–1121. DOI: 10.1016/j.cell.2016.02.007.

Dellino, G.I., Palluzzi, F., Chiariello, A.M., Piccioni, R., Bianco, S., Furia, L., De Conti, G., Bouwman, B.A.M., Melloni, G., Guido, D., Giacò, L., Luzi, L., Cittaro, D., Faretta, M., Nicodemi, M., Crosetto, N., and Pelicci, P.G. (2019), “Release of Paused RNA Polymerase II at Specific Loci Favors DNA Double-Strand-Break Formation and Promotes Cancer Translocations”, Nature Genetics, 51: 1011–1017. DOI: 10.1038/s41588-019-0421-z.

Dixon, J.R., Gorkin, D.U., and Ren, B. (2016), “Chromatin Domains: The Unit of Chromosome Organization”, Molecular Cell, 62 (5): 668–680. DOI: 10.1016/j.molcel.2016.05.018.

Feynman, R.P., Leighton, R.B., and Sands, M. (1964, revised edn. 2005), The Feynman Lectures on Physics, Reading, MA: Addison-Wesley.

Finn, E.H., and Misteli, T. (2019), “Molecular Basis and Biological Function of Variability in Spatial Genome Organization”, Science, 365 (6457). DOI: 10.1126/science.aaw9498.

Fiorillo, L., Musella, F., Conte, M., Kempfer, R., Chiariello, A.M., Bianco, S., Kukalev, A., Irastorza-Azcarate, I., Esposito, A., Abraham, A., Prisco, A., Pombo, A., and Nicodemi, M. (2021), “Comparison of the Hi-C, GAM and SPRITE Methods Using Polymer Models of Chromatin”, Nature Methods, 18: 482–487. DOI: 10.1038/s41592-021-01135-1.

Fraser, J., Ferrai, C., Chiariello, A.M., Schueler, M., Rito, T., Laudanno, G., Barbieri, M., Moore, B.L., Kraemer, D.C.A., Aitken, S., Xie, S.Q., Morris, K.J., Itoh, M., Kawaji, H., Jaeger, I., Hayashizaki, Y., Carninci, P., Forrest, A.R.R., The FANTOM Consortium, Semple, C.A., Dostie, J., Pombo, A., and Nicodemi, M. (2015), “Hierarchical Folding and Reorganization of Chromosomes Are Linked to Transcriptional Changes in Cellular Differentiation”, Molecular Systems Biology, 11 (12): 852-858. DOI: 10.15252/msb.20156492.

Kempfer, R., and Pombo, A. (2019), “Methods for Mapping 3D Chromosome Architecture”, Nature Reviews Genetics, 21 (4): 207–226. DOI: 10.1038/s41576-019-0195-2.

Kragesteen, B.K., Spielmann, M., Paliou, C., Heinrich, V., Schöpflin, R., Esposito, A., Annunziatella, C., Bianco, S., Chiariello, A.M., Jerkovic, I., Harabula, I., Guckelberger, P., Pechstein, M., Wittler, L., Chan, W.L., Franke, M., Lupiáñez, D.G., Kraft, K., Timmermann, B., Vingron, M., Visel, A., Nicodemi, M., Mundlos, S., and Andrey, G. (2018), “Dynamic 3D Chromatin Architecture Contributes to Enhancer Specificity and Limb Morphogenesis”, Nature Genetics, 50: 1463–1468. DOI: 10.1038/s41588-018-0221-x.

Sigal, Y.M., Zhou, R., and Zhuang, X. (2018), “Visualizing and Discovering Cellular Structures with Super-Resolution Microscopy”, Science, 361 (6405): 880–887. DOI: 10.1126/science.aau1044.

Spielmann, M., Lupianez, D.G., and Mundlos, S. (2018), “Structural Variation in the 3D Genome”, Nature Reviews Genetics, 19: 453–467. DOI: 10.1038/s41576-018-0007-0.




How to Cite

Nicodemi, M. (2022). Where Physics Meets Biology. PuntOorg International Journal, 7(1), 57–61. https://doi.org/10.19245/25.05.pij.7.1.6