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

• COST Action: CA15214 - An integrative action for multidisciplinary studies on cellular structural networks
• Modeling Angiogenesis in Type 2 Diabetes Mellitus - integrating experimental and theoretical approaches
• Cost Action: CA17139 - European Topology Interdisciplinary Action

Previous projects

• Physical Modelling of Tumours - Understanding the metastasis mechanism
• Angiogenesis in diabetic retinopathy – Integrating experiments and modeling
• The nature of the protein folding process

Recent Publications

Papers

International Journals

1 - 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)

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

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

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

5 - 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)

6 - 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)

7 - 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)

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

9 - The Automatic Identification and Tracking of Coronal Flux Ropes -- Part II: New Mathematical Morphology-based Flux Rope Extraction Method and Deflection Analysis
A. Wagner, S. Bourgeois, E. Kilpua, R. Sarkar, D. Price, A. Kumari, J. Pomoell, S. Poedts, T. Barata, R. Erdélyi, O. Oliveira, R. Gafeira
Astron. Astrophys. (2024)

10 - 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)

11 - 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 (2023)

12 - Gauge dependence of the quark gap equation: An exploratory study
JR Lessa, FE Serna, B El-Bennich, A Bashir, O Oliveira
Phys. Rev. D 107(7), 074017 (2023)

13 - A mathematical model of fibrinogen-mediated erythrocyte-erythrocyte adhesion
CS Lopes, J Curty, FA Carvalho, A Hernandez-Machado, K Kinoshita, NC Santos, RDM Travasso
Commun. Biol. 6(1), 192 (2023)

14 - The ECM and tissue architecture are major determinants of early invasion mediated by E-cadherin dysfunction
S Melo, P Guerrero, MM Soares, JR Bordin, F Carneiro, P Carneiro, MB Dias, J Carvalho, J Figueiredo, R Seruca, RDM Travasso
Commun. Biol. 6 (1), 1132 (2023)

15 - Looking at QED with Dyson-Schwinger Equations: Basic Equations, Ward-Takahashi Identities and the Two-Photon-Two-Fermion Irreducible Vertex
O Oliveira, HL Macedo, RC Terin
Few-Body Syst. 64(3), 67 (2023)

16 - A coupled logistic map lattice model for two competing species
J. Sales, R. Travasso, M. Buckeridge, S. A. Carvalho
Eur. Phys. J. Plus 138, 1020 (2023)

17 - Image-based angio-adaptation modelling: a playground to study cerebrovascular development
RDM Travasso, V Coelho-Santos
Front. Psychol. 14, 1223308 (2023)

Portuguese Journals

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

Proceedings

International Conferences

19 - Computation of the Kugo-Ojima function from lattice simulations
N. Brito, O. Oliveira, P.J. Silva, J. Papavassiliou, Ferreira M.N., A.C. Aguilar
PoS LATTICE2023 (2023)

20 - The four-gluon vertex in Landau gauge
M. Colaço, O. Oliveira, Paulo J. Silva
PoS LATTICE2023, 151 (2023)

21 - Spatially localized redox relays allow sensitive site-specific hydrogen peroxide signaling
M Griffith, A Araújo, R Travasso, A Salvador
Free Radic. Biol. Med. 208 (1), S29-S-30 (2023)

22 - The quark propagator and quark-gluon vertex from lattice QCD at finite temperature
J. Marques Leal Junior, G. Kalusche, T. Mendes, J.I. Skullerud, O. Oliveira, P. J. Silva
PoS LATTICE 2022, 280 (2023)

23 - How sensitive and site-specific hydrogen peroxide signaling can be achieved in human cells: spatially localized redox relays
A Salvador, M Griffith, A Araujo, R Travasso
Eur. Biophys. J. 52(SUPPL 1), 749 (2023)

24 - Generating Vascular Networks: A Reinforcement Learning Approach
J. Simoes, R Travasso, E Costa, T Baptista
8th Annual International Conference on Machine Learning, Optimization and Data science (LOD) 13811, 139-153 (2023)

Communications

Invited

25 - Multigluon correlation functions from lattice QCD
Oliveira, O.
From first-principles QCD to experiments, Trento, Italy, 26 May (2023)

26 - Multigluon correlation functions from lattice QCD
Oliveira, O.
Light Cone, Rio de Janeiro, 22 September (2023)

27 - How abundant are superoxide and hydrogen peroxide in the vasculature lumen, how far can they reach?
T. Sousa, M. Gouveia, RDM Travasso, A. Salvador
3rd Meeting of Young Biophysicists, Porto, Portugal, 1st – 2nd Jun (2023)

28 - How abundant are superoxide and hydrogen peroxide in the vasculature lumen, how far can they reach?
T. Sousa, M. Gouveia, RDM Travasso, A. Salvador
EBSA 2023, Stockholm, Sweden, 31st July – 4th Aug (2023)

29 - Movimento, Difusão, Tensão e Pressão - A Física na Biologia
Travasso, R.
IX Jornadas de Engenharia Física, Lisboa, Portugal, 22nd - 24th Feb (2023)

30 - Localised H2O2 gradients in the vasculature lumen and in the cellular cytoplasm
R. Travasso, A. Salvador, T. Santos, M. Gouveia, A. Itacarambi, F. Aidos, P. Abranches, A. Bayani
SFRR-E Webinar Series “Emerging leaders in redox biology”, 4th Jul (2023)

31 - Adhesion modulates cell migration, erythrocyte morphology and endothelial cell Dynamics
R. Travasso, et al.
Programa de Verão 2023, Laboratório Nacional de Computação Científica, 16th Jan – 17th Feb, Rio de Janeiro (remote talk), Brazil (2023)

32 - Adhesion modulates cell migration, erythrocyte morphology and endothelial cell Dynamics
R. Travasso, et al.
Immuno-engineering workshop, Turku, Finland, 14th-15th Mar (2023)

33 - Adhesion modulates cell migration, erythrocyte morphology and endothelial cell Dynamics
R. Travasso, et al.
LI Winter Meeting On Statistical Physics, Guanajuato, Mexico, 11th-14th Jan (2023)

Oral

34 - Recursos computacionais para o ensino de Física da Matéria Condensada
José António Paixão, Fernando Nogueira
5ª Conferência de Física de Países de Língua Portuguesa (2024)

35 - Atividades experimentais com supercondensadores
José António Paixão, Fernando Nogueira
5ª Conferência de Física de Países de Língua Portuguesa (2024)

36 - Lattice computation of the Kugo-Ojima function
N. Brito, O. Oliveira, P.J. Silva, J. Papavassiliou, Ferreira M.N., A.C. Aguilar
From first-principles QCD to experiments, Trento, Italy, 24 May (2023)

37 - Fibrinogen-Mediated Erythrocyte-Erythrocyte Adhesion: Clinical Relevance, Experimental Assessment and Mathematical Modeling
N. Santos, C. Lopes, J. Curty, F. Carvalho, A. Hernández-Machado, K. Kinoshita, R. Travasso
11th International Conference on Biological Physics, South Korea, 14th – 18th Aug (2023)

38 - Adhesion modulates cell migration and endothelial cell dynamics
R. Travasso, M. Gouveia, M. Palmeira, M. Soares, S. Cunha, J. Bordin
International Conference on Flow Dynamics 2023, Sendai, Japan (remote participation), 6th – 8th Nov (2023)

39 - Heart Rate in Mammals (contributed talk)
R. Travasso, C. Penick, R. Dunn, E. Poiré
International Conference on Flow Dynamics 2023, Sendai, Japan (remote participation), 6th – 8th Nov (2023)

Poster

40 - Numeric local pseudopotentials through evolutionary optimisation
Fernando Nogueira, Tiago Cerqueira
CMD31-General Conference of the Condensed Matter Division of the European Physical Society (2024)

41 - 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 (2024)

42 - Modeling the Transport of Hydrogen Peroxide in Human Tissues
A. Itacarambi, R. Travasso, A. Salvador
3rd Meeting of Young Biophysicists, Porto, Portugal, 1st – 2nd Jun (2023)

43 - Deconfinement in pure gauge SU(3) Yang-Mills theory: the ghost propagator
O. Oliveira, V. Paiva, P.J. Silva
19th International Conference on QCD in Extreme Conditions (XQCD 2023), 26 July (2023)

44 - Mathematical Modeling of Endothelial Cell Dynamics in Vascular Sprouts
M. Palmeira, M. Gouveia, R. Travasso
Building Bridges in Biology Symposium, 1st – 3rd Mar (2023)

45 - Spatially localized redox relays allow sensitive site-specific hydrogen peroxide signaling
A. Salvador, M. Griffith, A. Araújo, R. Travasso
SfRBM 23, Punta del Este, Uruguay, 15th – 18th Nov (2023)

Thesis

PhD thesis

46 - Modelling endothelial cell´s collective movement and keratin cytoskeleton dynamics using the phase field method
Marcos João do Carmo Gouveia
PhD Thesis in Physics (2023)

Other

47 - Graph-Based Strategies for Optimizing Wildfire Supression
J. Aveiro, D. Neves, Paulo J. Silva, O. Oliveira, F. Nogueira, Jaime Oliveira da Silva,
(2023)

48 - On the Photon-Fermion Vertex
Oliveira, O.
arXiv:2312.02886 [hep-ph] (2023)

49 - Deconfinement, Center Symmetry and the Ghost Propagator in Landau Gauge Pure SU(3) Yang-Mills Theory
V. Paiva, Paulo J. Silva, O. Oliveira
arXiv:2307.08662 [hep-lat] (2023)