Molecular Dynamics & Free Energy
Simulating atomic trajectories over microsecond scales to characterize protein conformational transitions, allosteric pathways, and compute binding free energy profiles with enhanced sampling techniques.
BIA LAB · UNIVERSITY OF COIMBRA · “DREAM, THINK, SOLVE!”
Simulate life.
Simulate life.
Engineer the future.
Explore biomolecular simulation and artificial intelligence at the interface of bioengineering, biotechnology, chemistry and biochemistry.
100% Laboratory Research
·
Erasmus+ Traineeships
·
Master’s Thesis (30 ECTS)
·
Visiting Scholars
EST. 1290 · ROYAL CAPITAL 1279 · COIMBRA, PORTUGAL
From 1279 to the future.
From Portugal to the world.
Seven centuries of university tradition. One forward-looking scientific mission.
In 1279, King D. Dinis established his royal capital in Coimbra. In 1290, he signed the historic charter that gave birth to one of the world's first universities.
For over seven hundred years, navigators, philosophers, and scientists left these hills to explore the unknown.
Today, the frontier is molecular. We do not sail across oceans. We navigate atomic trajectories, chemical bonds, and deep neural networks.
We model life atom by atom. We design targeted molecules to cure disease. We engineer biocatalysts for sustainable green chemistry.
Real science. Global collaboration. Future-ready capabilities.
“Dream without limits. Think with mathematical and chemical rigor. Solve the problems that matter to humanity.”
Laboratory Creed
Dream, Think, Solve.
Core Scientific Focus
Where Biomolecular Physics Meets AI
We apply rigorous computational modeling to unravel fundamental biological mechanisms and design next-generation molecular entities.
AI & Machine Learning in Chemistry
Leveraging deep learning, geometric graph neural networks, and generative molecular architectures to accelerate virtual screening, predict bioactivity, and discover novel chemical space for biotechnology.
Quantum Mechanics & QM/MM Catalysis
Investigating enzymatic reaction mechanisms, bond-breaking events, and catalytic transition states by seamlessly coupling high-accuracy quantum mechanics with macroscopic classical force fields.
Structure-Based Virtual Screening
High-throughput docking of massive compound libraries into macromolecular targets, assessing induced-fit effects, predicting pharmacokinetic properties, and guiding experimental hit optimization.
Authentic Crystallographic Model
PDB: 1IEP · 2.10 Å
Interactive Kinase-Inhibitor Complex (c-Abl + Imatinib)
Authentic biological structure of the c-Abl kinase catalytic domain in complex with the clinical inhibitor STI-571 (Imatinib / Gleevec). Explore the N-lobe and C-lobe fold, key catalytic residues (Lys271, Glu286, Thr315 gatekeeper, Met318 hinge), and directional binding pocket interactions in real-time WebGL.
- Direct access to dedicated local workstations and remote national supercomputing allocations (RNCA).
- Hands-on training in Python pipelines, MD trajectory analysis, and machine learning scoring functions.
- Co-authorship on peer-reviewed scientific contributions in international journals when projects yield publishable data.
Research Supervision & Direction
Scientific Mentorship & Collaborative Research
At BIA Lab, incoming researchers and mobility students are integrated directly into funded scientific initiatives, receiving individual mentorship, hands-on training, and co-authorship on peer-reviewed international publications.
Proven Mentorship Record
Over 7 PhD theses and 16 MSc dissertations successfully defended under Prof. Sérgio F. Sousa at the University of Coimbra. Currently directing 9 PhD candidates and 4 MSc researchers in international, highly collaborative stays.
7 PhD
Completed
16+ MSc
Completed
9 PhD & 4 MSc
Current Team
Major Research Grants
Selected for prestigious competitive programs including the CaixaResearch Health 2024 (€1,000,000 grant from “la Caixa” Foundation), the CaixaImpulse 2024 program, and Gilead Génese 2025.
Fully funded computational infrastructure & licenses
Global Standing & Output
Over 175 ISI papers with an h-index of 36 and >5,800 citations. Ranked among Stanford University's World Top 2% Most Cited Scientists (2022, 2023, 2024). Incoming students regularly co-author peer-reviewed publications.
175+
ISI Papers
36
h-index
5,800+
Citations
Laboratory Direction · Prof. Sérgio F. Sousa ↗
Principal Investigator & Group Leader · Department of Chemical Engineering (DEQ / FCTUC)
Future-Ready Capabilities
Skills That Bridge Science & Computation
A research stay at BIA Lab is an immersion in modern computational methodology. You develop analytical, programming, and biophysical skills that are in high demand across academia and biotechnology industries.
Scientific Computing
Linux environments, Bash scripting, Slurm cluster job scheduling, and high-performance computing (HPC) workflows on local and national architectures.
Python for Data & Biology
Data science pipelines with NumPy, Pandas, MDAnalysis, BioPython, and structural cheminformatics using RDKit for automated data extraction.
Simulation Engines
Setting up, parameterizing, equilibrating, and analyzing production simulations using GROMACS, Amber, and enhanced free energy sampling methods.
Applied Machine Learning
Training neural networks for QSAR/QSPR, molecular graph embeddings, AlphaFold structural predictions, and consensus scoring for drug discovery.
Molecular Visualization
Creating publication-grade structural figures, render pipelines with PyMOL, VMD, ChimeraX, and 3D scientific animation tools.
Scientific Communication
Writing reproducible protocols, drafting peer-reviewed manuscripts, presenting research in English lab meetings, and international conference posters.
Candidate Profiles & Opportunities
Who Can Join BIA Lab?
We welcome motivated students and researchers from European and international institutions looking to deepen their computational research experience in a collaborative, English-speaking environment.
Advanced Bachelor Students
Final-year undergraduate students (Licenciatura / BSc) seeking a focused research internship, a capstone graduation project, or an Erasmus+ Traineeship / summer stay.
Inquire about BSc Stays →Master’s Degree Candidates
MSc students wishing to conduct their full Master's Thesis research (30 ECTS track) or an Erasmus+ Traineeship in biomolecular modeling, QM/MM catalysis, or AI-guided drug design.
Inquire about MSc Thesis Stays →PhD Students & Visiting Scholars
Doctoral researchers looking for a collaborative research stay abroad, Sandwich PhD stays (CAPES, CNPq, FAPESP, TÜBİTAK, Erasmus+), or visiting scholars seeking joint computational projects.
Inquire about Doctoral Stays →
Graduate Study & Research Careers
MSc, PhD Degrees & Fellowships in Portugal
Beyond short-term mobility stays, you can pursue a full Master’s or Doctoral degree at FCTUC, conducting your thesis research inside BIA Lab with competitive national funding.
Primary Affiliation · Department of Chemical Engineering (DEQ / FCTUC)
BIA Lab is permanently anchored in the Department of Chemical Engineering at Pólo II. Candidates can enroll directly in DEQ graduate programs to conduct their full dissertation research with us:
Mestrado em Engenharia Química
Flagship master's degree offered by the Department of Chemical Engineering (DEQ / FCTUC). Advanced training in reaction engineering, transport phenomena, thermodynamics, and computational process modeling.
Thesis Research at BIA Lab: Molecular dynamics of complex fluids, membrane separation biophysics, solvation phenomena, and computational catalyst design.
Official DEQ Degree Page
Mestrado em Engenharia Biotecnológica
Offered by DEQ / FCTUC, this program bridges molecular biotechnology, cellular bioprocesses, biocatalysis, and protein engineering with industrial relevance.
Thesis Research at BIA Lab: Computational enzyme redesign, QM/MM biocatalytic reaction mechanisms, protein-ligand interactions, and synthetic biology modeling.
Official DEQ Degree Page
Programa Doutoral em Engenharia Química
Prestigious 3–4 year doctoral program hosted at DEQ / FCTUC and affiliated with the CERES research center. Develop cutting-edge computational methodologies and high-performance simulation workflows.
Doctoral Dissertation at BIA Lab: Multi-scale QM/MM calculations, atomistic simulations, high-throughput virtual screening, and AI-augmented biomolecular engineering.
Official DEQ Doctoral Page
Interdisciplinary Pathways · FCTUC
Associated Master’s & Doctoral Programs in Other FCTUC Departments
In addition to DEQ, BIA Lab actively collaborates and co-supervises Master's dissertations and PhD theses with students enrolled in other science and engineering departments across the Faculty of Sciences and Technology:
Dept. of Chemistry (DQ)
Chemistry & Medicinal Chemistry
- Mestrado em Química Medicinal
- Mestrado em Química
- Programa Doutoral em Química
Focus at BIA: Hit-to-lead molecular docking, structure-activity relationships (SAR) & rational ligand design.
Dept. of Life Sciences (DCV)
Biochemistry & Biosciences
- Mestrado em Bioquímica
- Mestrado em Biologia Celular e Molecular
- Programa Doutoral em Biociências
Focus at BIA: Structural biology, protein folding, allosteric pathways & biomolecular dynamics.
Dept. of Informatics (DEI)
AI, Data Science & Informatics
- Mestrado em Inteligência Artificial e Ciência de Dados
- Mestrado em Engenharia Informática
- Programa Doutoral em CTI
Focus at BIA: Geometric deep learning, molecular graph neural networks & HPC pipeline automation.
Dept. of Physics (DF)
Biomedical Engineering & Physics
- Mestrado em Engenharia Biomédica
- Programa Doutoral em Física
Focus at BIA: Biophysical modeling, multiscale physiological dynamics & biomolecular kinetics.
National & European Fellowships
Doctoral Fellowships in Portugal (FCT & Beyond)
Portugal offers dedicated, highly competitive multi-year doctoral grants through the Fundação para a Ciência e a Tecnologia (FCT). These fellowships provide comprehensive financial support for international PhD candidates:
100%
Full university tuition covered directly to University of Coimbra
~€1,250+ / mo
Monthly tax-free living allowance + social security + travel support
48 Months
Up to 4 full years of dedicated doctoral research funding
Global Eligibility
Open to all international candidates regardless of nationality
* Candidate Support: BIA Lab actively supports outstanding prospective PhD candidates in co-authoring winning FCT research work plans and securing institutional hosting letters.
Interested in a PhD?
Submit your CV, academic transcripts, and a brief statement of research interests. We evaluate alignment with upcoming FCT fellowship calls and European grant openings.
Discuss PhD Candidacy With Us →
Verified Pathways & Deadlines
Planning Your Mobility to Coimbra
Official deadlines, institutional application links, and transparent procedures to organize your stay at the Faculty of Sciences and Technology (FCTUC).
Portal Focus: Hands-On Research, Laboratory Projects & Theses
The emphasis of this mobility portal is specifically to attract and recruit students who want to conduct active scientific research, laboratory projects, master’s theses, or doctoral stays at BIA Lab under the guidance of Prof. Sérgio F. Sousa. Students do not need to come exclusively for a formal degree thesis — practical traineeships (e.g. Erasmus+ Traineeship / Staj) and computational research stays of all stages are warmly welcomed.
Looking Only to Attend Lecture Courses? Exchange students coming to the University of Coimbra solely to take traditional classroom curricular units / exams ("fazer cadeiras") should apply via the standard institutional channels at UC International Relations (DRI) ↗, as general course enrollment is coordinated through central university services independently of BIA Lab.
1
Pre-Approval & Scope with BIA Lab
Contact the laboratory with your academic CV, current transcript, and research interests to confirm supervisor availability and define a computational research topic.
2
Learning Agreement for Traineeship
Draft your Learning Agreement for Traineeship via your home institution's Erasmus+ coordinator, specifying DEQ / FCTUC at Universidade de Coimbra as your host institution.
3
Online Application on Nonio Portal
Complete your registration and document upload at the official UC Mobility Applications system.
4
Acceptance Letter & Welcome Session
Download your official Acceptance Letter from InforEstudante for visa procedures (if non-EU citizen) and book your arrival confirmation at the UC Student Hub.
1
Home University Nomination via EWP
Verify that your home university has an inter-institutional agreement with the University of Coimbra (DEQ / FCTUC). Your home Erasmus office nominates you for mobility.
2
Enrol in Master Dissertation / Research Project (30 ECTS)
For Master's thesis students, you enrol in the official Master Dissertation / Research Project unit (30 ECTS per semester) at DEQ / FCTUC, conducting your scientific investigation directly within BIA Lab under Prof. Sérgio F. Sousa.
3
Application & Timeline
Follow deadlines established by your home university and mobility program. Contact BIA Lab early to coordinate project scope.
1
Eligibility Verification
Students from non-partner universities must have completed at least 3 semesters at their home institution and possess agreement from their university.
2
Application on InforEstudante
Apply online directly as a Free Mover. Study plans must be validated by the FCTUC mobility coordinator.
1
Direct Collaborative Proposal
Doctoral candidates and visiting academics contact Prof. Sérgio F. Sousa directly with a targeted research proposal and CV.
2
Formal Host Invitation & DEQ Hosting
Once agreed, BIA Lab issues an official Letter of Invitation / Hosting Agreement to support scholarship applications, sabbatical leaves, or home university travel grants.
Interactive Tool
Find Your Tailored Mobility Path
Answer 4 brief questions to discover the ideal mobility framework, relevant deadlines, and direct application steps for your stay at BIA Lab.
1
2
3
4
1. What is your current academic stage?
Recommendation
Your Recommended Path
Description will appear here.
Official Application Window:
-
Required Portal / Route:
-
International Mobility & Practical Information
Portugal: Safe, Sunlit & Welcoming
Portugal is among the safest nations on Earth, offering exceptional quality of life, an Atlantic climate, and tailored visa and healthcare protocols for global scholars.
#7
Safest Country Worldwide
Global Peace Index · Peaceful, calm society
#8
English Proficiency Global
EF EPI Index · Very high international fluency
300+
Days of Sunshine
Temperate Mediterranean & Atlantic climate
20k+
International Community
Students & scholars from over 100 countries
Regional Administrative Frameworks
Visa & Healthcare Guidelines by Region
European Union & EEA
🇪🇺
European Union & Switzerland
EU/EEA and Swiss citizens enjoy unrestricted freedom of movement. No study or research visa is required to enter or live in Portugal.
- No Visa: Travel with valid National Identity Card or Passport.
- Healthcare: European Health Insurance Card (EHIC) provides full reciprocal SNS coverage.
- Registration: Stays over 90 days register easily at City Hall (CRUE certificate, ~€15).
- Funding: Direct eligibility for Erasmus+ SMS/SMP grants from home university.
Brazil · CPLP Accord
🇧🇷
Brazil
Brazilian students benefit from shared language, deep cultural affinity, and privileged bilateral treaties between Portugal and Brazil.
- CDAM (PB4): Bilateral healthcare accord granting free access to Portugal’s NHS (SNS) without private insurance.
- CPLP Mobility: Fast-track residence permits under the CPLP Mobility Agreement.
- Research Fellowships: Compatible with CAPES / CNPq Doutorado Sanduíche (PDSE) and FAPESP grants.
- Study Visa (D4): Submitted via VFS Global in Brazil with official UC Acceptance Letter.
PALOP · CPLP
🇦🇴
PALOP Countries (CPLP)
Candidates from Angola, Cape Verde, Guinea-Bissau, Mozambique, and São Tomé and Príncipe have access to dedicated cooperation agreements.
- CPLP Mobility Protocol: Simplified visa procedures and expedited consular evaluation.
- Fellowships: Calouste Gulbenkian Foundation, Camões I.P., and national grants (e.g. INAGBE).
- Institutional Support: Dedicated integration desks at the UC International Relations Unit (IRU).
- Academic Quotas: Preferential conditions for degree and exchange admissions.
Morocco & North Africa
🇲🇦
Morocco & North Africa
Direct geographic proximity, active Mediterranean bilateral protocols, and Erasmus+ International Credit Mobility (ICM) partnerships.
- Erasmus+ ICM (KA171): Mobility scholarships under bilateral inter-institutional agreements between UC and North African partner universities.
- Bilateral S&T Cooperation: Synergies under FCT (Portugal) and CNRST (Morocco) scientific cooperation frameworks.
- Study Visa (D4): Consular processing via the Portuguese Embassy in Rabat and VFS Global centers (Casablanca, Rabat).
- Academic Integration: 100% English working language in the lab with extensive campus support for international Maghreb scholars.
Turkey · Erasmus+ Member
🇹🇷
Turkey (Erasmus+ & TÜBİTAK)
Turkey is a full Erasmus+ Programme Country. Turkish students and researchers enjoy complete grant eligibility for research stays in Portugal.
- Erasmus+ Traineeship (Staj): Turkish BSc, MSc, and PhD students receive monthly allowances (~€600–€750/mo from home university's Ulusal Ajans grant) for 2 to 12 months at BIA Lab.
- TÜBİTAK Fellowships: Full support under 2214-A / 2219 International Doctoral & Postdoc Research Fellowships.
- Visa D4: Straightforward visa application via VFS Global (Ankara, Istanbul, Izmir) with official UC Acceptance Letter.
- Top Universities: Established ties with METU, ITU, Boğaziçi, Bilkent, Hacettepe, Koç, Sabancı, and Istanbul University.
Global · Non-EU International
🌎
Worldwide (North America, China, Latin America & Beyond)
Students and scholars from third countries (USA, Canada, China, India, Latin America) apply for the standard National Study / Research Visa (D4) with full institutional support:
1. Key Funding Schemes
Fulbright (USA), Mitacs Globalink (Canada), and China Scholarship Council (CSC) support.
2. Formal Acceptance Letter
Generated promptly via InforEstudante for visa submission at VFS Global / Consulates.
3. On-Arrival Support
Orientation at UC Student Hub, registration certificate, and AIMA / CMC assistance.
Living in Coimbra
An Inspiring Academic Heritage
Known throughout history as "A Cidade dos Estudantes", Coimbra combines seven centuries of university tradition with a vibrant, welcoming, and affordable European lifestyle.
UNESCO World Heritage · Rio Mondego
Where Tradition Fuels Cutting-Edge Science
The University of Coimbra was founded in 1290, making it one of the oldest operating universities in the world. As a visiting researcher at BIA Lab, your computational work takes place at the modern Pólo II (Campus 2) within the Department of Chemical Engineering (DEQ), surrounded by green spaces and state-of-the-art engineering laboratories, while the historic Alta and lively downtown are only a short bus or bike ride away.
Student-Centric City
Over 20,000 university students give Coimbra its unique rhythm, famous academic traditions, and welcoming international community.
High Safety & Walkability
Consistently ranked among the safest cities in Southern Europe, with pedestrian-friendly cobblestone avenues and river parks along the Mondego.
Strategic Central Location
Positioned on Portugal’s main rail artery: 1 hour from Porto, 1h30 from Lisbon, and 40 minutes from the Atlantic beaches of Figueira da Foz.
Pólo II Engineering Hub
Direct bus connections (SMTUC lines 34, 38) connecting DEQ with central Coimbra, student residences, and sports facilities.
Living Costs & Student Support
Affordable European Living
Compared to major European capitals, Coimbra offers exceptional value for students on Erasmus+ and research mobility grants. Quality housing, subsidised university canteens (SASUC), and affordable public transport make focused research stress-free.
| Item | Average Monthly Estimate |
|---|---|
| Private room in student apartment | €250 – €400 |
| Food & Groceries (canteen meals €2.75–€4.50) | €180 – €250 |
| City Transit (SMTUC Monthly Student Pass) | €15 – €20 |
| Leisure, culture & mobile connectivity | €80 – €120 |
| Estimated Total Monthly Budget | €525 – €790 / month |
Student Life · Historic Alta de Coimbra
Start the Conversation
Explore Your Stay with BIA Lab
Submit a qualified inquiry to discuss research alignment, hosting capacity, and guidance for your official University of Coimbra mobility application.
BIA Lab Host Laboratory
Laboratório de Bioengenharia, Inteligência Artificial e Simulação Molecular
Led by Prof. Sérgio F. Sousa
Location
Department of Chemical Engineering (DEQ), Pólo II da Universidade de Coimbra, Rua Sílvio Lima, 3030-790 Coimbra, Portugal
Official Lab Portal
Affiliated Research Unit
CERES - Research Centre for Chemical Process Engineering
Direct Inquiries
sergiofsousa@eq.uc.pt
Research Stay Inquiry
Please provide complete academic details so we can evaluate project alignment.