Group Parrinello

About

Our work focuses on development and application of classical and quantum simulation techniques for study of matter using high performance computing. The activities of the group have a strong interdisciplinary character ranging from solid state physics to chemical engineering to drug design. 

Recent projects have been the study of drug unbinding, protein conformational changes, crystal nucleation, phase change materials, and proton transport in water. Through our work we have been able to provide insight into the physics and chemistry of these and several other complex processes of great social and technological relevance.

Research on methodological aspects is an important part of our activity. Of particular relevance is the development of enhanced sampling algorithms based around metadynamics. This method has made major progress possible in the study of long timescale phenomena which are ubiquitous in nature, but were previously inaccessible due to fundamental limits of computational power. The group has also been the pioneer of the DFT-based ab initio molecular dynamics of Car and Parrinello, CPMD. This method allows calculating the static and dynamical properties of solids, liquids, disordered systems and complex molecules accurately and without adjustable parameters.

 


Research

Actual research directions

DRUG UNBINDING. It is of paramount importance in the early stages of drug discovery to predict both how strongly and for how long does a drug stay bound to the protein. So far the major emphasis has been on predicting the strength of interaction as determined by the binding affinity. In contrast it has not been possible to use computations to predict the duration for which a drug stays bound. The dissociative half-life of the protein-ligand complex is defined as the time during which the ligand remains in the binding site. In principle this should be amenable to calculations through molecular dynamics (MD) simulations. However, in spite of the potential of MD simulations no such simulation has yet been reported. This is a consequence of the limiting timescales of MD simulations.

Metadynamics developed in our group is a popular technique that complements MD and allows studying complex systems. Using our recent significant extensions of metadynamics, we can now for the first time study protein-ligand dissociation pathways and determine associated rates, reaching well into longer than seconds regime while maintaining full atomic resolution for protein, drug and solvent. This work will open up new horizons in the ability to calculate mechanisms and rate constants, and have a transformative effect on the process of drug design, hopefully making it cheaper and faster.

 

ALLOSTERIC REGULATION. Allosteric regulation plays an important role in a myriad of biomacromolecular processes. Specifically, in a protein, the process of allostery refers to the transmission of a local perturbation, such as ligand binding, to a distant site. Decades after the discovery of this phenomenon, models built on static images of proteins are being reconsidered with the knowledge that protein dynamics plays an important role in its function. Molecular dynamics simulations are a valuable tool for studying complex biomolecular systems, providing an atomistic description of their structure and dynamics.

Unfortunately, their predictive power has been limited by the complexity of the biomolecule free-energy surface and by the length of the allosteric timescale (in the order of milliseconds). Combing all-atom molecular dynamics with enhanced sampling methods developed in our group, we are able to probe the origins of the allosteric changes that transcription factor mixed lineage leukemia (MLL) causes to the interactions of KIX domain of CREB-binding protein (CBP) with phosphorylated kinase inducible domain (pKID). We compare our results with previous experimental studies. Through this research we are able to develop a general simulations protocol to study allosteric phenomena and many other biological processes that occur in the micro/milliseconds timescale.

 

PHASE CHANGE MATERIALS. Phase change materials are the building blocks of state of the art optical storage devices and of the next generation of non volatile memories, which foreshadow multi level programming, nanowires based architectures and an important role in neuromorphic computing. All of these applications rely on the fast and reversible switching from the disordered phase to the crystalline state, which takes place in the nano domain with respect to both the time and the length scales.

In order to unravel the atomistic details of the fast crystallization, we have taken advantage of Neural Network based interatomic potential for GeTe that obliterates the well known computational limitations of first principle calculations, in terms of system size and timescale while retaining the accuracy of a density functional theory framework. Thanks to this powerful tool, we have been able to perform large scale molecular dynamics simulations of the crystal growth of GeTe at the interface between the crystalline and the supercooled liquid phase, employing models that really bring our simulation playground extremely close to the actual crystallization scenario so extensively explored experimentally.

 

GROWTH OF ORGANIC CRYSTALS. Nucleation and growth of a crystal phase from solution is a ubiquitous phenomenon of primary importance both in natural and industrial processes. Biomineralization phenomena as well as the production of sophisticated synthetic drugs or expensive fine chemistry compounds are just some of the processes that crucially depend on the nucleation and growth of a crystal from a dispersed and disordered phase.

The identification of nucleation mechanisms, the mechanistic description of crystal shape evolution during the growth process or the influence of foreign molecules on both nucleation and growth, represent only a fraction of the open problems in this field.

In this framework, molecular simulations play a primary role, allowing to obtain an insight into the elusive phenomena that occur at the molecular scale. In our research we apply enhanced sampling simulations to investigate both nucleation and growth of organic molecules from solution.

 


 

Professor Michele Parrinello's Research Group

Dirac Medal and Marcel Benoist Prize

The Abdus Salam International Centre for Theoretical Physics has awarded Professor Michele Parrinello and Professor Roberto Car the 2009 Dirac Medal and Prize in recognition of their joint contribution in the development of the ab-initio simulation method in which they combined the quantum mechanical density functional method for the calculation of the electronic properties of matter with molecular dynamics methods for the Newtonian simulation of atomic motions.

The 2009 Dirac Medal and Prize awarded to Prof. Parrinello and Prof. Car

dirac
Prof. Parrinello (second from the left) and Prof. Dirac (second from the right) at ICTP in the late 70s

 

In 2011, the Board of Trustees of the Marcel Benoist Foundation under the chairmanship of Federal Councillor Didier Burkhalter has awarded the Marcel Benoist Prize to Michele Parrinello. The physicist and molecular scientist receiving the award in recognition of his computer-aided models in the field of molecular dynamics.

 

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Professor Parrinello's group and collaborators.

Publications

2016

"General Protein Data Bank-Based Collective Variables for Protein Folding"
A. Ardévol, f. Palazzesi, G. A. Tribello and M. Parrinello
J. Chem. Theory Comput., 2016, 12 (1), 29–35

"Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin"
P. Shaffer, O. Valsson and M. Parrinello
PNAS USA, 2016, 113 (5), 1150-1155

 

2015

"A perturbative solution to metadynamics ordinary differential equation"
P. Tiwary, J. Dama and M. Parrinello
J. Chem. Phys., 2015, 143, 234112

"de Broglie Swapping Metadynamics for Quantum and Classical Sampling"
M. Nava, R. Quhe, F. Palazzesi, P. Tiwary and M. Parrinello
J. Chem. Theory Comput., 2015, 11 (11), pp 5114–5119

"Variationally Optimized Free-Energy Flooding for Rate Calculation"
J. McCarty, O. Valsson, P. Tiwary and M. Parrinello
Phys. Rev. Lett., 2015, 115 (7), 070601

"Urea homogeneous nucleation mechanism is solvent dependent"
M. Salvalaglio, M. Mazzotti and M. Parrinello
The Royal Society of Chemistry 2015, Faraday Discuss. 179, 291–307

"Well-Tempered Variational Approach to Enhanced Sampling"
O. Valsson and M. Parrinello
J. Chem. Theory Comput., 2015, 11, 1996-2002

"Molecular dynamics simulations of solutions at constant chemical potential"
C. Perego, M. Salvalaglio and M. Parrinello
J. Chem. Phys., 2015, 142, 144113

"Heterogeneous Crystallization of the Phase Change Material GeTe via Atomistic Simulations"
G. C. Sosso, M. Salvalaglio, J. Behler, M. Bernasconi and M. Parrinello
J. Phys. Chem. C, 2015, 119 (11), 6428–6434

"Metadynamics Studies of Crystal Nucleation"
F. Giberti, M. Salvalaglio and M. Parrinello
IUCrJ, 2015, 2, 256–266

"Probing the Unfolded Configurations of a β-Hairpin Using Sketch-Map"
A. Ardévol, G. A. Tribello, M. Ceriotti and M Parrinello
J. Chem. Theory Comput., 2015, 11 (3), 1086-1093

"Path Integral Metadynamics"
R. Quhe, M. Nava, P. Tiwary and M. Parrinello
J. Chem. Theory Comput., 2015, 11 (4), 1383-1388

"Combustion Chemistry via Metadynamics: Benzyl Decomposition Revisited"
D. Polino and M. Parrinello
J. Phys. Chem. A, 2015, 119, 978 – 989

"Energetics and Structural Characterization of the large-scale Functional Motion of Adenylate Kinase"
E. Formoso, V. Limongelli and M. Parrinello
Scientific Reports, 2015, 5, 8425

"Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps"
P. Tiwary, V. Limongelli, M. Salvalaglio and M. Parrinello
PNAS, 2015, 112 (5), E386-E391

"Molecular dynamics simulations of urea nucleation from aqueous solution"
M. Salvalaglio, C. Perego, F. Giberti, M. Mazzotti and M. Parrinello
PNAS, 2015, 112 (1), E6 - E14

"A Time-Independent Free Energy Estimator for Metadynamics"
P. Tiwary and M. Parrinello
J. Phys. Chem. B, 2015, 119 (3), 736–742

"Insight into the nucleation of urea crystals from the melt"
F. Giberti, M. Salvalaglio, M. Mazzotti and M. Parrinello
Chemical Engineering Science, 2015, 121, 51–59

 

2014

"A Time-Independent Free Energy Estimator for Metadynamics"
P. Tiwary and M. Parrinello
J. Phys. Chem. B. 2014, , 504920

"Variational Approach to Enhanced Sampling and Free Energy Calculations"
O. Valsson and M. Parrinello
Phys. Rev. Lett. 2014, 113 (9), 090601 

"Well-Tempered Metadynamics Converges Asymptotically"
J. F. Dama, M. Parrinello and G. A. Voth
Phys. Rev. Lett. 2014, 112, 240602

 "1,3,5-Tris(4-bromophenyl)benzeneprenucleation clusters from meta-dynamics"
M. Salvalaglio, F. Giberti and M. Parrinello
Acta Cryst. 2014, C70, 132-136

"Evaluation functions of positive-definite matrices using colored-noise thermostats"
M. Nava, M. Ceriotti, C. Dryzun and M. Parrinello
Phys. Rev. E, 2014, 89 (2), 023302

"Anomalous water diffusion in salt solutions"
Y. Ding, A. A. Hassanali and M. Parrinello
PNAS 2014, 111 (9), 3310-3315

"Aqueous solutions: state of the art in ab initio molecular dynamics"
A. A. Hassanali, J. Cuny, V. Verdolino and M. Parrinello
Phil. Trans. R. Soc. A 2014, 372, 20120482

"Assessing the Reliability of the Dynamics Reconstructed from Metadynamics"
M. Salvalaglio, P. Tiwary and M. Parrinello
J. Chem. Theory Comput. 2014, 10, 1420-1425

"The role of the umbrella inversion mode in proton diffusion"
A. A. Hassanali, F. Giberti, G. C. Sosso and M. Parrinello
Chem. Phys. Lett. 2014, 599, 133-138

 

2013

"Controlling and Predictin Crystal Shapes: The Case of Urea"
M. Salvalaglio, T. Vetter, M. Mazzotti and M. Parrinello
Angew. Chem. Int. Ed. 2013, 52, 13369-13372

"Fre-energy landscape of protein oligomerization from atomistic simulations"
A. Barducci, M. Bonomi, M.K. Prakash and M. Parrinello
PNAS 2013, 110, E4708-E4713

"Thermodynamical Description of a Quasi-First-Order Phase Transition from the Well-Tempered Ensemble"
O. Valsson and M. Parrinello
J. Chem. Theory Comput. 2013, 9, 5267-5276

"From Metadynamics to Dynamics”
P. Tiwary and M. Parrinello
Phys. Rev. Lett. 2013, 111, 230602-230606

"Nuclear quantum effects and hydrogen bond fluctuations in water”
M. Ceriotti, J. Cuny, M. Parrinello and D. E. Manolopoulos
PNAS 2013, 110, 15591-15596

"The allosteric communication pathways in KIX domain of CBP”
F. Palazzesi, A. Barducci, M. Tollinger and M. Parrinello
PNAS 2013, 110, 142237-14242

"Proton transfer through the water gossamer”
A. Hassanali, F. Giberti, J. Cuny and M. Parrinello
PNAS 2013, 110, 13723-13728

"Chiral, Racemic, and Meso-Lithium Tartrate Framework Polymorphs: A Detailed Structural Analysis”
H. H.-M. Yeung, M. Kosa, M. Parrinello et al.
Crystal Growth & Design 2013, 13, 3705-3715

"Transient Polymorphism in NaCl”
F. Giberti, G. A. Tribello and M. Parrinello
J. Chem. Theory Comput. 2013, 9, 2526-2530

"Water Release from Pyrophyllite during the Dehydroxylation Process Explored by Quantum Mechanical Simulations”
E. Molina-Montes, D. Donadio, Alfonso Hernàndez-Laguna, M. Parrinello and C. I. Sainz-Díaz
J. Phys. Chem. C 2013, 117, 7526-7532

"Funnel metadynamics as accurate binding free-energy method”
V. Limongelli, M. Bonomi and M. Parrinello
PNAS 2013, 110, 6358-6363

"Density Functional Simulations of Hexagonal Ge2S2Te5 at High Pressure”
S. Caravati, G. C. Sosso, M. Bernasconi and M. Parrinello
Phys. Rev. B 2013, 87, 094117

"Demonstrating the Transferability and the Descriptive Power of Sketch-Map”
M. Ceriotti, G. A. Tribello and M. Parrinello
J. Chem. Theory Comput. 2013, 9, 1521-1532

"The G-Triplex DNA”
V. Limongelli, S. De Tito, L. Cerogolini, M. Fragai, B. Pagano, R. Trotta, S. Cosconati, L. Marinelli, E. Novellino, I. Bertini, A. Randazzo, C. Luchinat and M. Parrinello
Angew. Chem. Int. Ed 2013, 52, 2269-2273

"Combining Metadynamics Simulation and Experiments to Characterize Dendrimers in Solution”
G. M. Pavan, A. Barducci, L. Albertazzi and M. Parrinello
Soft Matter 2013, 9, 2593

 

2012

"Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA”
T. N. Do, E. Ippoliti, P. Carloni, G. Varani and M. Parrinello
J. Chem. Theory Comput. 2012, 8, 688-694

"Sampling protein motion and solvent effect during ligand binding”
V. Limongelli, L. Marinelli, S. Cosconati, C. La Motta, S. Sartini, L. Mugnaini, F. Da Settimo, E. Novellino and M. Parrinello
PNAS 2012, 109 (5), 1467-1472

"Investigating the Mechanism of Substrate Uptake and Release in the Glutamate Transporter Homologue GltPh through Metadynamics Simulations”
G. Grazioso, V. Limongelli, D. Branduardi, E. Novellino, C. De Micheli, A. Cavalli and M. Parrinello
J. Am. Chem. Soc. 2012, 134, 453-463

"Microscopic Origins of the Anomalous Melting Behavior of Sodium under Pressure”
H. Eshet, R. Z. Khaliullin, T. D. Kühne, J. Behler and M. Parrinello
Phys. Rev. Lett. 2012, 108 (11), 115701

"Using sketch-map coordinates to analyze and bias molecular dynamics simulations”
G. A. Tribello, M. Ceriotti and M. Parrinello
PNAS 2012, 109 (14), 5196-5201

"Locating binding poses in protein-ligand systems using reconnaissance metadynamics”
P. Söderhjelm, G. A. Tribello and M. Parrinello
PNAS 2012, 109 (14), 5170-5175

"The Fuzzy Quantum Proton in the Hydrogen Chloride Hydrates”
A. A. Hassanali, J. Cuny, M. Ceriotti, C. J. Pickard and M. Parrinello
J. Am. Chem. Soc. 2012, 134, 8557-8569

"Ab Initio Molecular Dynamics Study of the Dehydroxylation Reaction in a Smectite Model”
D. Munoz-Santiburcio, M. Kosa, A. Hernandez-Laguna, C. I. Saint-Diaz and M. Parrinello
J. Phys. Chem. C 2012, 116, 12203-12211

"Metadynamics with Adaptive Gaussians”
D. Branduardi, G. Bussi and M. Parrinello
J. Chem. Theory Comput. 2012, 8, 2247-2254

"Density functional simulations of Sb-rich GeSbTe phase change alloys”
S. Gabardi, S. Caravati, M. Bernasconi and M. Parrinello
J. Phys. Condens. Matter 2012, 24, 385803

"Uncovering Molecular Details of Urea Crystal Growth in the Presence of Additives”
M. Salvalaglio, T. Vetter, F. Giberti, M. Mazzotti and M. Parrinello
J. Am. Chem. Soc. 2012, 134, 17221-17233

"Combined Computational and Experimental NMR Study of Calix[4]arene Derivatives”
V. Verdolino, L. Baldini, F. Palazzesi, F. Giberti and M. Parrinello
J. Phys. Chem. C 2012, 116, 23441-23452

 

2011

"Effect of Urea on the β-Hairpin Conformational Ensemble and Protein Denaturation Mechanism”
A. Berteotti, A. Barducci and M. Parrinello
J. Am. Chem. Soc. 2011, 133, 17200-17206

"On the recombination of hydronium and hydroxide ions in water"
A. Hassanali, M. K. Prakash, H. Eshet and M. Parrinello
PNAS 2011, 108 (51), 20410-20415

"Hydrogen oxidation reaction at the Ni/YSZ anode of solid oxide fuel cells from first principles"
C. S. Cucinotta, M. Bernasconi and M. Parrinello
Phys. Rev. Lett. 2011, 107, 206103

"Esploring the free energy surfaces of clusters using reconnaissance metadynamics"
G. A. Tribello, J. Cuny, H. Eshet and M. Parrinello
J. Chem. Phys. 2011, 135, 114109

"Metadynamics
" A. Barducci, M. Bonomi and M. Parrinello
Comp. Mol. Sci. 2011, 1, 826-843

"A chirality-based metrics for free-energy calculations in biomolecular systems
A. Pietropaolo, D. Branduardi, M. Bonomi and M. Parrinello
J. Comput. Chem. 2011, 32, 2627-2637

Nucleation mechanism for the direct graphite-to-diamond phase transition
R.Z. Khaliullin, H. Eshet, T.D. Kühne, J. Behler and M. Parrinello
Nature Materials 2011, 10, 3078

Simplifying the representation of complex free-energy landscapes using sketch-map
M. Ceriotti, G.A. Tribello and M. Parrinello
PNAS 2011, 108 (32), 13023-13028

A quantitative measure of chirality inside nucleic acid databank
A. Pietropaolo and M. Parrinello
Chirality 2011, 23, 534-542

Replica temperatures for uniform exchange and efficient roundtrip times in explicit solvent parallel tempering simulations
M.K. Prakash, A. Barducci and M. Parrinello
J. Chem. Theory Comput. 2011, 7, 2025-2027

First-principles study of nitrogen doping in cubic and amorphous Ge2Sb2Te5
S. Caravati, D. Colleoni, R. Mazzarello, T.D. Kühne, M. Krack, M. Bernasconi and M. Parrinello
J. Phys. Cond. Matt. 2011, 23 (26), 265801

Momentum distribution, vibration dynamics, and the potential of mean force in ice
L. Lin, J.A. Morrone, R. Car and M. Parrinello
Phys. Rev. B 2011, 83 (22), 220302

First-principles study of the hight-temperature phase of Li2NH
G. Miceli, M. Ceriotti, S. Angioletti-Uberti, M. Bernasconi and M. Parrinello
J. Phys. Chem. C 2011, 115, 7076-7080

Accelerating the convergence of path integral dynamics with a generalized Langevin equation
M. Ceriotti, D.E. Manolopoulos and Michele Parrinello
J. Chem. Phys. 2011, 134 (8), 084104

Structural diversity and energetics in anhydrous lithium tartrates: experimental and computational studies of Novel Chiral Polymorphs and their racemic and meso analogues
H. H.-M. Yeung, M. Kosa, M. Parrinello, P.M. Forster and A.K. Cheetham
Crystal Growth & Design 2011, 11 (24),221-230

Static disorder and structural correlations in the low-temperature phase of lithium imide
G. Miceli, M. Ceriotti, M. Bernasconi and M. Parrinello
Phys. Rev. B 2011, 83 (5), 054119

 

2010

Nuclear quantum effects in ab initio dynamics: theory and experiments for lithium imide
M. Ceriotti, G. Miceli, A. Pietropaolo, D. Colognesi, A. Nale, M. Catti, M. Bernasconi and M. Parrinello
Phys. Rev. B 2010, 82, 174306

First principles study of the LiNh2Li2NH transformation
G. Miceli, C. S. Cucinotta, M. Bernasconi and M. Parrinello
J. Phys. Chem. C 2010, 114 (35), 15174-15183

A self-leraning algorithm for biased molecular dynamics
G. A. Tribello, M. Ceriotti and M. Parrinello
PNAS 2010, 107 (41), 17509-17514

The delta-thermostat: selective normal-modes excitation by colored-noise Langevin dynamics
M. Ceriotti and M. Parrinello
Procedia Computer Science 2010, 1, 1607-1614

Efficient stochastic thermostatting of path integral molecular dynamics
M. Ceriotti, M. Parrinello, T.E. Markland and D. E. Manolopoulos
J. Chem. Phys. 2010, 133, 124104

Multiple routes and milestones in the folding of HIV-1 protease monomer
M. Bonomi, A. Barducci, F. L. Gervasio and M. Parrinello
PLoS ONE 2010, 5 (10), 13208

A model approach to modeling
R. Car and M. Parrinello
Nature Materials 2010, 9 (9), 687

A method to break all barriers
F. Pulizzi and M. Parrinello
Nature Materials 2010, 9 (9), 693

Probing the mechanical properties of hybrid inorganic-organic frameworks: a computational and experimental study
M. Kosa, J.C. Tan, C.A. Merrill, M. Krack, A.K. Cheetham and M. Parrinello
ChemPhysChem 2010, 11 (11), 2332

Displaced path integral formulation for the momentum distribution of quantum particles
L. Lin, J.A. Morrone, R. Car, and M. Parrinello
Phys. Rev. Lett. 2010, 105 (11), 110602

Asprich peptides are occluded in calcite and permanently disorder biomineral crystals
R.A. Metzler, G.A. Tribello, M. Parrinello and P.U.P.A. Gilbert
J. Am. Chem. Soc. 2010, 132, 11585

First principles study of the optical contrast in phase change materials
S. Caravati, M. Bernasconi and M. Parrinello
J. Phys. Condens. Matter 2010, 22, 315801

Probing the mechanism of pH-induced large-scale conformational changes in Dengue virus envelope protein using atomistic simulations
M.K. Prakash, A. Barducci and M. Parrinello
Biophysical Journal 2010, 99, 588-594

Targeting biomolecular flexibility with metadynamics
V. Leone, F. Marinelli, P. Carloni and M. Parrinello
Structural Biology 2010, 20, 148-154

Linking well-tempered metadynamics simulations with experiments
A. Barducci, M. Bonomi and M. Parrinello
Biophysical Journal 2010, 98, L44-L46

Enhanced sampling in the well-tempered ensemble
M. Bonomi and M. Parrinello
J. Phys. Rev. Lett. 2010, 104(19), 190601

Ab initio quality neural-network potential for sodium
H. Eshet, R.Z. Khaliullin, T.D. Kühne, J. Behler and M. Parrinello
J. Phys. Rev. B 2010, 81, 184107

Colored-noise thermostats à la carte
M. Ceriotti, G. Bussi and M. Parrinello
J. Chem. Theory Comput. 2010, 6, 1170-1180

Graphite-diamond phase coexistence study employing a neural-network mapping of the ab-initio potential energy surface
R.Z. Khaliullin, H. Eshet, T.D. Kühne, J. Behler and M. Parrinello
J. Phys. Rev. B 2010, 81, 100103

Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition
V. Limongelli, M. Bonomi, L. Marinelli, F.L. Gervasio, A. Cavalli, E. Novellino and M. Parrinello
PNAS 2010, 107(12), 5411-5416

Signature of tetrahedral Ge in the Raman spectrum of amorphous phase-change materials
R. Mazzarello, S. Caravati, S. Angioletti-Uberti, M. Bernasconi and M. Parrinello
J. Phys. Rev. Lett. 2010, 104, 085503

First-principles study of liquid and amorphous Sb2Te3
S. Caravati, M. Bernasconi and M. Parrinello
J. Phys. Rev. B 2010, 81, 014201

 

2009

Phase selection and energetics in chiral alkaline earth tartrates and their racemic and meso analogues: synthetic, structural, computational and calorimetric studies
L.N. Appelhand, M. Kosa, A.V. Radha, P. Simoncic, A. Navrotsky, M. Parrinello and A.K. Cheetham
J. Am. Chem. Soc. 2009, 131, 15375-15386

Ensemble of transition state structures for the Cis-Trans Isomerization of N-Methylacetamide
Y.A. Mantz, D. Branduardi, G. Bussi and M. Parrinello
J. Phys. Chem. B 2009, 113, 12521-12529

Superionic conduction in substoichiometric LiAl alloy: an Ab initio study
C.S. Cucinotta, G. Miceli, P. Raiteri, M. Krack, T.D. Kühne, M. Bernasconi and M. Parrinello
Phys. Rev. Lett. 2009, 102, 125901

PLUMED: a portable plugin for free-energy calculations with molecular dynamics
M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Donadio, F. Marinelli, F. Pietrucci, R. A. Broglia and M. Parrinello
Comp. Phys. Comm. 2009, 180, 1961-1972

A molecular dynamics study of the early stages of calcium carbonate growth
G. A. Tribello, F. Bruneval, C. C. Liew, M. Parrinello
J. Phys. Chem. B. 2009, 113, 11680-11687

Nuclear quantum effects in solids using a colored-noise thermostat
M. Ceriotti, G. Bussi, M. Parrinello
Phys. Rev. Lett. 2009, 103 (3), 030603

Nucleotide-dependent conformational states of actin
J. Pfaendtner, D. Branduardi, M. Parrinello, T. D. Pollard, G. A. Voth
PNAS 2009, 106 (31), 12723-12728

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics
M. Bonomi, A. Barducci, M. Parrinello
J. Comput. Chem. 2009, 30, 1615-1621

First-principles study of crystalline and amorphous Ge2Sb2Te5 and the effects of stoichiometric defects"
S. Caravati, M. Bernasconi, T.D. Kühne, M. Krack, M. Parrinello
J. Phys.: Condens. Matter 2009, 21, 255501

Unravelling the mechanism of pressure induced amorphization of phase change materials
S. Caravati, M. Bernasconi, T.D. Kühne, M. Krack, M. Parrinello
Phys. Rev. Lett. 2009, 102, 205502

Binding of calcium and carbonate to polyacrylates
G.A. Tribello, C.C. Liew, M. Parrinello
J. Phys. Chem. B 2009, 113, 7081-7085

Protein conformational transitions: the closure mechanism of a kinase explored by atomistic simulations
A. Berteotti, A. Cavalli, D. Branduardi, F.L. Gervasio, M. Recanatini, M. Parrinello
J. Am. Chem. Soc. 2009, 131, 244-250

Langevin equation with colored noise for constant-temperature molecular dynamics simulations
M. Ceriotti, G. Bussi, M. Parrinello
Phys. Rev. Lett. 2009, 102, 020601

Static and dynamical properties of liquid water from first principles by a novel Car-Parrinello-like approach
T.D. Kuehne, M. Krack , M. Parrinello
J. Chem. Theory and Comput. 2009, 5 (2), 235-241

Isothermal-isobaric molecular dynamics using stochastic velocity rescaling
G. Bussi, T Zykova-Timan, M. Parrinello
J. Chem. Phys. 2009, 130, 074101

 

2008

Pressure-induced phase transitions in silicon studied by neural network-based metadynamics simulations
J. Behler, R. Martonak, D. Donadio, M. Parrinello
Phys. Stat. Sol. (b) 2008, 245 (12), 2618-2629

Modeling the hydrogen storage materials with Exposed M2+ Coordination sites
M. Kosa, M. Krack, A.K. Cheetham, M. Parrinello
J. Phys. Chem. C 2008, 112 (42), 16171-16173

Investigating the polymorphism in PR179: a combined crystal structure prediction and metadynamics study
T. Zykova-Timan, P. Raiteri, M. Parrinello
J. Phys. Chem. B 2008, 112, 13231-13237

Vacancy-vacancy interaction and oxygen diffusion in stabilized cubic ZrO2 from first principles
F. Pietrucci, M. Bernasconi, A. Laio, M. Parrinello
Phys. Rev. B 2008, 78, 094301

The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin
M. Bonomi, D. Branduardi, F.L. Gervasio, M. Parrinello
J. Am. Chem. Soc. 2008, 130, 13938-13944

An efficient and accurate decomposition of the Fermi operator
M. Ceriotti, T.D. Kühne, M. Parrinello
J. Chem. Phys. 2008, 129, 024707

New Lennard-Jones metastable phase
H. Eshet, F. Bruneval, M. Parrinello
J. Chem. Phys. 2008, 129, 026101

Conformational changes and gating at the selectivity filter of Potassium channels
C. Domene, M.L. Klein, D. Branduardi, F.L. Gervasio, M. Parrinello
J. Am. Chem. Soc.2008, 130, 9474-9480

Stochastic thermostats: comparison of local and global schemes
G. Bussi, M. Parrinello
Comp. Phys. Comm. 2008, 179, 26-29

Anharmonic infrared and Raman spectra in Car-Parrinello molecular dynamics simulations
M. Pagliai, C. Cavazzoni, G. Cardini, G. Erbacci, M. Parrinello, V. Schettino
J. Chem. Phys. 2008, 128, 224514

DFT research on the Dehydroxylation reaction of Pyrophyllite 1. first-principle molecular dynamics simulations
E. Molina-Montes, D. Donadio, A. Hernandez-Laguna, C.I. Saint-Diaz, M. Parrinello
J. Phys. Chem. B 2008, 112, 7051-7060

Metadynamics simulations of the high-pressure phases of Silicon employing a high-dimensional neural network potential
J. Behler, R. Martonak, D. Donadio, M. Parrinello
Phys. Rev. Lett. 2008, 100, 185501

Unravelling the shuttling mechanism in a photoswitchable multicomponent bistable rotaxane
P. Raiteri, G. Bussi, C.S. Cucinotta, A. Credi, J.F. Stoddart, M. Parrinello
Angew. Chem. Int. Ed. 2008, 47, 3536-3539

HCI Hydrates as model systems for protonated water
V. Buch, A. Dubrovskiy, F. Mohamed, M. Parrinello, J. Sadlej, A.D. Hammerich, J.P. Devlin
J. Phys. Chem. A 2008, 112, 2144-2161

The thermal stability of lattice-energy minima of 5-Fluorouracil: metadynamics as an aid to polymorph prediction
P.G. Karamertzanis, P. Raiteri, M. Parrinello, M. Leslie, S.L. Price
J. Phys. Chem. B 2008, 112, 4298-4308

Influence of temperature and anisotropic pressure on the phase transitions in alpha-Cristobalite
D. Donadio, R. Martonak, P. Raiteri, M. Parrinello
Phys. Rev. Lett. 2008, 100, 165502

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
A. Barducci, G. Bussi, M. Parrinello
Phys. Rev. Lett. 2008, 100, 020603

The role of Li+, Na+, and K+ in the ligand binding inside the human acetylcholinesterase gorge
G. Petraglio, M. Bartolini, D. Branduardi, V. Andrisano, M. Recanatini, F.L. Gervasio, A. Cavalli, M. Parrinello
Proteins 2008, 70, 779-785

 

2007

At the Water's Edge: Nitric Acid as a Weak Acid
E.S. Shamay, V. Buch, M. Parrinello, G.L. Richmond
J. Am. Chem. Soc. 2007, 129, 12910-12911

Molecular Dynamics Study of the Solvation of Calcium Carbonate in Water
F. Bruneval, D. Donadio, M. Parrinello
J. Phys. Chem. B 2007, 111, 12219-12227

Coexistence of tetrahedral- and octahedral-like sites in amorphous phase change materials
S. Caravati, M. Bernasconi, T.D. Kühne, M. Krack, M. Parrinello
Appl. Phys. Lett. 2007, 91, 171906

Insight into the folding inhibition of the HIV-1 protease by a small peptide
M. Bonomi, F.L. Gervasio, G. Tiana, D. Provasi, R.A. Broglia, M. Parrinello
Biophysical J. 2007, 93, 2813-2821

Conjugate gradient heat bath for ill-conditioned actions
M. Ceriotti, G. Bussi, M. Parrinello
Phys. Rev. E 2007, 76, 026707

Solvent effects on charge spatial extent in DNA and implications for transfer
Y.A. Mantz, F.L. Gervasio, T. Laino, M. Parrinello
Phys. Rev. Lett. 2007, 99, 058104

Linear scaling electronic structure Monte Carlo method for metals
F.R. Krajewski, M. Parrinello
Phys. Rev. B 2007, 75, 235108

The conformational free energy landscape of β-D-Glucopyranose. Implications for Substrate Practivation in β-Glucoside Hydrolases
X. Biarnés, a. Ardèvol, A. Planas, C. Rovira, A. Laio, M. Parrinello
J. Am. Chem. Soc. 2007, 129(35), 10686-10693

From four- to six-coordinated silica: Transformation pathways from metadynamics
R. Martonak, D. Donadio, A.R. Oganov, M. Parrinello
Phys. Rev. B 2007, 76, 014120

Energy conservation in adaptive hybrid atomistic/coarse-grain molecular dynamics
B. Ensing, S.O. Nielsen, P.B. Moore, M.L. Klein, M. Parrinello
J. Chem. Theory Comput. 2007, 3, 1100-1105

"Site binding" of Ca2+ ions to polyacrylates in water: a molecular dynamics study of coiling and aggregation
R.E. Bulo, D. Donadio, A. Laio, F. Molnar, J. Rieger, M. Parrinello
Macromolecules 2007, 40, 3437-3442

Accurate sampling using Langevin dynamics
G. Bussi, M. Parrinello
Phys. Rev. E 2007, 75, 056707

The interplay between surface-water and hydrogen bonding in a water adlayer on Pt(111)and Ag(111)
L. Delle Site, L.M. Ghiringhelli, O. Andreussi, D. Donadio, M. Parrinello
J. Phys. Condens. Matter 2007, 19, 242101

Defective pyrite (100) surface: An ab initio study
A. Stirling, M. Bernasconi, M. Parrinello
Phys. Rev. B 2007, 75 (16), 165406

Generalized neural-network representation of high-dimensional ptetntial-energy surfaces
J. Behler, M. Parrinello
Phys. Rev. Lett. 2007, 98 (14), 146401

Ab initio molecular dynamics study of heterogeneous Nitric acid decomposition reactions on graphite surfaces
A. Rodriguez-Fortea, M. Iannuzzi, M. Parrinello
J. Phys. Chem. C 2007, 111 (5), 2251-2258

Charge localisation and hopping in DNA
M. Boero, F.L. Gervasio, M. Parrinello
Molecular Simulation 2007, 33 (1-2), 57-60

Free energy ab initio metadynamics: A new tool for the theoretical study of organometallic reactivity? Example of the C-C and C-H reductive eliminations from platinum (IV) complexes
C. Michel, A. Laio, F. Mohamed, M. Krack, M. Parrinello, A. Milet
Organometallics 2007, 26 (5), 1241-1249

Elusive structure of HCI monohydrate
V. Buch, F. Mohamed, M. Parrinello, J.P. Devlin
J. Chem. Phys. 2007, 126, 074503

Efficient and accurate Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics
T.D. Kühne, M. Krack, F. Mohamed, M. Parrinello
Phys. Rev. Lett. 2007, 98 (6), 066401

From A to B in free energy space
D. Branduardi, F.L. Gervasio, M. Parrinello
J. Chem. Phys. 2007, 126 (5), Art. No. 054103

A new glance at HCI-monohydrate spectroscopy, using on-the-fly dynamics
V. Buch, F. Mohamed, J.P. Devlin, M. Parrinello
J. Chem. Phys. 2007, 126 (2), Art. No. 021102

Charge localization in stacked radical cation DNA base paris and the benzene dimer studied by self-interaction corrected density-functional theory
Y.A. Mantz, F.L. Gervasio, T. Laino, M. Parrinello
J. Phys. Chem. A 2007, 111 (1), 105-112

Canonical sampling through velocity rescaling
G. Bussi, D. Donadio, M. Parrinello
J. Chem. Phys. 2007, 126 (1), Art. No. 014101

 

2006

The amorphous analogs of the crystalline monohydrate of HCI: Structures and spectra
J.P. Devlin, V. Buch. F. Mohamed, M. Parrinello
Chem. Phys. Lett. 2006, 432 (4-6), 462-467

Free-Energy Landscape for Beta Hairpin Folding from Combined Parallel Tempering and Metadynamics
G. Bussi, F.L. Gervasio, A. Laio, M. Parrinello
J. Am. Chem. Soc. 2006, 128, 13435-13441

Stability and Structure of Oligomers of the Alzheimer Peptide ABeta16-22:From the Dimer to the 32-Mer
U.F. Röhrig, A. Laio, N. Tantalo, M. Parrinello, R. Petronzio
Biophysical Journal 2006, 91, 3217-3229

Linear scaling for quasi-one-dimensional systems
F.R. Krajewski, M. Parrinello
Phys. Rev. B, 2006, 74, 125107

Using Metadynamics to Understand the Mechanism of Calmodulin/Target Recognition at Atomic Detail
G. Giorin, A. Pastore, P. Carloni, M. Parrinello
J. Biophys. 2006, 91(8), 2768-2777

Freezing of a Lennard-Jones Fluid: From Nucleation to Spinodal Regime
F. Trudu, D. Donadio, M. Parrinello
Phys. Rev. Lett. 2006, 97(10), 105701

An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations
T. Laino, F. Mohamed, A. Laio, M. Parrinello
J. Chem. Theory Comput. 2006, 2, 1370-1378

Double Proton Coupled Charge Transfer in DNA
F.L. Gervasio, M. Boero, M. Parrinello
Angew. Chem. Int. Ed. 2006, 45(34), 5605-5609

Dissociation Mechanism of Acetic Acid in Water
J.M. Park, A. Laio, M. Iannuzzi, M. Parrinello
J. Am. Chem. Soc. 2006, 128, 11318-11319

Exploring the Gating Mechanism in the CIC Chloride Channel via metadynamics
F.L. Gervasio, M. Parrinello, M. Ceccarelli, M.L. Klein
J. Mol. Biol. 2006, 361, 390-398

Crystal structure transformations in SiO2 from classical and ab initio metadynamics
R. Martonak, D. Donadio, A. R. Oganov and M. Parrinello
Nat. Mat. 2006, 5, 623-626

Non-equilibrium dynamics and structure of interfacial ice
O. Andreussi, D. Donadio, M. Parrinello, A. H. Zewail
Chem. Phys. Lett. 2006, 426(1-3), 115-119

Exploration of NVE classical trajectories as a tool for molecular crystal structure prediction, with tests on ice polymorphs
V. Buch, R. Martonak and M. Parrinello
J. Chem. Phys. 2006, 124, 204705

A QUICKSTEP-based quantum mechanics molecular mechanics approach for silica
F. Zipoli, T. Laino, A. Laio, M. Bernasconi, and M. Parrinello
J. Chem. Phys. 2006, 124, 154707

Equilibrium Free Energies from Nonequilibrium Metadynamics
G. Bussi, A. Laio, and M. Parrinello
Phys. Rev. Lett. 2006, 96, 090601

Ab Initio Molecular Dynamics Study of Heterogeneous Oxidation of Graphite by Means of Gas-Phase Nitric Acid
A. Rodríguez-Fortea, M. Iannuzzi, and M. Parrinello
J. Phys. Chem. B 2006, 110(8), 3477-3484

Efficient Reconstruction of Complex Free Energy Landscapes by Multiple Walkers Metadynamics
P. Raiteri, A. Laio, F. L. Gervasio, C. Micheletti, and M. Parrinello
J. Phys. Chem. B 2006, 110(8), 3533-3539

Metadynamics Simulation of Prion Protein: beta-Structure Stability and the Early Stages of Misfolding
A. Barducci, R. Chelli, P. Procacci, V. Schettino, F. L. Gervasio, and M. Parrinello
J. Am. Chem. Soc. 2006, 128(8), 2705-2710

Linear scaling electronic structure calculations and accurate statistical mechanics sampling with noisy forces
F. R. Krajewski and M. Parrinello
Phys. Rev. B 2006, 73, 041105

Lithium Hydroxide Phase Transition under High Pressure: An Ab Initio Molecular Dynamics Study
M. Pagliai, M. Iannuzzi, G. Cardini, M. Parrinello, V. Schettino
ChemPhysChem 2006, 7(1), 141-147

 

2005

Anisotropy of Earth's D" layer and stacking faults in the MgSiO3 post-perovskite phase
A. R. Oganov, R. Martonak, A. Laio, P. Raiteri and M. Parrinello
Nature 2005, 438, 1142-1144

An efficient real space multigrid QM/MM electrostatic coupling
T. Laino, F. Mohamed, A. Laio, M. Parrinello
J. Chem. Theory Comput. 2005, 1(6), 1176-1184

The Microscopic Switching Mechanism of a [2]Catenane
M. Ceccarelli, F. Mercuri, D. Passerone, and M. Parrinello
J. Phys. Chem. B 2005, 109(36), 17094-17099

A new molecular-dynamics based approach for molecular crystal structure search
V. Buch, R. Martonak, and M. Parrinello
J. Chem Phys. 2005, 123, 051108

Nonperiodic boundary conditions for solvated systems
G. Petraglio, M. Ceccarelli, and M. Parrinello
J. Chem. Phys. 2005, 123, 044103

Stochastic linear scaling for metals and nonmetals
F. R. Krajewski and M. Parrinello
Phys. Rev. B 2005, 71, 233105

beta-Lactone Synthesis from Epoxide and CO: Reaction Mechanism Revisited
A. Stirling, M. Iannuzzi, M. Parrinello, F. Molnar, V. Bernhart, and G.A. Luinstra
Organometallics, 2005, 24(10), 2533-2537

The Role of the Peripheral Anionic Site and Cation-pi Interactions in the Ligand Penetration of the Human AChE Gorge
D. Branduardi, F. L. Gervasio, A. Cavalli, M. Recanatini, and M. Parrinello
J. Am. Chem. Soc. 2005, 127(25), 9147-9155

Exploring Polymorphism: The Case of Benzene
P. Raiteri, R. Martonak, M. Parrinello
Angew. Chem. Int. Ed. 2005, 44(24), 3769-3773

Toward a Monte Carlo program for simulating vapor–liquid phase equilibria from first principles
M. J. McGrath, J. I. Siepmann, I-Feng W. Kuo, C. J. Mundy, J. VandeVondele, M. Sprik, J. Hutter, F. Mohamed, M. Krack and M. Parrinello
Comput. Phys. Comm. 2005, 169(1-3), 289-294

Charge Localization in DNA Fibers
F. L. Gervasio, A. Laio, M. Parrinello, M. Boero
Phys. Rev. Lett. 2005, 94, 158103

Evolution of the structure of amorphous ice: From low-density amorphous through high-density amorphous to very high-density amorphous ice
R. Martonak, D. Donadio, and M. Parrinello
J. Chem. Phys. 2005, 122, 134501

QUICKSTEP: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach
J. VandeVondele, M. Krack, F. Mohamed, M. Parrinello, T. Chassaing and J. Hutter
Comput. Phys. Comm. 2005, 167(2), 103-128

Experimental and computational study of isotopic effects within the Zundel ion
J. P. Devlin, M. W. Severson, F. Mohamed, J. Sadlej, V. Buch and M. Parrinello
Chem. Phys. Lett. 2005, 408(4-6), 439-444

Simulation of structural phase transitions by metadynamics
R. Martonak, A. Laio, M. Bernasconi, C. Ceriani, P. Raiteri, F. Zipoli and M. Parrinello
Z. Kristallogr. 2005, 220(5-6), 489-498

Assessing the Accuracy of Metadynamics
A. Laio, A. Rodriguez-Fortea, F. L. Gervasio, M. Ceccarelli, and M. Parrinello
J. Phys. Chem. B 2005, 109(14), 6714-6721

Topological Defects and Bulk Melting of Hexagonal Ice
D. Donadio, P. Raiteri, and M. Parrinello
J. Phys. Chem. B 2005, 109(12), 5421-5424

A recipe for the Computation of the Free Energy Barrier and the Lowest Free Energy Path of Concerted Reactions
B. Ensing, A. Laio, M. Parrinello, and M. L. Klein
J. Phys. Chem. B 2005, 109(14), 6676-6687

Flexible Docking in Solution Using Metadynamics
F. L. Gervasio, A. Laio, and M. Parrinello
J. Am. Chem. Soc. 2005, 127(8), 2600-2607

The influence of temperature and density functional models in ab initio molecular dynamics simulation of liquid water
J. VandeVondele, F. Mohamed, M. Krack, J. Hutter, M. Sprik, M. Parrinello
J. Chem. Phys. 2005, 122, 014515

 

2004

Solvation states of HCl in mixed ether:acid crystals: A computational study
V. Buch, F. Mohamed, M. Krack, J. Sadley, J. P. Devlin, M. Parrinello
J. Chem. Phys. 2005, 121(24), 12135-12138

Azulene-to-Naphthalene Rearrangement: The Car-Parrinello Metadynamics Method Explores Various Reaction Mechanisms
A. Stirling, M. Iannuzzi, A. Laio, M. Parrinello
ChemPhysChem 2004, 5(10), 1558-1568

Influence of DNA Structure on the Reactivity of the Guanine Radical Cation
F. L. Gervasio, A. Laio, M. Iannuzzi, M. Parrinello
Chem. Eur. J. 2004, 10(19), 4846-4852

Molecular dynamics simulation of reconstructive phase transitions on an anhydrous zeolite
C. Ceriani, A. Laio, E. Fois, A. Gamba, R. Martonak, and M. Parrinello
Phys. Rev. B 2004, 70, 113403

Correlations among Hydrogen Bonds in Liquid Water
P. Raiteri, A. Laio, and M. Parrinello
Phys. Rev. Lett. 2004, 93, 087801

Liquid Water from First Principles: Investigation of Different Sampling Approaches
I-F. W. Kuo, C. J. Mundy, M. J. McGrath, J. I. Siepmann, J. VandeVondele, M. Sprik, J. Hutter, B. Chen, M. L. Klein, F. Mohamed, M. Krack, and M. Parrinello
J. Phys. Chem. B 2004, 108(34), 12990-12998

A Minimum Free Energy Reaction Path for the E2 Reaction between Fluoro Ethane and a Fluoride Ion
B. Ensing, A. Laio, F. L. Gervasio, M. Parrinello, and M. L. Klein
J. Am. Chem. Soc. 2004, 126(31), 9492-9493

Microscopic Mechanism of Antibiotics Translocation through a Porin
M. Ceccarelli, C. Danelon, A. Laio, and M. Parrinello
Biophys. J. 2004, 87(1), 58-64

Reconstructing the Density of States by History-Dependent Metadynamics
C. Micheletti, A. Laio, and M. Parrinello
Phys. Rev. Lett. 2004, 92, 170601

Ab Initio Study of Dehydroxylation-Carbonation Reaction on Brucite Surface
S. V. Churakov, M. Iannuzzi, and M. Parrinello
J. Phys. Chem. B 2004, 108(31), 11567-11574

Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: A new method for force-matching
S. Izvekov, M. Parrinello, C. J. Burnham, and G. A. Voth
J. Chem. Phys. 2004, 120(23), 10896-10913

Polyamorphism of Ice at Low Temperatures from Constant-Pressure Simulations
R. Martonak, D. Donadio, and M. Parrinello
Phys. Rev. Lett. 2004, 92, 225702

Dispersion corrections to density functionals for water aromatic interactions
U. Zimmerli, M. Parrinello, and P. Koumoutsakos
J. Chem. Phys. 2004, 120(6), 2693-2699

Proton Transfer in Heterocycle Crystals
M. Iannuzzi and M. Parrinello
Phys. Rev. Lett. 2004, 93, 025901

Hydrogen Bond Driven Chemical Reactions: Beckmann Rearrangement of Cyclohexanone Oxime into epsilon-Caprolactam in Supercritical Water
M. Boero, T. Ikeshoji, C. C. Liew, K. Terakura, and M. Parrinello
J. Am. Chem. Soc. 2004, 126(20), 6280-6286

Insights into the Electronic Dynamics in Chemical Reactions
D. Aktah, D. Passerone, and M. Parrinello
J. Phys. Chem. A, 2004, 108(5), 848-854

 

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