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001-es BibID:	BIBFORM031436
035-os BibID:	WOS:000298552800027
Első szerző:	Bernstein, Noam
Cím:	QM/MM simulation of liquid water with an adaptive quantum region / Noam Bernstein, Csilla Várnai, Iván Solt, Steven A. Winfield, Mike C. Payne, István Simon, Mónika Fuxreiter, Gábor Csányi
Dátum:	2012
ISSN:	1463-9076
Megjegyzések:	The simulation of complex chemical systems often requires a multi-level description, in which a region of special interest is treated using a computationally expensive quantum mechanical (QM) model while its environment is described by a faster, simpler molecular mechanical (MM) model. Furthermore, studying dynamic effects in solvated systems or bio-molecules requires a variable definition of the two regions, so that atoms or molecules can be dynamically re-assigned between the QM and MM descriptions during the course of the simulation. Such reassignments pose a problem for traditional QM/MM schemes by exacerbating the errors that stem from switching the model at the boundary. Here we show that stable, long adaptive simulations can be carried out using density functional theory with the BLYP exchange-correlation functional for the QM model and a flexible TIP3P force field for the MM model without requiring adjustments of either. Using a primary benchmark system of pure water, we investigate the convergence of the liquid structure with the size of the QM region, and demonstrate that by using a sufficiently large QM region (with radius 6 angstrom) it is possible to obtain radial and angular distributions that, in the QM region, match the results of fully quantum mechanical calculations with periodic boundary conditions, and, after a smooth transition, also agree with fully MM calculations in the MM region. The key ingredient is the accurate evaluation of forces in the QM subsystem which we achieve by including an extended buffer region in the QM calculations. We also show that our buffered-force QM/MM scheme is transferable by simulating the solvated Cl(-) ion.
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban egyetemen (Magyarországon) készült közlemény
Megjelenés:	Physical chemistry chemical physics. - 14 : 2 (2012), p. 646-656. -
További szerzők:	Várnai Csilla Solt Iván Winfield, Steven Payne, Mike C. Simon István Fuxreiter Mónika (1969-) (kutató vegyész) Csányi Gábor
Internet cím:	Intézményi repozitóriumban (DEA) tárolt változat DOI
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001-es BibID:	BIBFORM117812
035-os BibID:	(WoS)001137383100001 (Scopus)85181941112
Első szerző:	Shanmuga Sundar, Saravanabhavan
Cím:	In vitro study on the inflammatory response of chitosan nanoparticles as a potential siRNA carrier targeting towards osteosarcoma cells / Shanmuga Sundar S., Natarajan Kannan, Zsolt Sarang, Priya Lakshminarayanan Srimathi, Ayyar Manikandan, Anboo Sasikala, Nissapatorn Veeranoot, Jonna Narendranath, Vasanthapalaniappan Kamalakannan, Packirisamy Rajavelu, Dolma Karma Gyurmey
Dátum:	2024
ISSN:	0942-9352
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk
Megjelenés:	Zeitschrift Fur Physikalische Chemie-International Journal Of Research In Physical Chemistry & Chemical Physics. - [Epub ahead of print] (2024). -
További szerzők:	Kannan, Natarajan Sarang Zsolt (1976-) (mikrobiológus) Lakshminarayanan, Srimathi Priya Manikandan, Ayyar Sasikala, Anboo Veeranoot, Nissapatorn Narendranath, Jonna Kamalakannan, Vasanthapalaniappan Rajavelu, Packirisamy Karma, Gyurmey Dolma
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