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Tomás Fernandes da Silva. Concluiu o(a) Doutoramento em Bioquímica em 2023/01/10 pelo(a) Universidade de Lisboa Faculdade de Ciências, Mestrado em Bioquímica em 2017 pelo(a) Universidade de Lisboa Faculdade de Ciências e Licenciatura em Bioquímica em 2015 pelo(a) Universidade de Lisboa Faculdade de Ciências. É Pós-doutorado no(a) Scuola Internazionale Superiore di Studi Avanzati. Publicou 9 artigos em revistas especializadas. Possui 1 capítulo(s) de livros. Organizou 5 evento(s). Participou em 1 evento(s). Recebeu 1 prémio(s) e/ou homenagens. Participa e/ou participou como Bolseiro de Doutoramento em 1 projeto(s), Bolseiro de Mestrado em 1 projeto(s) e Bolseiro de Pós-Doutoramento em 1 projeto(s). Atua na(s) área(s) de Ciências Naturais com ênfase em Ciências Biológicas com ênfase em Biofísica e Ciências Naturais com ênfase em Ciências Biológicas com ênfase em Biofísica. No seu currículo Ciência Vitae os termos mais frequentes na contextualização da produção científica, tecnológica e artístico-cultural são: dinâmica-molecular; pH-replica-exchange; perfis-pKa; acidez-tumoral; mecânica-molecular; vesículas; Lípidos; Electrostática; Péptidos; Proteínas; pHLIP; fármacos; pH-gradient; Ácidos nucleicos; CpHMD; enhanced sampling techniques; tumor acidity; pH gradient; peptide-membrane models; tumoral acidity; Lewis Base drugs; pHRE; Nucleic Acids; Metadynamics; RNA; Biomolecules (q-bio; BM); Biological Physics (physics; bio-ph); Chemical Physics (physics; chem-ph); FOS: Biological sciences; FOS: Physical sciences; .
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Identification

Personal identification

Full name
Tomás Fernandes da Silva

Citation names

  • Silva, Tomás F.D.

Author identifiers

Ciência ID
A31B-EA41-A32E
ORCID iD
0000-0003-4608-2673

Email addresses

  • tfernand@sissa.it (Professional)
  • tfs94@protonmail.com (Personal)

Addresses

  • BioISI | Instituto de Biossistemas e Ciências Integrativas. Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Edifício C8 (sala 8.5.53), 1749-016, Lisboa, Lisboa, Portugal (Professional)
  • Scuola Internazionale Superiore di Studi Avanzati - via Bonomea, 265 room 331, 34136 , Trieste, Friuli-Venezia Giulia , Italy (Professional)

Knowledge fields

  • Natural sciences - Biological Sciences - Biophysics
  • Natural sciences - Biological Sciences - Biophysics

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Italian Intermediate (B1) Upper intermediate (B2) Intermediate (B1) Upper intermediate (B2) Beginner (A1)
Education
Degree Classification
2023/01/10
Concluded
 Bioquímica (Doutoramento)
Major in Bioquímica Teórica
Universidade de Lisboa Faculdade de Ciências, Portugal
"In silico tumor-targeting technologies for the evasion of acidity-induced multidrug resistance" (THESIS/DISSERTATION)
 Aprovado com Distinção e Louvor
2017
Concluded
 Bioquímica (Mestrado)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Computational study of pH-dependent membrane insertion mechanism of pHLIP peptides" (THESIS/DISSERTATION)
 18
2015
Concluded
 Bioquímica (Licenciatura)
Universidade de Lisboa Faculdade de Ciências, Portugal
"n/a" (THESIS/DISSERTATION)
 15
Affiliation

Science

Category
Host institution 		Employer
2023/01/15 - Current Postdoc (Research) Scuola Internazionale Superiore di Studi Avanzati, Italy
2018/03/01 - 2018/08/31 Researcher (Research) FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal
Projects

Grant

Designation Funders
2023/01 - 2025/01 Coupling CpHMD with metadynamics to study pH-dependent effects in nucleic acids
ALTF 399-2022
Post-doc Fellow
Gesellschaft zur Förderung der Lebenswissenschaften Heidelberg GmbH
2018/09/01 - 2022/11/01 Desenvolvimento e aplicação de técnicas de amostragem aumentada dependente do pH na optimização da tecnologia pHLIP como marcador tumoral
SFRH/BD/140886/2018
PhD Student Fellow
Universidade de Lisboa Faculdade de Ciências, Portugal

Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
Associação para a Inovação e Desenvolvimento da FCT
Concluded

Contract

Designation Funders
2018/10/01 - 2022/09/30 Deal with PAINS: strategies to spot membrane modulators
PTDC/BIA-BFS/28419/2017
Researcher
FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2019/01/01 - 2019/12/31 Instituto de Biosistemas & Ciências Integrativas
UID/Multi/04046/2019
154697UID
PhD Student Fellow
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal

Universidade do Minho, Portugal

Universidade do Porto Faculdade de Ciências, Portugal

Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal

FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal

Universidade de Lisboa Faculdade de Ciências, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2018/03/01 - 2018/09/01 CpHMD-L simulations of pHLIP peptides: design of new tumor-targeted drug delivery systems
PTDC/QEQ-COM/5904/2014
Master Student Fellow
FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências
Concluded
Outputs

Publications

Book chapter
  1. Oliveira, Nuno F. B.; Silva, Tomás F. D.; Reis, Pedro B. P. S.; Machuqueiro, Miguel. "pK a Calculations in Membrane Proteins from Molecular Dynamics Simulations". In Computational Design of Membrane Proteins, 185-195. Springer US, 2021.
    Published • 10.1007/978-1-0716-1468-6_11
Conference abstract
  1. Silva, Tomás F.D.; Bussi, Giovanni. "CpH-MetaD: coupling wt-metadynamics and CpHMD in the study of RNA oligomers". Paper presented in 2023 3D-BioInfo-PT Meeting, Coimbra, 2023.
  2. Silva, Tomás F.D.; Vila-Viçosa, Diogo; Machuqueiro, Miguel. "Tackling the realism: A pH gradient approach to transmembrane peptides’ simulations". Paper presented in 2022 3D-BioInfo-PT Meeting, Oeiras, 2022.
  3. Silva, Tomás; Vila-Viçosa, Diogo; Reis, Pedro; Victor, Bruno; Diem, Matthias; Oostenbrink, Chris; Machuqueiro, Miguel. "The impact of using single atomistic long range cutoff schemes with the GROMOS 54A7 force field". Paper presented in EJIBCE 2018, Porto, 2019.
    Published • 10.3390/mol2net-04-06146
  4. Silva, Tomás; Vila-Viçosa, Diogo; Reshetnyak, Yana; Andreev, Oleg; Machuqueiro, Miguel. "In silico studies on the pH induced membrane insertion of pHLIP peptides". Paper presented in EJIBCE 2017, Coimbra, 2017.
    10.3390/mol2net-03-05079
Conference poster
  1. Silva, Tomás F.D.; Bussi, Giovanni. Corresponding author: Silva, Tomás F.D.. "Coupling constant-pH MD simulations and metadynamics to study RNA oligomers". Paper presented in 3rd MOSBRI conference (Molecular-scale Biophysics Research Infrastructure), 2024.
  2. Silva, Tomás F.D.; Bussi, Giovanni. Corresponding author: Silva, Tomás F.D.. "Constant pH metadynamics simulations in the study of RNA oligomers". Paper presented in Emerging Theoretical Approaches to Compliment Single-Particle Cryo-Electron Microscopy BPS Thematic Meeting, 2024.
  3. Silva, Tomás F.D.; Suzano, Pedro; Pires, I.D.S.; Oliveira, Nuno F. B.; Reis, Pedro B P S; Machuqueiro, Miguel. Corresponding author: Suzano, Pedro. "MembIT - a tool to calculate membrane-insertion properties of solutes". Paper presented in 3D-BIOINFO-PT Annual Meeting, 2022.
  4. Suzano, Pedro; Silva, Tomás F.D.; Machuqueiro, Miguel. Corresponding author: Suzano, Pedro. "A Computational Method to Estimate pH Effects in Antitumor Drug Resistance". Paper presented in 2nd Chem & Biochem Students Meeting, 2022.
  5. Silva, Tomás F.D.; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "Improved realism of peptide-membrane simulations using a pH-Gradient/CpHMD protocol". Paper presented in 8º Encontro Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE2021), 2021.
  6. Silva, Tomás F.D.; Vila-Viçosa, Diogo; Machuqueiro, Miguel. "Computational Methods to Tackle the pH Effects on Membrane-Inserting Peptides". Paper presented in Computer Simulation and Theory of Macromolecules 2021, Online Workshop, 2021.
  7. Suzano, Pedro; Silva, Tomás F.D.; Machuqueiro, Miguel. Corresponding author: Suzano, Pedro. "In silico Study of Acid-Induced Anti-Tumor Drug Resistance". Paper presented in Computer Simulation and Theory of Macromolecules 2021, Online Workshop, 2021.
  8. Silva, Tomás F.D.; Machuqueiro, Miguel. "pH-dependent membrane crossing mechanism of lipophilic antitumoral drugs". Paper presented in EJIBCE 2019, 2019.
  9. Silva, Tomás F.D.; Vila-Viçosa, Diogo; Machuqueiro, Miguel. "Improving in silico membrane pKa calculations of pHLIP peptides,". Paper presented in EUROPIN Summer School on Drug Design, 2019.
  10. Silva, Tomás F.D.; Vila-Viçosa, Diogo; Machuqueiro, Miguel. "pH Replica Exchange simulations of pHLIP peptides". Paper presented in 12th EBSA - IUPAP Biophysics Congress, 2019.
  11. Silva, Tomás F.D.; Vila-Viçosa, Diogo; Machuqueiro, Miguel. "Applying a pHRE method to pHLIP Peptides". Paper presented in BioISI PhD Symposium, 2019.
  12. Silva, Tomás F.D.; Vila-Viçosa, Diogo; Machuqueiro, Miguel. "A pH Replica Exchange approach to pHLIP peptides". Paper presented in Integrative Approaches to Protein Folding & Aggregation, 2019.
  13. Silva, Tomás F.D.; Vila-Viçosa, Diogo; Slaybaugh, Gregory; Reshetnyak, Yana K.; Andreev, Oleg A.; Machuqueiro, Miguel. "Replica Exchange CpHMD simulations of pHLIP peptides". Paper presented in Protein Electrostatics, 2018.
  14. Vila-Viçosa, Diogo; Reis, Pedro B P S; Silva, Tomás F.D.; Machuqueiro, Miguel. "Coupling enhanced sampling and biased MD simulations with CpHMD". Paper presented in Protein Electrostatics, 2018.
  15. Magalhães, Pedro Rafael; Vila-Viçosa, Diogo; Silva, Tomás; Machuqueiro, Miguel. "pH effects on PG/PC and PS/PC lipid binary mixtures". Paper presented in Protein Electrostatics, 2018.
    10.3390/mol2net-04-05922
  16. Silva, Tomás F.D.; Reis, Pedro B P S; Victor, Bruno; Vila-Viçosa, Diogo; Machuqueiro, Miguel. "Evaluating GROMOS force fields without the twin-range cutoff scheme". Paper presented in Free Energy Calculations from Molecular Simulation: Aplications in Life and Medical Sciences, 2017.
Journal article
  1. Tomás F. D. Silva; Hannah Visca; Craig Klumpp; Oleg A. Andreev; Yana K. Reshetnyak; Miguel Machuqueiro. "Arginine Residues Modulate the Membrane Interactions of pHLIP Peptides". Journal of Chemical Information and Modeling (2023): https://doi.org/10.1021/acs.jcim.3c00360.
    10.1021/acs.jcim.3c00360
  2. Suzano, Pedro M. S.; Pires, Inês D. S.; Silva, Tomás F.D.; Oliveira, Nuno F. B.; Reis, Pedro B. P. S.; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "MembIT – A Tool to Calculate Solute Membrane Insertions and Deformations in Molecular Dynamics Simulations". Journal of Computational Biophysics and Chemistry (2023): 1-9. http://dx.doi.org/10.1142/s2737416523500254.
    Published • 10.1142/s2737416523500254
  3. Silva, Tomás F.D.; Diogo Vila-Viçosa; Miguel Machuqueiro. "Increasing the Realism of in Silico pHLIP Peptide Models with a Novel pH Gradient CpHMD Method". Journal of Chemical Theory and Computation (2022): https://doi.org/10.1021/acs.jctc.2c00880.
    Published • 10.1021/acs.jctc.2c00880
  4. Borges, Patrícia T.; Silva, Diogo; Silva, Tomás F.D.; Brissos, Vânia; Cañellas, Marina; Lucas, Maria Fátima; Masgrau, Laura; et al. Corresponding author: Martins, Lígia O.. "Unveiling molecular details behind improved activity at neutral to alkaline pH of an engineered DyP-type peroxidase". Computational and Structural Biotechnology Journal 20 (2022): 3899-3910. http://dx.doi.org/10.1016/j.csbj.2022.07.032.
    Open access • Published • 10.1016/j.csbj.2022.07.032
  5. Nícia Rosário-Ferreira; Salete J. Baptista; Carlos A. V. Barreto; Filipe E. P. Rodrigues; Tomás F. D. Silva; Sara G. F. Ferreira; João N. M. Vitorino; et al. "In Silico End-to-End Protein–Ligand Interaction Characterization Pipeline: The Case of SARS-CoV-2". ACS Synthetic Biology (2021): https://doi.org/10.1021/acssynbio.1c00368.
    10.1021/acssynbio.1c00368
  6. Tomás F. D. Silva; Diogo Vila-Viçosa; Miguel Machuqueiro. "Improved Protocol to Tackle the pH Effects on Membrane-Inserting Peptides". Journal of Chemical Theory and Computation 17 7 (2021): 3830-3840. https://doi.org/10.1021/acs.jctc.1c00020.
    10.1021/acs.jctc.1c00020
  7. Stark, Michal; Silva, Tomás F. D.; Levin, Guy; Machuqueiro, Miguel; Assaraf, Yehuda G.. "The Lysosomotropic Activity of Hydrophobic Weak Base Drugs is Mediated via Their Intercalation into the Lysosomal Membrane". Cells 9 5 (2020): 1082. http://dx.doi.org/10.3390/cells9051082.
    Open access • Published • 10.3390/cells9051082
  8. Silva, Tomás F. D.; Vila-Viçosa, Diogo; Reis, Pedro B. P. S.; Victor, Bruno L.; Diem, Matthias; Oostenbrink, Chris; Machuqueiro, Miguel. "The Impact of Using Single Atomistic Long-Range Cutoff Schemes with the GROMOS 54A7 Force Field". Journal of Chemical Theory and Computation 14 11 (2018): 5823-5833. http://dx.doi.org/10.1021/acs.jctc.8b00758.
    10.1021/acs.jctc.8b00758
  9. Vila-Viçosa, Diogo; Silva, Tomás F. D.; Slaybaugh, Gregory; Reshetnyak, Yana K.; Andreev, Oleg A.; Machuqueiro, Miguel. "Membrane-Induced pKa Shifts in wt-pHLIP and Its L16H Variant". Journal of Chemical Theory and Computation 14 6 (2018): 3289-3297. http://dx.doi.org/10.1021/acs.jctc.8b00102.
    Published • 10.1021/acs.jctc.8b00102
Preprint
  1. Tomas F. D. Silva; Giovanni Bussi. "Characterizing RNA oligomers using Stochastic Titration Constant-pH Metadynamics simulations". 2024. https://arxiv.org/abs/2410.16064.
    10.48550/ARXIV.2410.16064
Thesis / Dissertation
  1. "In silico tumor-targeting technologies for the evasion of acidity-induced multidrug resistance". PhD, 2023.
  2. Silva, Tomás F.D.. "Computational study of pH-dependent membrane insertion mechanism of pHLIP peptides". Master, 2017.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2024/12 Characterizing RNA oligomers using Stochastic Titration Constant-pH Metadynamics simulations 2024 3D-BioInfo-PT Meeting
(Lisboa, Portugal)
2023/12 CpH-MetaD: coupling wt-metadynamics and CpHMD in the study of RNA oligomers 2023 3D-BioInfo-PT Meeting
(Coimbra, Portugal)
2022/12 Tackling the realism: a pH-Gradient/CpHMD approach to transmembrane peptides’ simulations 2022 3D-BioInfo-PT Meeting
(Oeiras, Portugal)
2018/12 The impact of using single atomistic long range cutoff schemes with the GROMOS 54A7 EJIBCE 2018
2017/12 In silico studies on the pH induced membrane insertion of pHLIP peptides EJIBCE 2017
(Coimbra, Portugal)

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2024/07/12 - 2024/07/16 CECAM School 2024 Assistant lecturer on: - Calculations on small molecules: water and Zundel ion - Effect of solvation on small organic molecules - Normal modes and molecular properties (2024/07/08 - 2024/07/19)
Workshop (Other)
 Scuola Internazionale Superiore di Studi Avanzati, Italy
2024/07/09 - 2024/07/09 CECAM School 2024 - Lecturer on “Introduction to Force Fields” (2024/07/08 - 2024/07/19)
Workshop (Other)
 Scuola Internazionale Superiore di Studi Avanzati, Italy
2022/01/01 - 2022/07/20 2nd Chem & Biochem Students Meeting (2022/07/15 - 2022/07/15)
Conference (Co-organisor)
 Universidade de Lisboa Faculdade de Ciências, Portugal
2021/12 - 2021/12 3d-BioInfo-PT Intermediate Workshop "Computational Structural Biology Tools” - Molecular Dynamics Module (2021/12 - 2021/12)
Workshop (Other)
 Universidade de Coimbra, Portugal
2019/12/20 - 2019/12/20 EJIBCE 2019 (2019/12/20 - 2019/12/20)
Meeting (Member of the Organising Committee)
 Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2024/12/19 - 2024/12/20 Introduction to enhanced sampling: Meta-Dynamics
Workshop
 Intermediate Workshop 3D-BioInfo-Meeting
Universidade de Lisboa Faculdade de Ciências, Portugal
Distinctions

Award

2018 Best Scientific Poster Communication @ Protein Electrostatics 2018, Belgrade