68
A. Jayaraman et al.
4. Sijbesma RP, Meijer EW (1999) Self-assembly of well-defined structures by hydrogen
bonding. Curr Opin Colloid Interf Sci 4(1):24–32
5. Binder WH, Bouteiller L, Ten Brinke G, Ikkala O, Rotello V, Ruokolainen J, Srivastava S,
Xu H, Zirbs R (2007) Hydrogen bonded polymers, vol 207. Springer, New York
6. Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A (2016) Coarse-grained
protein models and their applications. Chem Rev 116(14):7898–7936
7. Shen T, Gnanakaran S (2009) The Stability of Cellulose: a statistical perspective from a
coarse-grained model of hydrogen-bond networks. Biophys J 96(8):3032–3040
8. Noid W (2013) Perspective: coarse-grained models for biomolecular systems. J Chem Phys
139(9):090901
9. Potoyan DA, Savelyev A, Papoian GA (2013) Recent successes in coarse-grained modeling
of DNA. Wiley Interdisc Rev Comput Mol Sci 3(1):69–83
10. Freeman GS, Hinckley DM, de Pablo JJ (2011) A coarse-grain three-site-per-nucleotide model
for DNA with explicit ions. J Chem Phys 135(16):10B625
11. Hinckley DM, Freeman GS, Whitmer JK, De Pablo JJ (2013) An experimentallyinformed coarse-grained 3-site-per-nucleotide model of DNA: structure, thermodynamics,
and dynamics of hybridization. J Chem Phys 139(14):10B604_1
12. Freeman GS, Hinckley DM, Lequieu JP, Whitmer JK, de Pablo JJ (2014) Coarse-grained
modeling of DNA curvature. J Chem Phys 141(16):10B615_1
13. Šulc P, Romano F, Ouldridge TE, Rovigatti L, Doye JP, Louis AA (2012) Sequence-dependent
thermodynamics of a coarse-grained DNA model. J Chem Phys 137(13):135101
14. Doye JP, Ouldridge TE, Louis AA, Romano F, Šulc P, Matek C, Snodin BE, Rovigatti L, Schreck JS, Harrison RM (2013) Coarse-graining DNA for simulations of DNA
nanotechnology. Phys Chem Chem Phys 15(47):20395–20414
15. Starr FW, Sciortino F (2006) Model for assembly and gelation of four-armed DNA dendrimers.
J Phys Condens Matter 18(26):L347
16. Largo J, Starr FW, Sciortino F (2007) Self-assembling DNA dendrimers: a numerical study.
Langmuir 23(11):5896–5905
17. Lara FV, Starr FW (2011) Stability of DNA-linked nanoparticle crystals I: effect of linker
sequence and length. Soft Matter 7(5):2085–2093
18. Knorowski C, Travesset A (2011) Materials design by DNA programmed self-assembly. Curr
Opin Solid State Mater Sci 15(6):262–270
19. Ghobadi AF, Jayaraman A (2016) Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study. Soft
Matter 12(8):2276–2287
20. Ghobadi AF, Jayaraman A (2016) Effects of polymer conjugation on hybridization thermodynamics of oligonucleic acids. J Phys Chem B 120(36):9788–9799
21. Seifpour A, Dahl SR, Jayaraman A (2014) Molecular simulation study of assembly of DNAgrafted nanoparticles: effect of bidispersity in DNA strand length. Mol Simul 40(14):1085–
1098
22. Seifpour A, Dahl SR, Lin B, Jayaraman A (2013) Molecular simulation study of the assembly
of DNA-functionalised nanoparticles: Effect of DNA strand sequence and composition. Mol
Simul 39(9):741–753
23. Denesyuk NA, Thirumalai D (2013) Coarse-grained model for predicting RNA folding
thermodynamics. J Phys Chem B 117(17):4901–4911
24. Watson JD, Crick FH (1953) Molecular structure of nucleic acids. Nature 171(4356):737–738
25. Liang H, Zhang X-B, Lv Y, Gong L, Wang R, Zhu X, Yang R, Tan W (2014) Functional
DNA-containing nanomaterials: cellular applications in biosensing, imaging, and targeted
therapy. Acc Chem Res 47(6):1891–1901
26. Tjong V, Tang L, Zauscher S, Chilkoti A (2014) Smart DNA interfaces. Chem Soc Rev
43(5):1612–1626
27. Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11(1):31
28. Chmielecki J, Meyerson M (2014) DNA sequencing of cancer: what have we learned? Annu
Rev Med 65:63–79
A. Jayaraman et al.
4. Sijbesma RP, Meijer EW (1999) Self-assembly of well-defined structures by hydrogen
bonding. Curr Opin Colloid Interf Sci 4(1):24–32
5. Binder WH, Bouteiller L, Ten Brinke G, Ikkala O, Rotello V, Ruokolainen J, Srivastava S,
Xu H, Zirbs R (2007) Hydrogen bonded polymers, vol 207. Springer, New York
6. Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A (2016) Coarse-grained
protein models and their applications. Chem Rev 116(14):7898–7936
7. Shen T, Gnanakaran S (2009) The Stability of Cellulose: a statistical perspective from a
coarse-grained model of hydrogen-bond networks. Biophys J 96(8):3032–3040
8. Noid W (2013) Perspective: coarse-grained models for biomolecular systems. J Chem Phys
139(9):090901
9. Potoyan DA, Savelyev A, Papoian GA (2013) Recent successes in coarse-grained modeling
of DNA. Wiley Interdisc Rev Comput Mol Sci 3(1):69–83
10. Freeman GS, Hinckley DM, de Pablo JJ (2011) A coarse-grain three-site-per-nucleotide model
for DNA with explicit ions. J Chem Phys 135(16):10B625
11. Hinckley DM, Freeman GS, Whitmer JK, De Pablo JJ (2013) An experimentallyinformed coarse-grained 3-site-per-nucleotide model of DNA: structure, thermodynamics,
and dynamics of hybridization. J Chem Phys 139(14):10B604_1
12. Freeman GS, Hinckley DM, Lequieu JP, Whitmer JK, de Pablo JJ (2014) Coarse-grained
modeling of DNA curvature. J Chem Phys 141(16):10B615_1
13. Šulc P, Romano F, Ouldridge TE, Rovigatti L, Doye JP, Louis AA (2012) Sequence-dependent
thermodynamics of a coarse-grained DNA model. J Chem Phys 137(13):135101
14. Doye JP, Ouldridge TE, Louis AA, Romano F, Šulc P, Matek C, Snodin BE, Rovigatti L, Schreck JS, Harrison RM (2013) Coarse-graining DNA for simulations of DNA
nanotechnology. Phys Chem Chem Phys 15(47):20395–20414
15. Starr FW, Sciortino F (2006) Model for assembly and gelation of four-armed DNA dendrimers.
J Phys Condens Matter 18(26):L347
16. Largo J, Starr FW, Sciortino F (2007) Self-assembling DNA dendrimers: a numerical study.
Langmuir 23(11):5896–5905
17. Lara FV, Starr FW (2011) Stability of DNA-linked nanoparticle crystals I: effect of linker
sequence and length. Soft Matter 7(5):2085–2093
18. Knorowski C, Travesset A (2011) Materials design by DNA programmed self-assembly. Curr
Opin Solid State Mater Sci 15(6):262–270
19. Ghobadi AF, Jayaraman A (2016) Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study. Soft
Matter 12(8):2276–2287
20. Ghobadi AF, Jayaraman A (2016) Effects of polymer conjugation on hybridization thermodynamics of oligonucleic acids. J Phys Chem B 120(36):9788–9799
21. Seifpour A, Dahl SR, Jayaraman A (2014) Molecular simulation study of assembly of DNAgrafted nanoparticles: effect of bidispersity in DNA strand length. Mol Simul 40(14):1085–
1098
22. Seifpour A, Dahl SR, Lin B, Jayaraman A (2013) Molecular simulation study of the assembly
of DNA-functionalised nanoparticles: Effect of DNA strand sequence and composition. Mol
Simul 39(9):741–753
23. Denesyuk NA, Thirumalai D (2013) Coarse-grained model for predicting RNA folding
thermodynamics. J Phys Chem B 117(17):4901–4911
24. Watson JD, Crick FH (1953) Molecular structure of nucleic acids. Nature 171(4356):737–738
25. Liang H, Zhang X-B, Lv Y, Gong L, Wang R, Zhu X, Yang R, Tan W (2014) Functional
DNA-containing nanomaterials: cellular applications in biosensing, imaging, and targeted
therapy. Acc Chem Res 47(6):1891–1901
26. Tjong V, Tang L, Zauscher S, Chilkoti A (2014) Smart DNA interfaces. Chem Soc Rev
43(5):1612–1626
27. Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11(1):31
28. Chmielecki J, Meyerson M (2014) DNA sequencing of cancer: what have we learned? Annu
Rev Med 65:63–79