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Dimension-free path-integral molecular dynamics without preconditioning.
Korol R, Rosa-Raíces JL, Bou-Rabee N, Miller TF 3rd. Korol R, et al. J Chem Phys. 2020 Mar 14;152(10):104102. doi: 10.1063/1.5134810. J Chem Phys. 2020. PMID: 32171215
However, an unfortunate property of existing non-preconditioned numerical integration schemes for path-integral molecular dynamics-including essentially all existing ring-polymer molecular dynamics (RPMD) and thermostatted RPMD (T-RPMD) methods-is that for a given MD time step, t …
However, an unfortunate property of existing non-preconditioned numerical integration schemes for path-integral molecular dynamics-including …
Pressure control using stochastic cell rescaling.
Bernetti M, Bussi G. Bernetti M, et al. J Chem Phys. 2020 Sep 21;153(11):114107. doi: 10.1063/5.0020514. J Chem Phys. 2020. PMID: 32962386
The usual recipe is to employ the Berendsen barostat first, which displays a first-order volume relaxation efficient in equilibration but results in incorrect volume fluctuations, followed by a second-order or a Monte Carlo barostat for production runs. In this paper, we i …
The usual recipe is to employ the Berendsen barostat first, which displays a first-order volume relaxation efficient in equilibration but re …
Analyzing and Biasing Simulations with PLUMED.
Bussi G, Tribello GA. Bussi G, et al. Methods Mol Biol. 2019;2022:529-578. doi: 10.1007/978-1-4939-9608-7_21. Methods Mol Biol. 2019. PMID: 31396917
Later parts of the chapter discuss how PLUMED can be used to perform enhanced sampling simulations that introduce simulation biases or multiple replicas of the system and Monte Carlo exchanges between these replicas. This section is then followed by a discussion on how fre …
Later parts of the chapter discuss how PLUMED can be used to perform enhanced sampling simulations that introduce simulation biases or multi …
ARIA-ITALY multidisciplinary consensus on nasal polyposis and biological treatments.
Lombardi C, Asero R, Bagnasco D, Blasi F, Bonini M, Bussi M, Canevari RF, Canonica GW, Castelnuovo P, Cecchi L, Cosmi L, Gelardi M, Heffler E, Indinnimeo L, Landi M, Licari A, Liotta F, Macchi A, Malvezzi L, Marseglia G, Micheletto C, Musarra A, Peroni D, Piacentini G, Poletti V, Richeldi L, Santoni A, Schiappoli M, Senna G, Vaghi A, Villani A, Passalacqua G; ARIA Italia. Lombardi C, et al. World Allergy Organ J. 2021 Nov 1;14(10):100592. doi: 10.1016/j.waojou.2021.100592. eCollection 2021 Oct. World Allergy Organ J. 2021. PMID: 34786034 Free PMC article.
Impact of lymph node ratio and number of lymph node metastases on survival and recurrence in laryngeal squamous cell carcinoma.
Molteni G, Nocini R, Mattioli F, Nakayama M, Dedivitis RA, Mannelli G, Crosetti E, Chiesa-Estomba CM, Sistiaga-Suarez JA, Giordano L, Galli A, Lionello M, Mercante G, Ralli M, Fermi M, Klein-Rodríguez A, Mayo-Yáñez M, Serafini E, Pirola F, Paderno A, Cambria F, Oridate N, Sano D, Boscolo-Rizzo P, Marcuzzo AV, Parrinello G, Marchi F, Saibene AM, Tucciarone M, Viscasillas G, Zeleník K, Ramos DM, Palacios-Garcia J, Tirelli G, Pellini R, Paludetti G, Galli J, Rossi G, De Vincentiis M, Cernea CR, Spriano G, Bussi M, Peretti G, Succo G, Piazza C, Bertolin A, Kowalski LP, Presutti L, Sacchetto A. Molteni G, et al. Head Neck. 2023 Sep;45(9):2274-2293. doi: 10.1002/hed.27471. Epub 2023 Jul 27. Head Neck. 2023. PMID: 37496499
Long-Term Outcome After Out-of-Hospital Cardiac Arrest: An Utstein-Based Analysis.
Baldi E, Compagnoni S, Buratti S, Primi R, Bendotti S, Currao A, Gentile FR, Sechi GM, Mare C, Bertona R, Raimondi Cominesi I, Taravelli E, Fava C, Danzi GB, Oltrona Visconti L, Savastano S; all the Lombardia CARe Researchers. Baldi E, et al. Front Cardiovasc Med. 2021 Dec 15;8:764043. doi: 10.3389/fcvm.2021.764043. eCollection 2021. Front Cardiovasc Med. 2021. PMID: 34977181 Free PMC article.
Metadynamics convergence law in a multidimensional system.
Crespo Y, Marinelli F, Pietrucci F, Laio A. Crespo Y, et al. Phys Rev E Stat Nonlin Soft Matter Phys. 2010 May;81(5 Pt 2):055701. doi: 10.1103/PhysRevE.81.055701. Epub 2010 May 7. Phys Rev E Stat Nonlin Soft Matter Phys. 2010. PMID: 20866290
Metadynamics is a powerful sampling technique that uses a nonequilibrium history-dependent process to reconstruct the free-energy surface as a function of the relevant collective variables s . In Bussi [Phys. Rev. Lett. 96, 090601 (2006)] it is proved that, in a Langevin p …
Metadynamics is a powerful sampling technique that uses a nonequilibrium history-dependent process to reconstruct the free-energy surface as …
Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems.
Fass J, Sivak DA, Crooks GE, Beauchamp KA, Leimkuhler B, Chodera JD. Fass J, et al. Entropy (Basel). 2018 May;20(5):318. doi: 10.3390/e20050318. Epub 2018 Apr 26. Entropy (Basel). 2018. PMID: 30393452 Free PMC article.
Here, we introduce a variant of this near-equilibrium estimator capable of measuring the error in the configuration-space marginal density, validating it against a complex but exact nested Monte Carlo estimator to show that it reproduces the KL divergence with high fidelit …
Here, we introduce a variant of this near-equilibrium estimator capable of measuring the error in the configuration-space marginal density, …
An INCA model for pathogens in rivers and catchments: Model structure, sensitivity analysis and application to the River Thames catchment, UK.
Whitehead PG, Leckie H, Rankinen K, Butterfield D, Futter MN, Bussi G. Whitehead PG, et al. Sci Total Environ. 2016 Dec 1;572:1601-1610. doi: 10.1016/j.scitotenv.2016.01.128. Epub 2016 Feb 11. Sci Total Environ. 2016. PMID: 26875602
Model equations are presented and the new pathogens model has been applied to the River Thames in order to assess total coliform (TC) responses under current and projected future land use. A Monte Carlo sensitivity analysis indicates that the input coliform estimates from …
Model equations are presented and the new pathogens model has been applied to the River Thames in order to assess total coliform (TC) respon …
11 results