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Items: 1 to 50 of 306

1.

Temperature Dependence of Homogeneous Nucleation in Ice.

Niu H, Yang YI, Parrinello M.

Phys Rev Lett. 2019 Jun 21;122(24):245501. doi: 10.1103/PhysRevLett.122.245501.

PMID:
31322390
2.

Blind search for complex chemical pathways using Harmonic Linear Discriminant Analysis.

Rizzi V, Mendels D, Sicilia E, Parrinello M.

J Chem Theory Comput. 2019 Jul 17. doi: 10.1021/acs.jctc.9b00358. [Epub ahead of print]

PMID:
31314521
3.

Kinetics of Aqueous Media Reactions via Ab Initio Enhanced Molecular Dynamics: The Case of Urea Decomposition.

Polino D, Parrinello M.

J Phys Chem B. 2019 Jul 9. doi: 10.1021/acs.jpcb.9b05271. [Epub ahead of print]

PMID:
31286763
4.

Calculation of phase diagrams in the multithermal-multibaric ensemble.

Piaggi PM, Parrinello M.

J Chem Phys. 2019 Jun 28;150(24):244119. doi: 10.1063/1.5102104.

PMID:
31255056
5.

Accurate Quantum Chemical Free Energies at Affordable Cost.

Piccini G, Parrinello M.

J Phys Chem Lett. 2019 Jul 5;10(13):3727-3731. doi: 10.1021/acs.jpclett.9b01301. Epub 2019 Jun 21.

PMID:
31244270
6.

Exhaustive Search of Ligand Binding Pathways via Volume-Based Metadynamics.

Capelli R, Carloni P, Parrinello M.

J Phys Chem Lett. 2019 Jun 20;10(12):3495-3499. doi: 10.1021/acs.jpclett.9b01183. Epub 2019 Jun 12.

PMID:
31188006
7.

A local fingerprint for hydrophobicity and hydrophilicity: From methane to peptides.

Pérez-Conesa S, Piaggi PM, Parrinello M.

J Chem Phys. 2019 May 28;150(20):204103. doi: 10.1063/1.5088418.

PMID:
31153166
8.

Chasing the Full Free Energy Landscape of Neuroreceptor/Ligand Unbinding by Metadynamics Simulations.

Capelli R, Bochicchio A, Piccini G, Casasnovas R, Carloni P, Parrinello M.

J Chem Theory Comput. 2019 May 14;15(5):3354-3361. doi: 10.1021/acs.jctc.9b00118. Epub 2019 Apr 4.

PMID:
30913388
9.

Improving collective variables: The case of crystallization.

Zhang YY, Niu H, Piccini G, Mendels D, Parrinello M.

J Chem Phys. 2019 Mar 7;150(9):094509. doi: 10.1063/1.5081040.

PMID:
30849916
10.

Making the Best of a Bad Situation: A Multiscale Approach to Free Energy Calculation.

Invernizzi M, Parrinello M.

J Chem Theory Comput. 2019 Apr 9;15(4):2187-2194. doi: 10.1021/acs.jctc.9b00032. Epub 2019 Mar 13.

PMID:
30822383
11.

Multithermal-Multibaric Molecular Simulations from a Variational Principle.

Piaggi PM, Parrinello M.

Phys Rev Lett. 2019 Feb 8;122(5):050601. doi: 10.1103/PhysRevLett.122.050601.

PMID:
30822009
12.

Enhanced Sampling of Transition States.

Debnath J, Invernizzi M, Parrinello M.

J Chem Theory Comput. 2019 Apr 9;15(4):2454-2459. doi: 10.1021/acs.jctc.8b01283. Epub 2019 Mar 6.

PMID:
30779567
13.

Microscopic description of acid-base equilibrium.

Grifoni E, Piccini G, Parrinello M.

Proc Natl Acad Sci U S A. 2019 Feb 14. pii: 201819771. doi: 10.1073/pnas.1819771116. [Epub ahead of print]

PMID:
30765522
14.

The Onset of Dehydrogenation in Solid Ammonia Borane: An Ab Initio Metadynamics Study.

Rizzi V, Polino D, Sicilia E, Russo N, Parrinello M.

Angew Chem Int Ed Engl. 2019 Mar 18;58(12):3976-3980. doi: 10.1002/anie.201900134. Epub 2019 Feb 18.

PMID:
30689299
15.

Silicon Liquid Structure and Crystal Nucleation from Ab Initio Deep Metadynamics.

Bonati L, Parrinello M.

Phys Rev Lett. 2018 Dec 28;121(26):265701. doi: 10.1103/PhysRevLett.121.265701.

PMID:
30636123
16.

Enhanced Sampling of Protein Conformational Transitions via Dynamically Optimized Collective Variables.

Brotzakis ZF, Parrinello M.

J Chem Theory Comput. 2019 Feb 12;15(2):1393-1398. doi: 10.1021/acs.jctc.8b00827. Epub 2019 Jan 3.

PMID:
30557019
17.

Accelerating the Calculation of Protein-Ligand Binding Free Energy and Residence Times Using Dynamically Optimized Collective Variables.

Brotzakis ZF, Limongelli V, Parrinello M.

J Chem Theory Comput. 2019 Jan 8;15(1):743-750. doi: 10.1021/acs.jctc.8b00934. Epub 2018 Dec 28.

PMID:
30537822
18.

Folding a small protein using harmonic linear discriminant analysis.

Mendels D, Piccini G, Brotzakis ZF, Yang YI, Parrinello M.

J Chem Phys. 2018 Nov 21;149(19):194113. doi: 10.1063/1.5053566.

PMID:
30466286
19.

Combining Metadynamics and Integrated Tempering Sampling.

Yang YI, Niu H, Parrinello M.

J Phys Chem Lett. 2018 Nov 15;9(22):6426-6430. doi: 10.1021/acs.jpclett.8b03005. Epub 2018 Oct 26.

PMID:
30354148
20.

Quantum Symmetry from Enhanced Sampling Methods.

Runeson J, Nava M, Parrinello M.

Phys Rev Lett. 2018 Oct 5;121(14):140602. doi: 10.1103/PhysRevLett.121.140602.

PMID:
30339452
21.

Predicting polymorphism in molecular crystals using orientational entropy.

Piaggi PM, Parrinello M.

Proc Natl Acad Sci U S A. 2018 Oct 9;115(41):10251-10256. doi: 10.1073/pnas.1811056115. Epub 2018 Sep 20.

22.

Metadynamics with Discriminants: A Tool for Understanding Chemistry.

Piccini G, Mendels D, Parrinello M.

J Chem Theory Comput. 2018 Oct 9;14(10):5040-5044. doi: 10.1021/acs.jctc.8b00634. Epub 2018 Sep 26.

PMID:
30222350
23.

Frequency adaptive metadynamics for the calculation of rare-event kinetics.

Wang Y, Valsson O, Tiwary P, Parrinello M, Lindorff-Larsen K.

J Chem Phys. 2018 Aug 21;149(7):072309. doi: 10.1063/1.5024679.

PMID:
30134721
24.

Chemical potential calculations in non-homogeneous liquids.

Perego C, Valsson O, Parrinello M.

J Chem Phys. 2018 Aug 21;149(7):072305. doi: 10.1063/1.5024631.

PMID:
30134712
25.

Molecular dynamics simulations of liquid silica crystallization.

Niu H, Piaggi PM, Invernizzi M, Parrinello M.

Proc Natl Acad Sci U S A. 2018 May 22;115(21):5348-5352. doi: 10.1073/pnas.1803919115. Epub 2018 May 7.

26.

Collective Variables from Local Fluctuations.

Mendels D, Piccini G, Parrinello M.

J Phys Chem Lett. 2018 Jun 7;9(11):2776-2781. doi: 10.1021/acs.jpclett.8b00733. Epub 2018 May 11.

PMID:
29733652
27.

Refining Collective Coordinates and Improving Free Energy Representation in Variational Enhanced Sampling.

Yang YI, Parrinello M.

J Chem Theory Comput. 2018 Jun 12;14(6):2889-2894. doi: 10.1021/acs.jctc.8b00231. Epub 2018 May 11.

PMID:
29715017
28.

A Cannibalistic Approach to Grand Canonical Crystal Growth.

Karmakar T, Piaggi PM, Perego C, Parrinello M.

J Chem Theory Comput. 2018 May 8;14(5):2678-2683. doi: 10.1021/acs.jctc.8b00191. Epub 2018 Apr 4.

PMID:
29589924
29.

A variational conformational dynamics approach to the selection of collective variables in metadynamics.

McCarty J, Parrinello M.

J Chem Phys. 2017 Nov 28;147(20):204109. doi: 10.1063/1.4998598.

PMID:
29195289
30.
31.

Concentration gradient driven molecular dynamics: a new method for simulations of membrane permeation and separation.

Ozcan A, Perego C, Salvalaglio M, Parrinello M, Yazaydin O.

Chem Sci. 2017 May 1;8(5):3858-3865. doi: 10.1039/c6sc04978h. Epub 2017 Mar 20.

32.

Entropy based fingerprint for local crystalline order.

Piaggi PM, Parrinello M.

J Chem Phys. 2017 Sep 21;147(11):114112. doi: 10.1063/1.4998408.

PMID:
28938808
33.

Conformational Entropy as Collective Variable for Proteins.

Palazzesi F, Valsson O, Parrinello M.

J Phys Chem Lett. 2017 Oct 5;8(19):4752-4756. doi: 10.1021/acs.jpclett.7b01770. Epub 2017 Sep 18.

PMID:
28906117
34.

Identifying Slow Molecular Motions in Complex Chemical Reactions.

Piccini G, Polino D, Parrinello M.

J Phys Chem Lett. 2017 Sep 7;8(17):4197-4200. doi: 10.1021/acs.jpclett.7b01889. Epub 2017 Aug 22.

PMID:
28829135
35.

Prion protein β2-α2 loop conformational landscape.

Caldarulo E, Barducci A, Wüthrich K, Parrinello M.

Proc Natl Acad Sci U S A. 2017 Sep 5;114(36):9617-9622. doi: 10.1073/pnas.1712155114. Epub 2017 Aug 21.

36.

Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations.

Salvalaglio M, Tiwary P, Maggioni GM, Mazzotti M, Parrinello M.

J Chem Phys. 2016 Dec 7;145(21):211925. doi: 10.1063/1.4966265.

PMID:
28799374
37.

Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations.

Piaggi PM, Valsson O, Parrinello M.

Phys Rev Lett. 2017 Jul 7;119(1):015701. doi: 10.1103/PhysRevLett.119.015701. Epub 2017 Jul 6.

PMID:
28731736
38.

The impact of methylphenidate and its enantiomers on dopamine synthesis and metabolism in vitro.

Bartl J, Palazzesi F, Parrinello M, Hommers L, Riederer P, Walitza S, Grünblatt E.

Prog Neuropsychopharmacol Biol Psychiatry. 2017 Oct 3;79(Pt B):281-288. doi: 10.1016/j.pnpbp.2017.07.002. Epub 2017 Jul 8.

PMID:
28690202
39.

Novel nonresectional posterior leaflet remodeling approach for minimally invasive mitral repair.

Agnino A, Parrinello M, Panisi P, Anselmi A.

J Thorac Cardiovasc Surg. 2017 Oct;154(4):1247-1249. doi: 10.1016/j.jtcvs.2017.04.076. Epub 2017 May 23. No abstract available.

PMID:
28606395
40.

Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model.

Invernizzi M, Valsson O, Parrinello M.

Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):3370-3374. doi: 10.1073/pnas.1618455114. Epub 2017 Mar 14.

41.

Unbinding Kinetics of a p38 MAP Kinase Type II Inhibitor from Metadynamics Simulations.

Casasnovas R, Limongelli V, Tiwary P, Carloni P, Parrinello M.

J Am Chem Soc. 2017 Apr 5;139(13):4780-4788. doi: 10.1021/jacs.6b12950. Epub 2017 Mar 24.

PMID:
28290199
42.

Nonorgan-specific autoantibodies in HIV-infected patients in the HAART era.

Iordache L, Bengoufa D, Taulera O, Rami A, Lascoux-Combe C, Day N, Parrinello M, Sellier PO, Molina JM, Mahr A.

Medicine (Baltimore). 2017 Mar;96(10):e6230. doi: 10.1097/MD.0000000000006230.

43.

Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations.

Moraca F, Amato J, Ortuso F, Artese A, Pagano B, Novellino E, Alcaro S, Parrinello M, Limongelli V.

Proc Natl Acad Sci U S A. 2017 Mar 14;114(11):E2136-E2145. doi: 10.1073/pnas.1612627114. Epub 2017 Feb 23.

44.

Analyzing and Driving Cluster Formation in Atomistic Simulations.

Tribello GA, Giberti F, Sosso GC, Salvalaglio M, Parrinello M.

J Chem Theory Comput. 2017 Mar 14;13(3):1317-1327. doi: 10.1021/acs.jctc.6b01073. Epub 2017 Feb 8.

PMID:
28121147
45.

Variational Flooding Study of a SN2 Reaction.

Piccini G, McCarty JJ, Valsson O, Parrinello M.

J Phys Chem Lett. 2017 Feb 2;8(3):580-583. doi: 10.1021/acs.jpclett.6b02852. Epub 2017 Jan 17.

PMID:
28071915
46.

Dimer Metadynamics.

Nava M, Palazzesi F, Perego C, Parrinello M.

J Chem Theory Comput. 2017 Feb 14;13(2):425-430. doi: 10.1021/acs.jctc.6b00691. Epub 2017 Jan 10.

PMID:
28005387
47.

New methods: general discussion.

Angulo G, Astumian RD, Beniwal V, Bolhuis PG, Dellago C, Ellis J, Ensing B, Glowacki DR, Hammes-Schiffer S, Kästner J, Lelièvre T, Makri N, Manolopoulos D, Menzl G, Miller TF, Mulholland A, Oprzeska-Zingrebe EA, Parrinello M, Pollak E, Proppe J, Reiher M, Richardson J, Roy Chowdhury P, Sanz E, Schütte C, Shalashilin D, Szabla R, Taraphder S, Tiwari A, Vanden-Eijnden E, Vijaykumar A, Zinovjev K.

Faraday Discuss. 2016 Dec 22;195:521-556. doi: 10.1039/C6FD90075E. No abstract available.

PMID:
27929586
48.

Application to large systems: general discussion.

Althorpe S, Angulo G, Astumian RD, Beniwal V, Bolhuis PG, Brandão J, Ellis J, Fang W, Glowacki DR, Hammes-Schiffer S, Hele TJ, Jónsson H, Lelièvre T, Makri N, Manolopoulos D, Mebel AM, Menzl G, Miller TF, Parrinello M, Piaggi PM, Pollak E, Roy Chowdhury P, Sanz E, Shalashilin D, Skúlason E, Spezia R, Taraphder S.

Faraday Discuss. 2016 Dec 8. [Epub ahead of print] No abstract available.

PMID:
27929584
49.

Hierarchical Protein Free Energy Landscapes from Variationally Enhanced Sampling.

Shaffer P, Valsson O, Parrinello M.

J Chem Theory Comput. 2016 Dec 13;12(12):5751-5757. Epub 2016 Nov 4.

PMID:
27813415
50.

Communication: Role of explicit water models in the helix folding/unfolding processes.

Palazzesi F, Salvalaglio M, Barducci A, Parrinello M.

J Chem Phys. 2016 Sep 28;145(12):121101.

PMID:
27782670

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