214 related articles for article (PubMed ID: 35394775)
1. Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA.
Assenza S; Pérez R
J Chem Theory Comput; 2022 May; 18(5):3239-3256. PubMed ID: 35394775
[TBL] [Abstract][Full Text] [Related]
2. Temperature dependence of DNA elasticity: An all-atom molecular dynamics simulation study.
Zhang Y; He L; Li S
J Chem Phys; 2023 Mar; 158(9):094902. PubMed ID: 36889965
[TBL] [Abstract][Full Text] [Related]
3. Computing the Elastic Mechanical Properties of Rodlike DNA Nanostructures.
Chhabra H; Mishra G; Cao Y; Prešern D; Skoruppa E; Tortora MMC; Doye JPK
J Chem Theory Comput; 2020 Dec; 16(12):7748-7763. PubMed ID: 33164531
[TBL] [Abstract][Full Text] [Related]
4. From rigid base pairs to semiflexible polymers: coarse-graining DNA.
Becker NB; Everaers R
Phys Rev E Stat Nonlin Soft Matter Phys; 2007 Aug; 76(2 Pt 1):021923. PubMed ID: 17930081
[TBL] [Abstract][Full Text] [Related]
5. Martini Coarse-Grained Force Field: Extension to DNA.
Uusitalo JJ; Ingólfsson HI; Akhshi P; Tieleman DP; Marrink SJ
J Chem Theory Comput; 2015 Aug; 11(8):3932-45. PubMed ID: 26574472
[TBL] [Abstract][Full Text] [Related]
6. Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations.
Shi Z; Castro CE; Arya G
ACS Nano; 2017 May; 11(5):4617-4630. PubMed ID: 28423273
[TBL] [Abstract][Full Text] [Related]
7. Mechanical properties of DNA and DNA nanostructures: comparison of atomistic, Martini and oxDNA models.
Naskar S; Maiti PK
J Mater Chem B; 2021 Jun; 9(25):5102-5113. PubMed ID: 34127998
[TBL] [Abstract][Full Text] [Related]
8. An experimentally-informed coarse-grained 3-Site-Per-Nucleotide model of DNA: structure, thermodynamics, and dynamics of hybridization.
Hinckley DM; Freeman GS; Whitmer JK; de Pablo JJ
J Chem Phys; 2013 Oct; 139(14):144903. PubMed ID: 24116642
[TBL] [Abstract][Full Text] [Related]
9. Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence.
Isami S; Sakamoto N; Nishimori H; Awazu A
PLoS One; 2015; 10(12):e0143760. PubMed ID: 26624614
[TBL] [Abstract][Full Text] [Related]
10. Coarse-grained simulation of DNA using LAMMPS : An implementation of the oxDNA model and its applications.
Henrich O; Gutiérrez Fosado YA; Curk T; Ouldridge TE
Eur Phys J E Soft Matter; 2018 May; 41(5):57. PubMed ID: 29748779
[TBL] [Abstract][Full Text] [Related]
11. A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality.
Morriss-Andrews A; Rottler J; Plotkin SS
J Chem Phys; 2010 Jan; 132(3):035105. PubMed ID: 20095755
[TBL] [Abstract][Full Text] [Related]
12. Molecular renormalization group coarse-graining of polymer chains: application to double-stranded DNA.
Savelyev A; Papoian GA
Biophys J; 2009 May; 96(10):4044-52. PubMed ID: 19450476
[TBL] [Abstract][Full Text] [Related]
13. Coarse-grained simulations of RNA and DNA duplexes.
Cragnolini T; Derreumaux P; Pasquali S
J Phys Chem B; 2013 Jul; 117(27):8047-60. PubMed ID: 23730911
[TBL] [Abstract][Full Text] [Related]
14. Coarse-Grained Molecular Dynamics Model of Double-Stranded DNA for DNA Nanostructure Design.
Yagyu H; Lee JY; Kim DN; Tabata O
J Phys Chem B; 2017 May; 121(19):5033-5039. PubMed ID: 28448145
[TBL] [Abstract][Full Text] [Related]
15. Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis.
Liebl K; Drsata T; Lankas F; Lipfert J; Zacharias M
Nucleic Acids Res; 2015 Dec; 43(21):10143-56. PubMed ID: 26464435
[TBL] [Abstract][Full Text] [Related]
16. Chemically accurate coarse graining of double-stranded DNA.
Savelyev A; Papoian GA
Proc Natl Acad Sci U S A; 2010 Nov; 107(47):20340-5. PubMed ID: 21059937
[TBL] [Abstract][Full Text] [Related]
17. The temperature dependence of the helical twist of DNA.
Kriegel F; Matek C; Dršata T; Kulenkampff K; Tschirpke S; Zacharias M; Lankaš F; Lipfert J
Nucleic Acids Res; 2018 Sep; 46(15):7998-8009. PubMed ID: 30053087
[TBL] [Abstract][Full Text] [Related]
18. Coarse-Grained Double-Stranded RNA Model from Quantum-Mechanical Calculations.
Cruz-León S; Vázquez-Mayagoitia A; Melchionna S; Schwierz N; Fyta M
J Phys Chem B; 2018 Aug; 122(32):7915-7928. PubMed ID: 30044622
[TBL] [Abstract][Full Text] [Related]
19. Understanding the Relative Flexibility of RNA and DNA Duplexes: Stretching and Twist-Stretch Coupling.
Bao L; Zhang X; Shi YZ; Wu YY; Tan ZJ
Biophys J; 2017 Mar; 112(6):1094-1104. PubMed ID: 28355538
[TBL] [Abstract][Full Text] [Related]
20. A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment.
Maffeo C; Ngo TT; Ha T; Aksimentiev A
J Chem Theory Comput; 2014 Aug; 10(8):2891-2896. PubMed ID: 25136266
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
