Papers

Habilitation thesis (27 Nov 2017): see bottom of page

A. France-Lanord, H. Vroylandt, M. Salanne, B. Rotenberg, A.M. Saitta, F. Pietrucci

Data-driven path collective variables

J. Chem. Theory Comput. 20, 3069 (2024) (link) (arxiv)

D.D. Girardier, H. Vroylandt, S. Bonella, F. Pietrucci

Inferring free-energy barriers and kinetic rates from molecular dynamics via underdamped Langevin models

J. Chem. Phys. 159, 164111 (2023) (link)

C. Ma, F. Pietrucci, W. Andreoni

CO2 capture and release in amine solutions: to what extent can molecular simulations help understand the trends?

Molecules 28, 6447 (2023) (link)

F. Angiolari, S. Huppert, F. Pietrucci, R. Spezia

Environmental and nuclear quantum effects on double proton transfer in the guanine-cytosine base pair

J. Phys. Chem. Lett. 14, 5102 (2023) (link) (chemrxiv)

L. Mouaffac, K. Palacio-Rodriguez, F. Pietrucci

Optimal reaction coordinates and kinetic rates from the projected dynamics of transition paths

J. Chem. Theory Comput. 19, 5701 (2023) (link) (arxiv)

J. Lam, F. Pietrucci

A critical comparison of general-purpose collective variables for crystal nucleation

Phys. Rev. E 107, L012601 (2023) (link)

A. Jedrecy, A.M. Saitta, F. Pietrucci

Free energy calculations and unbiased molecular dynamics targeting the liquid-liquid transition in water no man’s land

J. Chem. Phys. 158, 014502 (2023) (link) (arxiv)

T. Magrino, L. Huet, A.M. Saitta, F. Pietrucci

Critical assessment of data-driven versus heuristic reaction coordinates in solution chemistry

J. Phys. Chem. A, 126, 8887 (2022) (link)

K. Palacio-Rodriguez, F. Pietrucci

Free energy landscapes, diffusion coefficients and kinetic rates from transition paths

J. Chem. Theory Comput. 18, 4639 (2022) (link) (arxiv)

K. Palacio-Rodriguez, H. Vroylandt, L.S. Stelzl, F. Pietrucci, G. Hummer, P. Cossio

Transition rates, survival probabilities, and quality of bias from time-dependent biased simulations

J. Phys. Chem. Lett. 13, 7490 (2022) (link) arXiv:2109.11360

T. Devergne, T. Magrino, F. Pietrucci, A.M. Saitta

Combining machine learning approaches and accurate ab initio enhanced sampling methods for prebiotic chemical reactions in solution

J. Chem. Theory Comput. 18, 5410 (2022) (link)

A. France-Lanord, F. Pietrucci, A.M. Saitta, J.M. Tarascon, A. Grimaud, M. Salanne

Chemical Decomposition of the TFSI Anion Under Aqueous Basic Conditions

Phys. Rev. X Energy 1, 013005 (2022) (link)

A. Krygier, ..., G. Mogni, F. Pietrucci, et al,

X-ray diffraction study of phase transformation dynamics of Fe and Fe-Si alloys along the shock

Hugoniot using an x-ray free electron laser

Phys. Rev. B 105, L220102 (2022) (link)

H. Vroylandt, L. Goudenège, P. Monmarché, F. Pietrucci, B. Rotenberg

Likelihood-based parametric estimator for memory kernel in molecular dynamics

Proc. Natl. Acad. Sci. U. S. A. 119, e2117586119 (2022) (arxiv) (link)

F. Siro Brigiano, M. Gierada, F. Tielens, F. Pietrucci

Mechanism and free-energy landscape of peptide bond formation at the silica-water interface

ACS Catalysis 12, 2821 (2022) (link)

D. Nelli, F. Pietrucci, R. Ferrando

Impurity diffusion in magic-size icosahedral clusters

J. Chem. Phys. 155, 144304 (2021) (link)

M. Moog, F. Pietrucci, A.M. Saitta

Carbon dioxide at Earth mantle conditions: from a molecular liquid through a reactive fluid to polymeric regimes

J. Phys. Chem. A 125, 5863 (2021) (link)

A. Sinopoli, A. Abotaleb, F. Pietrucci, I. Gladich

Stability of Monoethanolamine-CO2 Zwitterion at the Vapour/Liquid Water Interface: Implications for Low Partial Pressure Carbon Capture Technologies

J. Phys. Chem. B 125, 4890 (2021) (link)

T. Magrino, F. Pietrucci, A.M. Saitta

Step by Step Strecker Amino Acid Synthesis from ab Initio Prebiotic Chemistry

J. Phys. Chem. Lett. 12, 2630 (2021) (link)

F. Pietrucci, M. Boero, W. Andreoni

How Natural Materials Remove Heavy Metals from Water: Mechanistic Insights from Molecular Dynamics Simulations

Chem. Sci. 12, 2979 (2021) (link) (ChemRxiv) covered in Chemistry World & Prace success stories

J. Amodeo, F. Pietrucci, J. Lam

Out of equilibrium polymorph selection during nanoparticle freezing

J. Phys. Chem. Lett. 11, 8060 (2020) (link)

P. Gkeka, G. Stoltz, A.B. Farimani, Z. Belkacemi, M. Ceriotti, J. Chodera, A.R. Dinner, A. Ferguson, J.B. Maillet, H. Minoux, C. Peter, F. Pietrucci, A. Silveira, A. Tkatchenko, Z. Trstanova, R. Wiewiora, T. Leliévre

Machine learning force fields and coarse-grained variables in molecular dynamics: application to materials and biological systems

J. Chem. Theory Comput. 16, 4757 (2020) (link) - arXiv:2004.06950 (link)

S. Laporte, F. Pietrucci, F. Guyot, A.M. Saitta

Formic acid synthesis in a water-mineral system: major role of the interface

J. Phys. Chem. C 124, 5125 (2020) (link)

S. Schaack, P. Depondt, M. Moog, F. Pietrucci, F. Finocchi

How methane hydrate recovers at very high pressure the hexagonal ice structure

J. Chem. Phys. 152, 024504 (2020) (link)

M. Moog, S. Schaack, F. Pietrucci, A.M. Saitta

Exploration of MoS2 nanoclusters configurations: structures, energetics, and electronic properties

J. Phys. Chem. C 123, 22564 (2019) (link)

M. Bonomi, G. Bussi, C. Camilloni, G. Tribello, ..., F. Pietrucci, et al.

Promoting transparency and reproducibility in enhanced molecular simulations

Nature Methods 16, 670 (2019) (link)

L.E. Bove, F. Pietrucci, A.M. Saitta, S. Klotz, J. Teixeira

On the link between polyamorphism and liquid liquid transition: the case of salty water

J. Chem. Phys. 151, 044503 (2019) (link)

M. Ferus, F. Pietrucci, A.M. Saitta, O. Ivanek, A. Knizek, P. Kubelík, M. Krus, L. Juha, R. Dudzak, J. Dostál, A. Pastorek, L. Petera, J. Hrncirova, H. Saeidfirozeh, V. Shestivská, J. Sponer, J.E. Sponer, P. Rimmer, S. Civiš, G. Cassone

Prebiotic synthesis initiated in formaldehyde by laser plasma simulating high-velocity impacts

Astronomy & Astrophysics 626, A52 (2019) (link)

G. Cassone, F. Pietrucci, F. Saija, A.M. Saitta

Free Energy Calculations of Electric Field-Induced Chemistry

in "Computational Approaches for Chemistry Under Extreme Conditions", Springer (2019) (link)

A. Basciu, G. Malloci, F. Pietrucci, A.M.J.J. Bonvin, A.V. Vargiu

Holo-like and druggable protein conformations from enhanced sampling of binding pocket shape

J. Chem. Inf. Model. 59, 1515 (2019) (link) - bioRxiv 434092 (2018) (link)

A. Pérez-Villa, F. Pietrucci

Free energy, friction, and mass profiles from short molecular dynamics trajectories

arXiv 1810.00713 (2018) (link)

C. Camilloni, F. Pietrucci

Advanced simulation techniques for the thermodynamic and kinetic characterization of biological systems

Adv. Phys. X 3, 1477531 (2018) (link)

A. Pérez-Villa, F. Pietrucci, A.M. Saitta

Prebiotic chemistry and origins of life research with atomistic computer simulations

Phys. Life Rev. 34-35, 105 (2020) (link) (pdf)

A. Pérez-Villa, A.M. Saitta, T. Georgelin, J.F. Lambert, F. Guyot, M.C. Maurel, F. Pietrucci

Synthesis of RNA nucleotides in plausible prebiotic conditions from ab initio computer simulations

J. Phys. Chem. Lett. 9, 4981 (2018) (link) ChemRxiv (link)

F. Pietrucci

Novel enhanced sampling strategies for transitions between ordered and disordered structures

in Handbook of Materials Modeling, Springer, ISBN 978-3-319-42913-7 (2018) (link) (pdf)

B. Hoffmann, A. Elbahnsi, P. Lehn, J.L. Décout, F. Pietrucci, J.P. Mornon, I. Callebaut

Combining theoretical and experimental data to decipher CFTR 3D structures and functions

Cell. Mol. Life Sci. 75, 3829 (2018) (link)

F. Pietrucci, J. Aponte, R.D. Starr, A. Pérez-Villa, J.E. Elsila, J.P. Dworkin, A.M. Saitta

Hydrothermal decomposition of amino acids and origins of prebiotic meteoritic organic compounds

ACS Earth Space Chem. 2, 588 (2018) (link)

M.P. Kroonblawd, F. Pietrucci, A.M. Saitta, N. Goldman

Generating converged accurate free energy surfaces for chemical reactions with a force-matched semi-empirical model

J. Chem. Theory Comput. 14, 2207 (2018) (link)

G. Cassone, J. Šponer, J.E. Šponer, F. Pietrucci, A.M. Saitta, F. Saija

Synthesis of (D)-erythrose from glycolaldehyde aqueous solutions under electric field

Chem. Commun. 54, 3211 (2018) (link)

E. Balan, J. Noireaux, V. Mavromatis, G. Saldi, V. Montouillout, M. Blanchard, F. Pietrucci, C. Gervais, J.R. Rustad, J. Schott, J. Gaillardet

Theoretical isotopic fractionation between structural boron in carbonates and aqueous boric acid and borate ion

Geochim. Cosmochim. Acta 222, 117 (2018) (link)

M. Fitzner, G.C. Sosso, F. Pietrucci, S. Pipolo, A. Michaelides

Pre-critical fluctuations and what they disclose about heterogeneous crystal nucleation

Nat. Commun. 8, 2257 (2017) (link)

S. Pipolo, M. Salanne, G. Ferlat, S. Klotz, A.M. Saitta, F. Pietrucci

Navigating at will on the water phase diagram

Phys. Rev. Lett. 119, 245701 (2017) (link) arXiv 1703.00753 (link)

C. Liu, A. Mafety, J.A. Queyroux, C. Wilson, K. Beneut, G. Le Marchand, B. Baptiste, P. Dumas, G. Garbarino, F. Finocchi, J.S. Loveday, F. Pietrucci, A.M. Saitta, F. Datchi, S. Ninet

Topologically frustrated ionisation in a water-ammonia ice mixture

Nat. Commun. 8, 1065 (2017) (link)

M. Bernetti, M. Masetti, F. Pietrucci, M. Blackledge, M. Jensen, M. Recanatini, L. Mollica, A. Cavalli

Structural and kinetic characterization of the intrinsically disordered protein SeV NTAIL through enhanced sampling simulations

J. Phys. Chem. B 121, 9572 (2017) (link)

G. Cassone, F. Pietrucci, F. Saija, F. Guyot, J. Sponer, J.E. Sponer, A.M. Saitta

Novel electrochemical route to cleaner fuel dimethyl ether

Sci. Rep. 7, 6901 (2017) (link)

M. Ducher, F. Pietrucci, E. Balan, G. Ferlat, M. Blanchard

Van der Waals contribution to the relative stability of aqueous Zn(2+) coordination states

J. Chem. Theory Comput. 13, 3340 (2017) (link)

F. Pietrucci

Strategies for the exploration of free energy landscapes: unity in diversity and challenges ahead

Rev. Phys. 2, 32 (2017) (link) (pdf)

M. Ferus, F. Pietrucci, A.M. Saitta, A. Knizek, P. Kubelik, O. Ivanek, V. Shestivska, S. Civis

Formation of nucleobases in a Miller-Urey reducing atmosphere

Proc. Natl. Acad. Sci. U.S.A. 114, 4306 (2017) (link) (pdf)

F. Datchi, M. Moog, F. Pietrucci, A.M. Saitta

Polymeric phase V of carbon dioxide has not been recovered at ambient pressure and has a unique structure

Proc. Natl. Acad. Sci. U. S. A. 114, E656 (2017) (link)

G. Cassone, F. Pietrucci, F. Saija, F. Guyot, A.M. Saitta

One-step electric-field driven methane and formaldehyde synthesis from liquid methanol

Chem. Sci. 8, 2329 (2017) (link)

W. Andreoni, F. Pietrucci

CO2 capture in amine solutions: modelling and simulations with non-empirical methods

J. Phys. Condens. Matter 58, 503003 (2016) (link) (pdf)

S. Klotz, K. Komatsu, F. Pietrucci, H. Kagi, A.A. Ludl, S. Machida, T. Hattori, A. Sano-Furukawa, L.E. Bove

Ice VII from aqueous salt solutions: From a glass to a crystal with broken H-bonds

Sci. Rep. 6, 32040 (2016) (link)

E. Balan, F. Pietrucci, C. Gervais, M. Blanchard, J. Schott, J. Gaillardet

First-principles study of boron speciation in calcite and aragonite

Geochim. Cosmochim. Acta 193, 119 (2016) (link) (pdf)

J.E. Sponer, R. Szabla, R.W. Gora, A.M. Saitta, F. Pietrucci, F. Saija, E. Di Mauro, R. Saladino, M. Ferus, S. Civis, J. Sponer

Prebiotic synthesis of nucleic acids and their building blocks at the atomic level – merging models and mechanisms from advanced computations and experiments

Phys. Chem. Chem. Phys. 18, 20047 (2016) (link) (pdf)

C. Ma, F. Pietrucci, W. Andreoni

Reaction dynamics of CO2 in aqueous amines from ab initio molecular dynamics: 2‑amino‑2‑methyl‑1,3‑propanediol (AMPD) compared to monoethanolamine (MEA)

Theor. Chem. Acc. 135, 60 (2016) (link)

J.M.H. Kroes, F. Pietrucci, K. Chikkadi, C. Roman, C. Hierold, W. Andreoni

The response of single-walled carbon nanotubes to NO2 and the search for a long-living adsorbed species

Appl. Phys. Lett. 108, 033111 (2016) (link)

F. Pietrucci, A.V. Vargiu, A. Kranjc

HIV-1 protease dimerization dynamics reveals a transient druggable binding pocket at the interface

Sci. Rep. 5, 18555 (2015) (link) (pdf)

F. Pietrucci, A.M. Saitta

Formamide reaction network in gas phase and solution via a unified theoretical approach: toward a reconciliation of different prebiotic scenarios

Proc. Natl. Acad. Sci. U. S. A. 112, 15030 (2015) (link) (pdf)

J.M.H. Kroes, F. Pietrucci, A.C.T. van Duin, W. Andreoni

Atom vacancies on a carbon nanotube: to what exent can we simulate their effect?

J. Chem. Theory Comput. 11, 3393 (2015) (link)

C. Ma, F. Pietrucci, W. Andreoni

Capture and Release of CO2 in Monoethanolamine Aqueous Solutions: New Insights from First-Principles Reaction Dynamics

J. Chem. Theory Comput. 11, 3189 (2015) (link)

F. Pietrucci and R. Martonak

Systematic Comparison of Crystalline and Amorphous Phases: Charting the Landscape of Water Structures and Transformations

J. Chem. Phys. 142, 104704 (2015) (link) (pdf)

A.M. Saitta, F. Saija, F. Pietrucci, F. Guyot

Reply to Bada and Cleaves: Ab initio free-energy landscape of Miller-like prebiotic reactions

Proc. Natl. Acad. Sci. U. S. A. 112, E343 (2015) (link)

J.M.H. Kroes, F. Pietrucci, A. Curioni, W. Andreoni

Characterizing and Understanding Divalent Adsorbates on Carbon Nanotubes with Ab-Initio and Classical Approaches: Size, Chirality and Coverage Effects

J. Chem. Theory Comput. 10, 4672 (2014) (link)

C. Ma, F. Pietrucci, W. Andreoni

Capturing CO2 in monoethanolamine (MEA) aqueous solutions: fingerprints of carbamate formation assessed with first-principles simulations

J. Phys. Chem. Lett. 5, 1672 (2014) (link)

X.L. Hu, R. Ciaglia, F. Pietrucci, G.A. Gallet, W. Andreoni

DFT-derived reactive potentials for the simulation of activated processes: the case of CdTe and CdTe:S

J. Phys. Chem. B 118, 6531 (2014) (link)

F. Pietrucci and W. Andreoni

The fate of a graphene flake: a new route towards fullerenes disclosed with ab initio simulations

J. Chem. Theory Comput. 10, 913 (2014) (link)

G.A. Gallet and F. Pietrucci

Structural cluster analysis of chemical reactions in solution

J. Chem. Phys. 139, 074101 (2013) (link) (journal cover)

F. Pietrucci, L. Mollica, and M. Blackledge

Mapping the native conformational ensemble of proteins from a combination of simulations and experiments: new insight into the src-SH3 domain

J. Phys. Chem. Lett. 4, 1943 (2013) (link) (pdf)

F. Baftizadeh, F. Pietrucci, X. Biarnes, and A. Laio

Nucleation process of a fibril precursor in the C-terminal segment of amyloid-beta

Phys. Rev. Lett. 110, 168103 (2013) (link)

J.M.H. Kroes, F. Pietrucci, A. Curioni, R. Jaafar, O. Groening, and W. Andreoni

Atomic Oxygen Chemisorption on Carbon Nanotubes Revisited with Theory and Experiments

J. Phys. Chem. C 117, 1948 (2013) (link)

C.A. Guido, F. Pietrucci, G. Gallet, and W. Andreoni

The Fate of a Zwitterion in Water from ab initio MD: Mono-ethanolamine(MEA)-CO2

J. Chem. Theory Comput. 9, 28 (2013) (link)

G. Gallet, F. Pietrucci, and W. Andreoni

Bridging static and dynamical descriptions of chemical reactions: an ab initio study of CO2 interacting with water molecules

J. Chem. Theory Comput. 8, 4029 (2012) (link) (journal cover)

F. Baftizadeh, X. Biarnes, F. Pietrucci, F. Affinito, and A. Laio

A multidimensional view of amyloid fibril nucleation in atomistic detail

J. Am. Chem. Soc. 134, 3886 (2012) (link)

W. Andreoni, A. Curioni, J. Kroes, F. Pietrucci, and O. Groening

Exohedral hydrogen chemisorption on a carbon nanotube: the clustering effect

J. Phys. Chem. C 116, 269 (2012) (link)

F. Baftizadeh, P. Cossio, F. Pietrucci, and A. Laio

Protein folding and ligand-enzyme binding from bias-exchange metadynamics simulations

Curr. Phys. Chem. 2, 79 (2012) (link) (pdf)

X. Biarnes, F. Pietrucci, F. Marinelli, and A. Laio

METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations

Comput. Phys. Commun. 183, 203 (2012) (link)

F. Pietrucci and W. Andreoni

Graph theory meets ab initio molecular dynamics: atomic structures and transformations at the nanoscale

Phys. Rev. Lett. 107, 085504 (2011) (link) (pdf)

P. Cossio, A. Laio, and F. Pietrucci

Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

Phys. Chem. Chem. Phys. 13, 10421 (2011) (link)

F. Pietrucci, G. Gerra, and W. Andreoni

CdTe surfaces: characterizing dynamical processes with first-principles metadynamics

Appl. Phys. Lett. 97, 141914 (2010) (link)

P. Cossio, A. Trovato, F. Pietrucci, F. Seno, A. Maritan, and A. Laio

Exploring the universe of protein structures beyond the Protein Data Bank

PLoS Comput. Biol. 6, e1000957 (2010) (link)

Y. Crespo, F. Marinelli, F. Pietrucci, and A. Laio

Metadynamics convergence law in a multidimensional system

Phys. Rev. E 81, 055701(R) (2010) (link)

P. Cossio, F. Marinelli, A. Laio, and F. Pietrucci

Optimizing the performance of bias-exchange metadynamics: folding a 48-residue LysM domain using a coarse-grained model

J. Phys. Chem. B 114, 3259 (2010) (link)

R. Di Meo, F. Pietrucci, A. Laio, and S. Cozzini

Protein folding by bias exchange metadynamics on a Grid infrastructure

ICTP Lecture Notes Series 24 (ISBN 92-95003-42-X) (link)

F. Pietrucci and A. Laio

A collective variable for the efficient exploration of protein beta-sheet structures: application to SH3 and GB1

J. Chem. Theory Comput. 5, 2197 (2009) (link)

F. Pietrucci, F. Marinelli, P. Carloni, and A. Laio

Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations

J. Am. Chem. Soc. 131, 11811 (2009) (link) (pdf)

M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Donadio, F. Marinelli, F. Pietrucci, R. A. Broglia, M. Parrinello

PLUMED: a portable plugin for free-energy calculations with molecular dynamics

Comput. Phys. Commun. 180, 1961 (2009) (link) (arxiv)

F. Marinelli, F. Pietrucci, A. Laio, and S. Piana

A kinetic model of TRP-cage folding from multiple biased molecular dynamics simulations

PLoS Comput. Biol. 5, e100045 (2009) (link)

A. Kranjc, F. W. Grillo, J. Rievaj, A. Boccaccio, F. Pietrucci, A. Menini, P. Carloni, and C. Anselmi

Regulation of Bestrophins by Ca2+: A Theoretical and Experimental Study

PLoS ONE 4, e4672 (2009) (link)

F. Pietrucci, M. Bernasconi, A. Laio, and M. Parrinello

Vacancy-vacancy interaction and oxygen diffusion in stabilized cubic ZrO2 from first principles

Phys. Rev. B 78, 094301 (2008) (link)

F. Pietrucci, S. Caravati, and M. Bernasconi

TeO2 glass properties from first principles

Phys. Rev. B 78, 064203 (2008) (link)

L. D'Alessio, F. Pietrucci, and M. Bernasconi

First principles study of the vibrational properties of Li2TeO3

J. Phys. Chem. Solids 68, 438-444 (2007) (link)

F. Pietrucci, M. Bernasconi, C. Di Valentin, F. Mauri, and C. J. Pickard

EPR g-tensor of paramagnetic centers in yttria-stabilized zirconia from first-principles calculations

Phys. Rev. B 73, 134112 (2006) (link)

M. Ceriotti, F. Pietrucci, and M. Bernasconi

Ab initio study of the vibrational properties of crystalline TeO2: The alpha, beta, and gamma phases

Phys. Rev. B 73, 104304 (2006) (link)

G. Ballabio, M. Bernasconi, F. Pietrucci, and S. Serra

Ab initio study of yttria-stabilized cubic zirconia surfaces

Phys. Rev. B 70, 075417 (2004) (link)

HDR-thesis-Pietrucci.pdf