About
My independent research focuses on the biophysics of large biological molecules involved in processes related to life sciences: heme proteins, Photosystem II light-harvesting complexes, SARS-CoV-2 proteins, intrinsically disordered proteins and condensates, protein thermostability, and the CRISPR-Cas and Fanzor systems.
In the lab we employ elaborate computational techniques based on the Molecular Dynamics (MD) method (accelerated MD, metadynamics in the multiwalkers variant, or parallel tempering metadynamics at the well-tempered ensemble variant), in combination with ab-initio Density Functional Theory (DFT) methods. Model setup and analysis draw on bioinformatics tools — protein-protein docking algorithms, sequence and structural alignments, and Markov State Modeling. The lab has benefited from High Performance Computing (HPC) allocations awarded within the EuroHPC JU and PRACE/DECI schemes (Joliot Curie-Irene ROME TGCC, Salomon iT4i, SuperMUC-NG LRZ Munich, HLRS Stuttgart, MareNostrum Barcelona Supercomputing Center). Combining computational and experimental biochemistry, biophysics, and biological chemistry underpins the lab's approach.
Position
September 2023 – Present
Assistant Professor, Biomolecular Engineering
Department of Chemical Engineering, University of Patras
March 2025 – Present
Visiting Faculty Member
Foundation for Research and Technology Hellas / Institute of Chemical Engineering Sciences (FORTH/ICE-HT)
Education
2000 – 2006
MSc & PhD, Computational Biophysical Chemistry
Department of Chemistry, University of Crete — Final grade: 9.75/10
PhD Thesis: "Bioenergetic Mechanisms of O2 and NO by Density Functional Theory." MSc Thesis: "The mechanism of O-O cleavage in Cytochrome c Oxidase as revealed by Density Functional Theory and resonance Raman."
1996 – 2000
Bachelor's Degree in Chemistry
Department of Chemistry, University of Crete — Final grade: 8.87/10
Academic Career
May 2022 – August 2023
Associate Professor, Department of Chemical Engineering
Cyprus University of Technology, Limassol, Cyprus
December 2014 – April 2022
Assistant Professor, Department of Chemical Engineering
Cyprus University of Technology, Limassol, Cyprus
November 2010 – December 2014
Lecturer, Department of Chemical Engineering
Cyprus University of Technology, Limassol, Cyprus
2006 – 2010
Research Collaborator
Institute of Electronic Structure and Laser, Foundation for Research and Technology Hellas — Heraklion, Greece
Grid Computational Chemistry (GRID-COMPCHEM) — Marie-Curie Host Fellowship for the Transfer of Knowledge, EU ToK grant No. MTKD-CT-2005-029583; HPC-Europa2 Scholarship.
2000 – 2006
Visiting Postdoc
Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
Current Research Grants
- SPROUT (2027–2031) — Horizon Europe MSCA Doctoral Networks. "Stress and Photosynthesis: Research to Optimize Understanding, Training and Applications." Total budget €4,269,525.4 (UPAT €269,484.48); PI: Vangelis Daskalakis.
- DALiA (2025–2026) — EuroHPC Extreme Scale Access. "Digital zoom into the All-atom dynamics of Light-harvesting complexes." 255,160 node hours, MareNostrum5 ACC; PI: Vangelis Daskalakis.
- SECure (2025–2026) — EuroHPC Regular Access. "Decoding the Disorder and Promiscuity of Sec14-like SFH Proteins Through Molecular Dynamics." 230,000 node hours, MareNostrum5 GPP; PI: Vangelis Daskalakis.
- PhotoCaM (2024–2028) — Horizon Europe MSCA Doctoral Networks. "Photosynthetic Antennas in a Computational Microscope: Training a new generation of computational scientists." Total budget €2,589,847.19 (vice-Coordinator UPAT €240,098.39); PI: Vangelis Daskalakis.
- SUNDIAL (2024–2025) — Hellenic Foundation for Research and Innovation (H.F.R.I.). "Seeing Diatoms under a Computational Sunlight." Coordinator UPAT €207,000; PI: Vangelis Daskalakis.
- Peptaibols: How to kill a bacterium (2023–2024) — EuroHPC Regular Access. 6,400,000 CPU-core hrs on MeluXina; PI: Vangelis Daskalakis.
- Five further Production Project awards on the Greek ARIS HPC infrastructure (2024–2026) as PI or collaborator, spanning light-harvesting complex dynamics, bacterial transporters, biocatalyst engineering, and RNA-guided nuclease dynamics.
Research Output & Recognition
57 publications: 49 peer-reviewed journal articles, 7 book chapters/reviews, and 1 conference proceeding — first author on 22 and corresponding author on 27, with an h-index of 19 (Scopus) / 24 (Google Scholar) and an i10-index of 32. Work published in J. Am. Chem. Soc., Proc. Natl. Acad. Sci. USA, Biochim. Biophys. Acta, Nature Communications Chemistry, Scientific Reports, J. Phys. Chem. B/C, Phys. Chem. Chem. Phys., Chem. Commun., and J. Biomolecular Struct. and Dynamics, among others.
Reviewer for Nature journals, ACS Physical Chemistry journals, RSC Phys. Chem. Chem. Phys., RSC Advances, and Springer J. Molecular Modeling (290+ reviews recorded on Web of Science / Publons; Outstanding Reviewer, Phys. Chem. Chem. Phys. 2024 and 2025). Reviewer for HPC proposals to Cyclone/CyTera (Cyprus Institute), GRNET ARIS, CSCS, JSC, GCS, and NIC, and evaluator for BBSRC and the Czech Science Foundation. 46 conference/seminar participations including 15+ invited lectures; research featured in the PRACE DIGEST 2017 and 2020.
Publications — Journal Articles
01
A dual gating mechanism controls target-strand cleavage in Cas12j: implications for engineering efficient nickases
Karvounis IG, Daskalakis V (2026) Protein Science 35(10): e70792. doi.org/10.1002/pro.70792
02
Role of Small Membrane Proteins in the Green Sulfur Bacterial Reaction Center
Lyratzakis A, Konstantopoulou A, Fragkaki EV, Sousani TI, Karvounis IG, Tsiotis G, Daskalakis V (2026) J. Phys. Chem. Au. doi.org/10.1021/acsphyschemau.5c00142 — selected for the ACS 150th-anniversary journal cover.
03
Structural insights into an engineered feruloyl esterase with improved MHET degrading properties
Karampa P, Makryniotis K, Sousani TI, Topakas E, Daskalakis V, Dimarogona M (2026) FEBS Letters. doi.org/10.1002/1873-3468.70322
04
Conformational plasticity enables functional switching in diatom light-harvesting complexes
Sousani TI, Zender B, Maity S, Kleinekathöfer U, Daskalakis V (2025) Commun Chem 8, 392. doi.org/10.1038/s42004-025-01774-x
05
An Unexpected Water Channel in the Light-Harvesting Complex of a Diatom: Implications for the Switch between Light Harvesting and Photoprotection
Daskalakis V, Maity S, Kleinekathöfer U (2025) ACS Phys. Chem. Au 5(1), 47–61. doi.org/10.1021/acsphyschemau.4c00069 — January 2025 journal cover.
06
Hydrophobic mismatch in the thylakoid membrane regulates photosynthetic light harvesting
Wilson S, Clarke C, Carbajal MA, Buccafusca R, Fleck R, Daskalakis V, Ruban A (2024) J. Am. Chem. Soc. 146(21), 14905–14914. doi.org/10.1021/jacs.4c05220
07
Acclimation mechanism of microalgal photosynthetic apparatus under low atmospheric pressures – New astrobiological perspectives in a Mars-like atmosphere
Gritsi CS, Sarmas E, Daskalakis V, Kotzabasis K (2024) Functional Plant Biology 51, FP24058. doi.org/10.1071/FP24058
08
Electric Field Susceptibility of Chlorophyll c Leads to Unexpected Excitation Dynamics in the Major Light-Harvesting Complex of Diatoms
Maity S, Daskalakis V, Jansen LCT, Kleinekathöfer U (2024) J. Phys. Chem. Lett. 15(9), 2499–2510.
09
The synergy between the PscC subunits for electron transfer to the P840 special pair in Chlorobaculum tepidum
Daskalakis V, Lyratzakis A, Xie H, Tsiotis G (2024) Photosynth Res 160, 87–96. doi.org/10.1007/s11120-024-01093-7
11
Recognition motifs for Importin 4 [(L)PPRS(G/P)P] and Importin 5 [KP(K/Y)LV] binding, identified by bio-informatic simulation and experimental in vitro validation
Panagiotopoulos AA, Kalyvianaki K, Tsodoulou PK, Darivianaki MN, Dellis D, Notas G, Daskalakis V, Theodoropoulos PA, Panagiotidis CA, Castanas E, Kampa M (2022) Comp. Struct. Biotechnol. J. doi.org/10.1016/j.csbj.2022.10.015
13
Trivial Excitation Energy Transfer to Carotenoids is an Unlikely Mechanism for Non-Photochemical Quenching in LHCII
Gray C, Wei T, Polívka T, Daskalakis V, Duffy CDP (2022) Front. Plant Sci. 12: 797373.
14
Natural polyphenols inhibit the dimerization of the SARS-CoV-2 main protease: the case of fortunellin and its structural analogs
Panagiotopoulos AA, Karakasiliotis I, Kotzampasi D-M, Dimitriou M, Sourvinos G, Kampa M, Pirintsos S, Castanas E, Daskalakis V (2021) Molecules (MDPI), 26, 6068.
15
Robust Strategy for Photoprotection in the Light-Harvesting Antenna of Diatoms: A Molecular Dynamics Study
Chrysafoudi A, Maity S, Kleinekathöfer U, Daskalakis V (2021) J. Phys. Chem. Lett. 12, 9626–9633.
16
Time-Dependent Atomistic Simulations of the CP29 Light-Harvesting Complex
Maity S, Sarngadharan P, Daskalakis V, Kleinekathöfer U (2021) J. Chem. Phys. 155, 055103.
17
Hydrogen gas as a central on-off functional switch of reversible metabolic arrest – New perspectives for biotechnological applications
Zerveas S, Kydonakis E, Mente M-S, Daskalakis V, Kotzabasis K (2021) J. Biotechnology 335: 9–18.
18
p-cymene impairs SARS-CoV-2 and Influenza A (H1N1) viral replication: In silico predicted interaction with SARS-CoV-2 nucleocapsid protein and H1N1 nucleoprotein
Panagiotopoulos A, Tseliou M, Karakasiliotis I, Kotzampasi D-M, Daskalakis V, Kesesidis N, Notas G, Lionis C, Kampa M, Pirintsos S, Sourvinos G, Castanas E (2021) Pharmacol Res Perspect. 9:e00798.
19
Multiscale QM/MM Molecular Dynamics Simulations of the Trimeric Major Light-Harvesting Complex II
Maity S, Daskalakis V, Elstner M, Kleinekathöfer U (2021) Phys. Chem. Chem. Phys. 23, 7407–7417.
20
The conformational phase space of the photoprotective switch in the major Light Harvesting Complex II
Daskalakis V, Papadatos S, Stergiannakos T (2020) Chem. Commun. 56, 11215–11218.
21
Structure and Dynamics of a Thermostable Alcohol Dehydrogenase from the Antarctic Psychrophile Moraxella sp. TAE123
Petratos K, Gessmann R, Daskalakis V, Papadovasilaki M, Papanikolau Y, Tsigos I, Bouriotis V (2020) ACS Omega 5(24), 14523–14534.
22
Structural Basis for Allosteric Regulation in the Major Antenna Trimer of Photosystem II
Daskalakis V, Maity S, Hart CL, Stergiannakos T, Duffy CDP, Kleinekathöfer U (2019) J. Phys. Chem. B 123(45), 9609–9615.
23
Fine tuning of the photosystem II major antenna mobility within the thylakoid membrane of higher plants
Daskalakis V, Papadatos S, Kleinekathoefer U (2019) Biochim. Biophys. Acta – Biomembranes 1861, 183059.
24
On a Chlorophyll-Carotenoid Coupling in LHCII
Maity S, Gelessus A, Daskalakis V, Kleinekathoefer U (2019) Chem. Phys. 526, 110439.
25
Protein-Protein Interactions within Photosystem II under Photoprotection: The Synergy between CP29 Minor Antenna, Subunit S (PsbS) and Zeaxanthin at all-atom resolution
Daskalakis V (2018) Phys. Chem. Chem. Phys. 20, 11843–11855.
26
The Photosystem II Subunit S under Stress
Daskalakis V, Papadatos S (2017) Biophys. J. (Cell) 113(11), 2364–2372.
27
A pathway for protective quenching in antenna proteins of Photosystem II
Papadatos S, Charalambous CA, Daskalakis V (2017) Scientific Reports (NPG) 7, 2523. doi.org/10.1038/s41598-017-02892-w
28
Detection of Maillard reaction products by a coupled HPLC-Fraction collector technique and FTIR characterization of Cu(II)-complexation with the isolated species
Ioannou A, Daskalakis V, Varotsis C (2017) J. Mol. Struct. 1141, 634–642.
29
Coupling of helix E-F motion with the O-nitrito and 2-nitrovinyl coordination in myoglobin
Ioannou A, Lambrou A, Daskalakis V, Pinakoulaki E (2017) Biophys. Chem. 221, 10–16.
30
Nitrite coordination in myoglobin
Ioannou A, Lambrou A, Daskalakis V, Pinakoulaki E (2017) J. Inorg. Biochemistry 166, 49–54.
31
Energizing the Light Harvesting Antenna: Insight from CP29
Ioannidis NE, Papadatos S, Daskalakis V (2016) BBA – Bioenergetics 1857(10), 1643–1650.
32
Correlation Between Surface Tension and the Bulk Dynamics in Salty Atmospheric Aquatic Droplets
Salameh A, Vorka F, Daskalakis V (2016) J. Phys. Chem. C 120(21), 11508–11518.
33
Structure and properties of the catalytic site of nitric oxide reductase at ambient temperature
Daskalakis V, Ohta T, Kitagawa T, Varotsis C (2015) Biochim. Biophys. Acta – Bioenergetics 1847(10), 1240–1244.
34
Surface-Active Organic Matter induces salt morphology transitions during new atmospheric particle formation and growth
Daskalakis V, Charalambous F, Demetriou DC, Georgiou AG (2015) RSC Adv. 5, 63240–63251.
35
Effects of Surface Activity on Carbon Dioxide Nucleation in Atmospheric Wet Aerosols: A Molecular Dynamics Study
Daskalakis V, Charalambous F, Panagiotou F, Nearchou I (2014) Phys. Chem. Chem. Phys. 16, 23723–23734.
36
Hexagonal Ice Stability and Growth in the presence of Glyoxal and Secondary Organic Aerosols
Daskalakis V, Hadjicharalambous M (2014) Phys. Chem. Chem. Phys. 16(33), 17799–17810.
37
The protein effect in the structure of two ferryl-oxo intermediates at the same oxidation level in the heme-copper binuclear center of cytochrome c oxidase
Pinakoulaki E, Daskalakis V, Ohta T, Richter OM, Budiman K, Kitagawa T, Ludwig B, Varotsis C (2013) J. Biol. Chem. 288(28), 20261–20266.
38
Exploring the Topography of Free Energy Surfaces and Kinetics of Cytochrome c Oxidases interacting with small ligands
Porrini M, Daskalakis V, Farantos SC (2012) RSC Adv. 2, 5828–5836.
39
Non-Linear Vibrational Modes in Biomolecules: a periodic orbits description
Kampanarakis A, Farantos SC, Daskalakis V, Varotsis C (2012) Chem. Phys. 399, 258–263.
40
The origin of the FeIV=O intermediates in cytochrome aa3 oxidase
Pinakoulaki E, Daskalakis V, Varotsis C (2012) BBA Bioenergetics 1817, 552–557.
41
Regulation of Electron and Proton Transfer by the Protein Matrix of Cytochrome c Oxidase
Daskalakis V, Farantos SC, Guallar V, Varotsis C (2011) J. Phys. Chem. B 115(13), 3648–3655.
42
Vibrational Resonances and CuB displacement controlled by proton motion in Cytochrome c Oxidase
Daskalakis V, Farantos SC, Guallar V, Varotsis C (2010) J. Phys. Chem. B 114(2), 1136–1143.
43
Binding and Docking Interactions of NO, CO and O2 in Heme Proteins as Probed by Density Functional Theory
Daskalakis V, Varotsis C (2009) Int. J. Mol. Sci. 10, 4137–4156. Review.
44
Heme Cavity Dynamics of Photodissociated CO from ba3-Cytochrome c Oxidase: The Role of Ring-D Propionate
Porrini M, Daskalakis V, Farantos SC, Varotsis C (2009) J. Phys. Chem. B 113(35), 12129–12135.
45
Assigning vibrational spectra of ferryl-oxo intermediates of cytochrome c oxidase by periodic orbits and Molecular Dynamics
Daskalakis V, Farantos SC, Varotsis C (2008) J. Am. Chem. Soc. 130(37), 12385–12393.
46
Probing the environment of CuB in heme-copper oxidases
Daskalakis V, Pinakoulaki E, Stavrakis S, Varotsis C (2007) J. Phys. Chem. B 111, 10502–10509.
47
Two ligand binding sites in the O2-sensing signal transducer HemAT: Implications for ligand recognition/discrimination and signaling
Pinakoulaki E, Yoshimura H, Daskalakis V, Yoshioka S, Aono S, Varotsis C (2006) Proc. Natl. Acad. Sci. USA 103, 14796–14801.
48
Structural dynamics of Heme-copper oxidases and Nitric oxide reductases: Time-Resolved step-scan FTIR and Time-resolved Resonance Raman studies
Pinakoulaki E, Koutsoupakis C, Stavrakis S, Marialena A, Papadopoulos G, Daskalakis V, Varotsis C (2005) J. Raman Spec. 36, 337–349.
49
Time-resolved step-scan Fourier transform infrared investigation of heme-copper oxidases: implications for O2 input and H2O/H+ output channels
Koutsoupakis C, Pinakoulaki E, Stavrakis S, Daskalakis V, Varotsis C (2004) Bioch. Biophys. Acta 1655, 347–352.
Book Chapters, Reviews & Conference Proceedings
BC
A Practical Guide to Investigating Biomolecular Condensates: A Comment from the Plant Community
Peng J, Agudo-Canalejo J, Chodasiewicz M, Van Damme D, Daskalakis V, et al. (2026) Sci China Life Sci. doi.org/10.1007/s11427-026-3459-x
BC
From Traditional Ethnopharmacology to Modern Natural Drug Discovery: A Methodology Discussion and Specific Examples
Pirintsos S, Panagiotopoulos A, Bariotakis M, Daskalakis V, Lionis C, Sourvinos G, Karakasiliotis I, Kampa M, Castanas E (2022) MDPI Molecules 27(13), 4060.
BC
A perspective on the Major Light Harvesting Complex Dynamics Under the Effect of pH, Salts and the Photoprotective PsbS Protein
Navakoudis E, Stergiannakos T, Daskalakis V (2022) Photosynthesis Research — book chapter.
BC
Atmospheric Ice Nucleation by Glassy Organic Compounds: A Review
Salameh A, Daskalakis V (2017) Chem. Comp. J 1(1), 13–23.
BC
Probing the Action of Cytochrome c Oxidase
Daskalakis V, Varotsis C (2014) Advances in Photosynthesis and Respiration 39(10). The Structural Basis of Biological Energy Generation.
BC
Tuning heme functionality: the cases of Cytochrome c Oxidase and Myoglobin Oxidation
Daskalakis V, Farantos SC, Varotsis C (2012) LNCS, Springer-Verlag Berlin Heidelberg, p. 304–315.
BC
Grid Computing Multiple Shooting Algorithms for Extended Phase Space Sampling and Long Time Propagation in Molecular Dynamics
Daskalakis V, Giatromanolakis M, Porrini M, Farantos SC, Gervasi O (2011) Computer Physics, Chapter 4, pp. 1–18, Nova Science Publishers.
CNF
Protein Dynamics and Spectroscopy for Ferryl Intermediate of Cytochrome c Oxidase: A Molecular Dynamics Approach
Daskalakis V, Farantos SC, Varotsis C (2007) AIP Computation in Modern Science and Engineering, Proc. 963(2), 31–34.
Selected Invited Talks
- 2026 — "When Structural Diversity Converges: Functional Macrostates of Diatom Light Harvesting Complexes," Light Harvesting satellite meeting, International Conference on Photosynthesis Research 2026, Liverpool, UK.
- 2026 — "Where Crystallography Fails: Probing Intrinsically Disordered Proteins by Computational Tools," 12th Conference of the Hellenic Crystallographic Association, Athens, Greece.
- 2025 — "Baila Morena: The Choreography of Proteins Under a Computational Microscope," ICFO Frontiers Research School: Physics for Biology and Medicine, Barcelona, Spain.
- 2024 — "Biomolecular Simulations: From Dynamics to Engineering," FORTH/ICE-HT, Patras, Greece.
- 2023 — "Biomolecular Engineering: Structures and Dynamics," Department of Physics, Constructor University, Bremen, Germany.
- 2021 — "The mechanics of photoprotection in the major antenna of Photosystem II," SuperMUC-NG Status and Results Workshop (online).
- 2021 — "Epitope vaccines based on the dynamics of mutated SARS-CoV-2 proteins at all atom resolution," EuroHPC Summit Week (online).
- 2019 — Photosynthesis Gordon Research Conference, Sunday River, ME, USA (by invitation only).
- 2018 — 62nd Annual Meeting of the Biophysical Society, San Francisco, USA.
57 publications, 46 conference participations and 15+ invited lectures in total.
Mentoring
Research Collaborators
Panos Koukos (postdoc, current). Former: Ariadni Konstantopoulou (postdoc), Konstantinos Chatzikyriakos (research associate).
Languages
Greek — Native
English — C2
French — B1
