A5049972739- Cellular Mechanics and Interactions
- Mathematical Biology Tumor Growth
- Angiogenesis and VEGF in Cancer
- Cancer Cells and Metastasis
- Theoretical and Computational Physics
- Protein Structure and Dynamics
- Enzyme Structure and Function
- Block Copolymer Self-Assembly
- Advanced Polymer Synthesis and Characterization
- Mitochondrial Function and Pathology
- Advanced Neuroimaging Techniques and Applications
- Cardiovascular Health and Disease Prevention
- Redox biology and oxidative stress
- Advanced MRI Techniques and Applications
- Material Dynamics and Properties
- Skin and Cellular Biology Research
- Blood properties and coagulation
- 3D Printing in Biomedical Research
- Rheology and Fluid Dynamics Studies
- Fluid Dynamics and Turbulent Flows
- Alzheimer's disease research and treatments
- Electron Spin Resonance Studies
- Cell Image Analysis Techniques
- Sulfur Compounds in Biology
- Solidification and crystal growth phenomena
University of Coimbra
2016-2025
University of Trento
2024
University of Southern Denmark
2024
Association for Innovation and Biomedical Research on Light and Image
2012-2014
University of Lisbon
2007-2012
University of Warwick
2008
Harvard University
2008
Universidade do Porto
2008
University of Pittsburgh
2005-2006
University of Manchester
2000-2001
The last years have witnessed remarkable advances in our understanding of the emergence and consequences topological constraints biological soft matter. Examples are abundant relation to (bio)polymeric systems range from characterization knots single polymers proteins that whole chromosomes polymer melts. At same time, considerable been made description interplay between physical properties complex fluids, with development techniques now allow researchers control formation interaction...
Understanding tumor induced angiogenesis is a challenging problem with important consequences for diagnosis and treatment of cancer. Recently, strong evidences suggest the dual role endothelial cells on migrating tips proliferating body blood vessels, in consonance further events behind lumen formation vascular patterning. In this paper we present multi-scale phase-field model that combines benefits continuum physics description capability tracking individual cells. The allows us to discuss...
Biophysical cues influence many aspects of cell behavior. Stiffness the extracellular matrix is probed by cells and transduced into biochemical signals through mechanotransduction protein networks, strongly influencing stem Cellular stemness intimately related with mechanical properties cell, like intracellular contractility stiffness, which in turn are influenced microenvironment. Pluripotency associated soft low-contractility cells. Hence, we postulated that culture substrates, presumably...
Hydrogen peroxide (H2O2) is a key signaling agent. Its best characterized actions in mammalian cells involve the early oxidation of thiols cytoplasmic phosphatases, kinases and transcription factors. However, these redox targets are orders magnitude less H2O2-reactive abundant than peroxiredoxins. How can they be oxidized time frame? Here we investigate this question using computational reaction-diffusion models H2O2 signaling. The results show that at supply rates commensurate with...
Sprouting angiogenesis, where new blood vessels grow from pre-existing ones, is a complex process biochemical and mechanical signals regulate endothelial cell proliferation movement. Therefore, mathematical description of sprouting angiogenesis has to take into consideration biological as well relevant physical processes, in particular the interplay between adjacent cells extracellular microenvironment. In this work, we introduce first phase-field continuous model capable predicting sprout...
Angiogenesis - the growth of new blood vessels from a pre-existing vasculature is key in both physiological processes and on several pathological scenarios such as cancer progression or diabetic retinopathy. For vascular networks to be functional, it required that growing sprouts merge either with an existing functional mature vessel another sprout. This process called anastomosis. We present systematic 2D 3D computational study tissue address capability angiogenic factor gradients drive...
During angiogenesis, new blood vessels sprout and grow from existing ones. This process plays a crucial role in organ development repair, wound healing numerous pathological processes such as cancer progression or diabetes. Here, we present mathematical model of early stage angiogenesis that permits exploration the relative importance mechanical, chemical cellular cues. Endothelial cells proliferate move over an extracellular matrix by following external gradients Vessel Growth Factor,...
We carry out systematic Monte Carlo simulations of Gō lattice proteins to investigate and compare the folding processes two model whose native structures differ from each other due presence a trefoil knot located near terminus one protein chains. show that time knotted fold is larger than unknotted this difference in particularly striking temperature region below optimal temperature. Both display similar transition temperatures, which indicative thermal stabilities. By using probability...
Systematic Monte Carlo simulations of simple lattice models show that the final stage protein folding is an ordered process where native contacts get locked (i.e., residues come into contact and remain in for duration process) a well-defined order. The detailed study dynamics protein-like sequences designed as to exhibit different energy distributions, well degrees sequence optimization participation non-native interactions process), reveals significant differences corresponding locking...
We develop a fluid mechanical model of the arterial tree in order to address key question what determines heart rate mammals. propose that frequency pulsatile pressure gradient, which minimizes resistance flow and facilitates movement, coincides with physiological rate. Using data from literature on 95 mammals as function body mass, radius aorta we construct target curve cardiac versus aortic radius. This serves benchmark for comparison our model's results. Our elastic one-dimensional flow,...
The dynamics of tumor growth and associated events cover multiple time spatial scales, generally including extracellular, cellular intracellular modifications. main goal this study is to model the biological physical behavior evolution in presence normal healthy tissue, considering a variety involved process. These include hyper hypoactivation signaling pathways during growth, vessels' intratumoral vascularization competition cancer cells with host tissue. work addresses two distinctive...
Recent work has suggested the existence of glassy behavior in a ferromagnetic model with four-spin interaction. Motivated by these findings, we have studied dynamics this using Monte Carlo simulations particular attention being paid to two-time quantities. We find that system shares many features common glass forming liquids. In particular, exhibits: (i) very long-lived metastable state, (ii) autocorrelation functions show stretched exponential relaxation, (iii) non-equilibrium timescale...
Computational modeling of biological systems is a powerful tool to clarify diverse processes contributing cancer. The aim the complex biochemical and mechanical interactions between cells, relevance intracellular signaling pathways in tumor progression related events cancer treatments, which are largely ignored previous studies.A three-dimensional multiscale cell-based model developed, covering multiple time spatial scales, including intracellular, cellular, extracellular processes....
Computer simulations reveal how photoinduced chemical reactions can be exploited to create long-range order in binary and ternary polymeric materials. The process is initiated by shining a spatially uniform light over photosensitive AB blend, which thereby undergoes both reversible reaction phase separation. We then introduce well-collimated, higher intensity source. Rastering this secondary the sample locally increases rate causes formation of defect-free, periodic structures. These...
Tumor growth is becoming a central problem in biophysics both from its social and medical interest and, more fundamentally, because it remarkable example of an emergent complex system. Focusing on the description spatial dynamical features tumor growth, this paper we review recent modeling approaches using technique borrowed materials science: phase-field models. These models allow us, with large degree generality, to identify paramount mechanisms causing uncontrolled cells as well propose...
For almost 15 years, the experimental correlation between protein folding rates and contact order parameter has been under scrutiny. Here, we use a simple simulation model combined with native-centric interaction potential to investigate physical roots of this empirical observation. We simulate large set circular permutants, thus eliminating dependencies rate on other properties (e.g. stability). show that rate-contact is consequence fact that, in high structures, transition state ensemble...
Abstract Germline mutations of E-cadherin cause Hereditary Diffuse Gastric Cancer (HDGC), a highly invasive cancer syndrome characterised by the occurrence diffuse-type gastric carcinoma and lobular breast cancer. In this disease, E-cadherin-defective cells are detected invading adjacent stroma since very early stages. Although loss is well established as triggering event, other determinants process persist largely unknown. Herein, we develop an experimental strategy that comprises in vitro...
In the cytosol of human cells under low oxidative loads, hydrogen peroxide is confined to microdomains around its supply sites, due fast consumption by peroxiredoxins. So are sulfenic and disulfide forms 2-Cys peroxiredoxins, according a previous theoretical analysis [Travasso et al., Redox Biology 15 (2017) 297]. Here, an extended reaction-diffusion model that for first time considers differential properties peroxiredoxins 1 2 thioredoxin redox cycle predicts important new aspects dynamics...
Abstract Motivation Trajectories, which are sequentially measured quantities that form a path, an important presence in many different fields, from hadronic beams physics to electrocardiograms medicine. Trajectory analysis requires the quantification and classification of curves, either by using statistical descriptors or physics-based features. To date, no extensive user-friendly package for trajectory has been readily available, despite its importance potential application across various...
We consider the interplay of thermal fluctuations and shear on surface domains in various systems coarsening under an imposed flow. These include with nonconserved conserved dynamics, a order parameter advected by fluid whose velocity field satisfies Navier-Stokes equation. In each case equation motion for interface height reduces to anisotropic Burgers The scaling exponents that describe growth are calculated exactly any dimension dynamics. For fluid-advected we determine exponents, but...