Soft and Biological Matter

This group works in soft condensed matter physics with a direct application to biological systems, aiming at a far-reaching impact in science and society. The research developed has a strong focus on cellular morphology and movement, tissue irrigation, and tumor and vessel growth. Within the topic of vessel growth, we explore the consequences of physical mechanisms in the development of complex processes in both health and disease such as organogenesis, wound healing, inflammation, endometriosis or diabetes. We collaborate with several multidisciplinary international teams and bring together the know-how of researchers with proven expertise in theoretical, computational and experimental tasks.

Current projects

Previous projects

• COST Action: CA15214 - An integrative action for multidisciplinary studies on cellular structural networks
• Physical Modelling of Tumours - Understanding the metastasis mechanism
• Angiogenesis in diabetic retinopathy – Integrating experiments and modeling
• The nature of the protein folding process
• Modeling Angiogenesis in Type 2 Diabetes Mellitus - integrating experimental and theoretical approaches
• Cost Action: CA17139 - European Topology Interdisciplinary Action

Recent Publications

Papers

International Journals

1 - A 3D Computational Study on the Formation and Progression of Tumor Cells in Diffuse Gastric Cancer
V. Lopes, J. Figueiredo, P. Carneiro, M. Gouveia, RDM Travasso, J. Carvalho
Bull. Math. Biol. 87(2), 28 (2025)

2 - On the momentum space structure of the quark propagator
O. Oliveira, T. Frederico, W. de Paula
Eur. Phys. J. C 85(3), 280 (2025)

3 - Lattice determination of the Batalin-Vilkovisky function and the strong running interaction
AC Aguilar, N Brito, MN Ferreira, J Papavassiliou, O Oliveira, PJ Silva
Phys. Lett. B 858, 139054 (2024)

4 - Effect of hypoxia and KCl depolarization in autofluorescence and ROS changes at the hippocampal CA3 area
M.I.G. Batista, C.M.F. Miranda, S.M. Figueiredo, M. Bosio, J.L. Alves, M.S. Sousa, F. Sampaio dos Aidos, C.M. Matias, R.M. Quinta-Ferreira, M.E. Quinta-Ferreira
Gen Physiol Biophys 43 (6), 585-592 (2024)

5 - Sunspots Identification Through Mathematical Morphology
S Bourgeois, T Barata, R Erdélyi, R Gafeira, O Oliveira
Sol. Phys. 299(2), 10 (2024)

6 - Four Gluon Vertex from Lattice QCD
M. Colaço, O. Oliveira, Paulo J. Silva
Phys. Rev. D 109 (7), 074502 (2024)

7 - The architecture of redox microdomains: Cascading gradients and peroxiredoxins´ redox-oligomeric coupling integrate redox signaling and antioxidant protection
M Griffith, A Araûjo, R Travasso, A Salvador
Redox Biol. 69, 103000 (2024)

8 - TrajPy: empowering feature engineering for trajectory analysis across domains
M Moreira-Soares, E Mossmann, RDM Travasso, JR Bordin
Bioinform. Adv. 4(1), vbae026 (2024)

9 - On the conformal limit of a QED-inspired model
O. Oliveira, T. Frederico, W. de Paula
Eur. Phys. J. C 84(851) (2024)

10 - Deconfinement, center symmetry and the ghost propagator in Landau gauge pure SU(3) Yang-Mills theory
V. Paiva, P.J. Silva, O. Oliveira
J. High Energy Phys. 5, 164 (2024)

11 - High-refractive-index materials screening from machine learning and ab initio methods
Pedro J.M.A. Carriço, Márcio Ferreira, Tiago F.T. Cerqueira, Fernando Nogueira, Pedro Borlido
Phys. Rev. Mater. 8, 015201 (2024)

12 - E-cadherin variants associated with oral facial clefts trigger aberrant cell motility in a REG1A-dependent manner
J. Pereira, S. Melo, R.M. Ferreira, P. Carneiro, V.T. Yang, A.F. Maia, J. Carvalho, C. Figueiredo, J.C. Machado, E. Morais-de-Sá, R. Seruca, J. Figueiredo
Cell Commun. Signal. 22 (1), 152 (2024)

13 - Topology in soft and biological matter
L Tubina, R. Travasso et al.
Phys. Rep. 1075, 1-137 (2024)

14 - The automatic identification and tracking of coronal flux ropes II. New mathematical morphology-based flux rope extraction method and deflection analysis
A. Wagner, S. Bourgeois, EKJ Kilpua, R. Sarkar, D.J. Price, A. Kumari, J. Pomoell, S. Poedts, T. Barata, R. Erdélyi, O. Oliveira, R. Gafeira
Astron. Astrophys. 683, A39 (2024)

Portuguese Journals

15 - Quarenta anos de Olimpíadas de Física
F. Nogueira
Gazeta de Física 47(2), 34 (2024)

Proceedings

International Conferences

16 - High statistical computation of the Landau gauge ghost-gluon vertex
N. Brito, O. Oliveira, Paulo J. Silva
PoS LATTICE2024 (2024)

Communications

Invited

17 - The Formation of Loops in Blood Vessel Networks - Resilience, Flow and Therapy
Travasso, RDM et al.
BIRS Workshop, Formation of Looping Networks - from Nature to Models, Banff, Canada, 7th - 12th Jul (2024)

18 - Christmas Seminar: Machine Learning in the Physics Department
RDM Travasso, V. Carvalho
Universidade de Coimbra, Coimbra, Portugal, Dec 13 (2024)

19 - Lattice gluon propagator in the center-symmetric Landau gauge
D. van Egmond, O. Oliveira, U. Reinosa, J. Serreau, Paulo J. Silva, M. Tissier
QuantFunc2024, Valência, Espanha, 2 - 6 September (2024)

Oral

20 - Mathematical Modeling of Wild Type and Mutant Keratin-14 Network Dynamics and Keratin Aggregate Formation
M. Gouveia, T. Sorcan, S. Zemljic-Jokhadar, RDM Travasso, M. Liovic
ECMTB 2024, Toledo, Spain, 22nd – 26th Jul (2024)

21 - Modelling the Influence of Loss of E-Cadherin and Stroma Attachment in Cancer Cell Invasion: Mathematical Approach
P. Guerrero, S. Melo, M. Moreira-Soares, JR Bordin, F. Carneiro, P. Carneiro, MB Dias, J. Carvalho, J. Figueiredo, R. Seruca, RDM. Travasso
ECMTB 2024, Toledo, Spain, 22nd – 26th Jul (2024)

22 - Atividades experimentais com supercondensadores
José António Paixão, Fernando Nogueira
5ª Conferência de Física de Países de Língua Portuguesa. Coimbra, Portugal. 8-10 September. (2024)

23 - Recursos computacionais para o ensino de Física da Matéria Condensada
José António Paixão, Fernando Nogueira
5ª Conferência de Física de Países de Língua Portuguesa. Coimbra, Portugal. 8-10 September (2024)

24 - Microenvironment Anisotropy drives Cell Migration and Large-Scale Nuclear Deformations – a coupled in silico and in vitro study
A. Paulino, C. Leclech, M. Gouveia, J. Carvalho, RDM Travasso, A. Barakat
ECMTB 2024, Toledo, Spain, 22nd – 26th Jul (2024)

25 - Notch Flow-Driven Polarisation and Signalling in Vessels - a Mathematical Model
RDM Travasso, M.M. Sá, M. Gouveia, M. Palmeira, E. Ferreira, C. Sahlgren
ECMTB 2024, Toledo, Spain, 22nd – 26th Jul (2024)

26 - Towards Prostate Cancer Predicative in Silico Models – the Early Stages and Vascular Growth
RDM Travasso, et al.
9th ECCOMAS Congress, Lisbon, Portugal, 3rd – 7th Jun (2024)

27 - The ECM and Tissue Architecture are Major Determinants of Early Invasion Mediated by E-Cadherin Dysfunction
RDM Travasso, et al.
IUTAM 2024 – Theoretical and numerical developments in cellular mechanobiology, Seville, Spain, 3rd – 5th Jun (2024)

28 - Identifying and Tracking Solar Flux Ropes in Simulation Data and Deflection Analysis of AR11176 and AR12473 Flux Ropes
A. Wagner, S. Bourgeois, E. Kilpua, R. Sarkar, D. Price, A. Kumari, J. Pomoell, S. Poedts, T. Barata, R. Erdélyi, O. Oliveira, R. Gafeira
EGU General Assembly 2024, Vienna, Austria, 14–19 April EGU24-8257 (2024)

29 - Solar Magnetic Flux Ropes and their Early-Stage Evolution
A. Wagner, S. Bourgeois, E.K.J. Kilpua, R. Sarkar, D.J. Price, A. Kumari, J. Pomoell, S. Poedts, T. Barata, R. Erdélyi, O. Oliveira, R. Gafeira
Austrian Early Career Conference 2024, Vega Observatory, Haus der Natur, Salzburg/Austria, 8-9 March (2024)

30 - Center-symmetric Landau gauge, the deconfinement transition and the gluon propagator as seen in lattice QCD
D. van Egmond, O. Oliveira, U. Reinosa, J. Serreau, Paulo J. Silva, M. Tissier
24a Conferência Nacional de Física (FÍSICA 2024), Departamento de Física da Universidade de Coimbra, 11 a 14 de Setembro (2024)

31 - Center-symmetric Landau gauge, the deconfinement transition and the gluon propagator as seen in lattice QCD
D. van Egmond, O. Oliveira, U. Reinosa, J. Serreau, Paulo J. Silva, M. Tissier
XVIth Quark Confinement and the Hadron Spectrum, Cairns, Austrália, 18-24 August (2024)

Poster

32 - High statistical computation of the Landau gauge ghost-gluon vertex
N. Brito, O. Oliveira, Paulo J. Silva,
41th International Symposium on Lattice Field Theory (Lattice 2024), Liverpool, Reino Unido, 28 July - 3 August (2024)

33 - The four-gluon and ghost-gluon vertices in the Landau gauge from lattice simulations
M. Colaço, N. Brito, O. Oliveira, Paulo J. Silva
XVIth Quark Confinement and the Hadron Spectrum, Cairns, Austrália, 18-24 August (2024)

34 - The four-gluon and ghost-gluon vertices in the Landau gauge from lattice simulations
M. Colaço, N. Brito, O. Oliveira, Paulo J. Silva
24a Conferência Nacional de Física (FÍSICA 2024), Departamento de Física da Universidade de Coimbra, 11-14 September (2024)

35 - Numeric local pseudopotentials through evolutionary optimisation
Fernando Nogueira, Tiago Cerqueira
CMD31-General Conference of the Condensed Matter Division of the European Physical Society, Braga - Portugal, 2-6 September (2024)

36 - Deconfinement in pure gauge SU(3) Yang-Mills theory: the ghost propagator
O. Oliveira, V. Paiva, Paulo J. Silva
24a Conferência Nacional de Física (FÍSICA 2024), Departamento de Física da Universidade de Coimbra, 11-14 September (2024)

37 - High-throughput search of B-C-X superconductors
Pedro Borlido, Tiago F.T. Cerqueira, Fernando Nogueira
CMD31-General Conference of the Condensed Matter Division of the European Physical Society, Braga - Portugal, 2-6 September (2024)

38 - The ECM and Tissue Architecture are Major Determinants of Early Invasion Mediated by E-Cadherin Dysfunction
RDM Travasso, et al.
Curvobio 2024, Warsaw, Poland, 28th – 30th Aug (2024)

Thesis

MSc thesis

39 - Modelização computacional dos efeitos da radiação ionizante na Síndrome Hereditária para cancro da mama e do ovário associada aos genes BRCA1/2
Carolina Costa Alves
Master in Biomedical Engineering (2024)

Other

40 - Gulbenkian New Talents in Physics Program
Travasso, RDM.
Mentor of New Talents in Physics awardee, Ana Bensabat Paulino. (2024)

41 - The center-symmetric Landau gauge meets the lattice
D. van Egmond, O. Oliveira, U. Reinosa, J. Serreau, Paulo J. Silva, M. Tissier
Submitted (2024)