# 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 - Sunspots Identification Through Mathematical Morphology

S Bourgeois, T Barata, R Erdélyi, R Gafeira, O Oliveira

Sol. Phys. **299(2)**, 10 (2024)

2 - Four Gluon Vertex from Lattice QCD

M. Colaço, O. Oliveira, Paulo J. Silva

Phys. Rev. D **109 (7)**, 074502 (2024)

3 - 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)

4 - 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)

5 - 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)

6 - 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)

7 - 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)

8 - 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)

9 - 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)

10 - 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)

11 - 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)

12 - 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)

13 - 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)

14 - Image-based angio-adaptation modelling: a playground to study cerebrovascular development

RDM Travasso, V Coelho-Santos

Front. Psychol. **14**, 1223308 (2023)

## Proceedings

### International Conferences

15 - 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)

16 - The four-gluon vertex in Landau gauge

M. Colaço, O. Oliveira, Paulo J. Silva

PoS **LATTICE2023**, 151 (2023)

17 - 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)

18 - 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)

19 - 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)

20 - 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

21 - Multigluon correlation functions from lattice QCD

Oliveira, O.

From first-principles QCD to experiments, Trento, Italy, 26 May (2023)

22 - Multigluon correlation functions from lattice QCD

Oliveira, O.

Light Cone, Rio de Janeiro, 22 September (2023)

23 - 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)

24 - 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)

25 - Movimento, Difusão, Tensão e Pressão - A Física na Biologia

Travasso, R.

IX Jornadas de Engenharia Física, Lisboa, Portugal, 22nd - 24th Feb (2023)

26 - 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)

27 - 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)

28 - 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)

29 - Adhesion modulates cell migration, erythrocyte morphology and endothelial cell Dynamics

R. Travasso, et al.

Immuno-engineering workshop, Turku, Finland, 14th-15th Mar (2023)

### Oral

30 - 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)

31 - 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)

32 - 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)

33 - 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

34 - Avaliação Crítica das Atividades Práticas e de Laboratório no Ensino de Física: Um Estudo Longitudinal do 3º Ciclo do Ensino Básico ao Ensino Secundário, considerando o Impacto da Pandemia de COVID-19 e das Escolhas Opcionais

J.C.S. Simões, M.N. Manaia, Esperança T.

Trabalho apresentado em XX Encontro Nacional de Educação em Ciências VI International Seminar on Science Education (2024)

35 - 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)

36 - 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)

37 - Mathematical Modeling of Endothelial Cell Dynamics in Vascular Sprouts

M. Palmeira, M. Gouveia, R. Travasso

Building Bridges in Biology Symposium, 1st – 3rd Mar (2023)

38 - 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

39 - 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

40 - Graph-Based Strategies for Optimizing Wildfire Supression

J. Aveiro, D. Neves, Paulo J. Silva, O. Oliveira, F. Nogueira, Jaime Oliveira da Silva,

(2023)

41 - On the Photon-Fermion Vertex

Oliveira, O.

arXiv:2312.02886 [hep-ph] (2023)

42 - 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)