Papers
88
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)
87
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)
86
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)
85
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)
84
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)
83
J. Lam, F. Pietrucci
A critical comparison of general-purpose collective variables for crystal nucleation
Phys. Rev. E 107, L012601 (2023) (link)
82
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)
81
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)
80
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)
79
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
78
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)
77
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)
76
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)
75
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)
74
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)
73
D. Nelli, F. Pietrucci, R. Ferrando
Impurity diffusion in magic-size icosahedral clusters
J. Chem. Phys. 155, 144304 (2021) (link)
72
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)
71
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)
70
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)
69
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
68
J. Amodeo, F. Pietrucci, J. Lam
Out of equilibrium polymorph selection during nanoparticle freezing
J. Phys. Chem. Lett. 11, 8060 (2020) (link)
67
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)
66
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)
65
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)
64
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)
63
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)
62
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)
61
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)
60
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)
59
C. Camilloni, F. Pietrucci
Advanced simulation techniques for the thermodynamic and kinetic characterization of biological systems
Adv. Phys. X 3, 1477531 (2018) (link)
58
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)
57
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)
56
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)
55
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)
54
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)
53
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)
52
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)
51
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)
50
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)
49
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)
48
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)
47
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)
46
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)
45
F. Pietrucci
Strategies for the exploration of free energy landscapes: unity in diversity and challenges ahead
Rev. Phys. 2, 32 (2017) (link) (pdf)
44
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)
43
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)
42
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)
41
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)
40
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)
39
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)
38
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)
37
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)
36
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)
35
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)
34
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)
33
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)
32
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)
31
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)
30
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)
29
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)
28
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)
27
G.A. Gallet and F. Pietrucci
Structural cluster analysis of chemical reactions in solution
J. Chem. Phys. 139, 074101 (2013) (link) (journal cover)
26
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)
25
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)
24
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)
23
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)
22
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)
21
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)
20
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)
19
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)
18
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)
17
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)
16
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)
15
F. Pietrucci, G. Gerra, and W. Andreoni
CdTe surfaces: characterizing dynamical processes with first-principles metadynamics
Appl. Phys. Lett. 97, 141914 (2010) (link)
14
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)
13
Y. Crespo, F. Marinelli, F. Pietrucci, and A. Laio
Metadynamics convergence law in a multidimensional system
Phys. Rev. E 81, 055701(R) (2010) (link)
12
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)
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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)
11
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)
10
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)
9
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)
8
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)
7
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)
6
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)
5
F. Pietrucci, S. Caravati, and M. Bernasconi
TeO2 glass properties from first principles
Phys. Rev. B 78, 064203 (2008) (link)
4
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)
3
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)
2
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)
1
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)