References
1. Xiang H, Lin H, Yu L, Chen Y. Hypoxia-irrelevant photonic
thermodynamic cancer nanomedicine. ACS Nano.2019;13(2):2223-2235.
2. Tila D, Ghasemi S, Yazdani-Arazi SN, Ghanbarzadeh S. Functional
liposomes in the cancer-targeted drug delivery. J. Biomater.
Appl. 2015;30(1):3-16.
3. He Y, Hong C, Li J, Howard MT, Li Y, Turvey ME, Uppu DSSM, Martin JR,
Zhang K, Irvine DJ, Hammond PT. Synthetic charge-invertible polymer for
rapid and complete implantation of layer-by-layer microneedle drug films
for enhanced transdermal vaccination. ACS Nano.2018;12(10):10272-10280.
4. Radha B, Senesi AJ, O’Brien MN, Wang MX, Auyeung E, Lee B, Mirkin CA.
Reconstitutable nanoparticle superlattices. Nano Lett.2014;14(4):2162-2167.
5. Zhang CY, Xiong D, Sun Y, Zhao B, Lin WJ, Zhang LJ. Self-assembled
micelles based on pH-sensitive PAE-g-MPEG-cholesterol block copolymer
for anticancer drug delivery. Int. J. Nanomed. 2014;9:4923-4933.
6. Yoo HS, Park TG. Folate receptor targeted biodegradable polymeric
doxorubicin micelles. J. Controlled Release. 2004;96(2):273-283.
7. Guo XD, Tan JPK, Kim SH, Zhang LJ, Zhang Y, Hedrick JL, Yang YY, Qian
Y. Computational studies on self-assembled paclitaxel structures:
Templates for hierarchical block copolymer assemblies and sustained drug
release. Biomaterials. 2009;30(33):6556-6563.
8. Hu Q, Li H, Wang L, Gu H, Fan C. DNA nanotechnology-enabled drug
delivery systems. Chem. Rev. 2019;119(10):6459-6506.
9. Ha D-H, Islam MA, Robinson RD. Binder-free and carbon-free
nanoparticle batteries: A method for nanoparticle electrodes without
polymeric binders or carbon black. Nano Lett.2012;12(10):5122-5130.
10. Tan HN, Wang W, Yu CY, Zhou YF, Lu ZY, Yan DY. Dissipative particle
dynamics simulation study on self-assembly of amphiphilic hyperbranched
multiarm copolymers with different degrees of branching. Soft
Matter. 2015;11(43):8460-8470.
11. Feng YH, Zhang XP, Zhao ZQ, Guo XD. Dissipative particle dynamics
aided design of drug delivery systems: A review. Mol.
Pharmaceutics. 2020;17(6):1778-1799.
12. Liang L, Fu J, Qiu L. Design of pH-sensitive nanovesicles via
cholesterol analogue incorporation for improving in vivo delivery of
chemotherapeutics. ACS Appl. Mater. Interfaces.2018;10(6):5213-5226.
13. Wang B, Kuo J, Bae SC, Granick S. When Brownian diffusion is not
Gaussian. Nature Mater. 2012;11(6):481-485.
14. Whitehead KA, Langer R, Anderson DG. Knocking down barriers:
advances in siRNA delivery. Nat. Rev. Drug Discov.2009;8(2):129-138.
15. Verma A, Stellacci F. Effect of surface properties on
nanoparticle–cell interactions. Small. 2010;6(1):12-21.
16. Yan Y, Wang Y, Heath JK, Nice EC, Caruso F. Cellular association and
cargo release of redox-responsive polymer capsules mediated by exofacial
thiols. Adv. Mater. 2011;23(34):3916-3921.
17. Li X, Tang Y-H, Liang H, Karniadakis GE. Large-scale dissipative
particle dynamics simulations of self-assembled amphiphilic systems.Chem. Commun. 2014;50(61):8306-8308.
18. Becker OM, Karplus M. Guide to biomolecular simulations. Vol
4: Springer Science & Business Media; 2006.
19. Gupta R, Badhe Y, Mitragotri S, Rai B. Permeation of nanoparticles
across the intestinal lipid membrane: dependence on shape and surface
chemistry studied through molecular simulations. Nanoscale.2020;12(11):6318-6333.
20. Zhang Q, Lin JP, Wang LQ, Xu ZW. Theoretical modeling and
simulations of self-assembly of copolymers in solution. Prog.
Polym. Sci. 2017;75:1-30.
21. Guo XD, Qian Y, Zhang CY, Nie SY, Zhang LJ. Can drug molecules
diffuse into the core of micelles? Soft Matter.2012;8(39):9989-9995.
22. Zheng LS, Yang YQ, Guo XD, Sun Y, Qian Y, Zhang LJ. Mesoscopic
simulations on the aggregation behavior of pH-responsive polymeric
micelles for drug delivery. J. Colloid Interface Sci.2011;363(1):114-121.
23. Xia Q-s, Ding H-m, Ma Y-q. Design strategy of pH-sensitive triblock
copolymer micelles for efficient cellular uptake by computer
simulations. J. Phys. D: Appl. Phys. 2018;51(12):124002.
24. Pivkin IV, Karniadakis GE. Accurate coarse-grained modeling of red
blood cells. Phys. Rev. Lett. 2008;101(11):118105.
25. Wang S, Guo H, Li Y, Li X. Penetration of nanoparticles across a
lipid bilayer: effects of particle stiffness and surface hydrophobicity.Nanoscale. 2019;11(9):4025-4034.
26. Chen L, Li X, Zhang Y, Chen T, Xiao S, Liang H. Morphological and
mechanical determinants of cellular uptake of deformable nanoparticles.Nanoscale. 2018;10(25):11969-11979.
27. Zhang S, Gao H, Bao G. Physical principles of nanoparticle cellular
endocytosis. ACS Nano. 2015;9(9):8655-8671.
28. Wang W, Yang R, Zhang F, Yuan B, Yang K, Ma Y. Partner-facilitating
transmembrane penetration of nanoparticles: a biological test in silico.Nanoscale. 2018;10(24):11670-11678.
29. Huang LY, Yu YS, Lu X, Ding HM, Ma YQ. Designing a
nanoparticle-containing polymeric substrate for detecting cancer cells
by computer simulations. Nanoscale. 2019;11(5):2170-2178.
30. Liu YC, Li SX, Liu XJ, Sun HN, Yue TT, Zhang XR, Yan B, Cao DP.
Design of small nanoparticles decorated with amphiphilic ligands:
Self-preservation effect and translocation into a plasma membrane.ACS Appl. Mater. Interfaces. 2019;11(27):23822-23831.
31. Yang K, Ma Y-Q. Computer simulation of the translocation of
nanoparticles with different shapes across a lipid bilayer. Nature
Nanotech. 2010;5(8):579-583.
32. Groot RD. Electrostatic interactions in dissipative particle
dynamics—simulation of polyelectrolytes and anionic surfactants.J. Chem. Phys. 2003;118(24):11265-11277.
33. Liang J, Chen P, Dong B, Huang Z, Zhao K, Yan L-T. Ligand–receptor
interaction-mediated transmembrane transport of dendrimer-like soft
nanoparticles: Mechanisms and complicated diffusive dynamics.Biomacromolecules. 2016;17(5):1834-1844.
34. Groot RD, Rabone KL. Mesoscopic simulation of cell membrane damage,
morphology change and rupture by nonionic surfactants. Biophys.
J. 2001;81(2):725-736.
35. Kranenburg M, Smit B. Phase behavior of model lipid bilayers.J. Phys. Chem. B. 2005;109(14):6553-6563.
36. Shillcock JC, Lipowsky R. Equilibrium structure and lateral stress
distribution of amphiphilic bilayers from dissipative particle dynamics
simulations. J. Chem. Phys. 2002;117(10):5048-5061.
37. Li X, Gao L, Fang W. Dissipative particle dynamics simulations for
phospholipid membranes based on a four-to-one coarse-grained mapping
scheme. Plos One. 2016;11(5):0154568.
38. Wan MW, Gao LH, Fang WH. Implicit-solvent dissipative particle
dynamics force field based on a four-to-one coarse grained mapping
scheme. Plos One. 2018;13(5).
39. Alexeev A, Uspal WE, Balazs AC. Harnessing Janus nanoparticles to
create controllable pores in membranes. ACS Nano.2008;2(6):1117-1122.
40. Sun C, Sun J, Xiao G, Zhang H, Qiu X, Li H, Chen L. Mesoscale
organization of nearly monodisperse flowerlike ceria microspheres.J. Phys. Chem. B. 2006;110(27):13445-13452.
41. Shillcock JC, Lipowsky R. Tension-induced fusion of bilayer
membranes and vesicles. Nature Mater. 2005;4(3):225-228.
42. Wenwen L, Zhao L, Bing Y, Kai Y. Tail-structure regulated phase
behaviors of a lipid bilayer. Chinese Physics B.2020;29(12):128701.
43. Wong-Ekkabut J, Baoukina S, Triampo W, Tang IM, Tieleman DP,
Monticelli L. Computer simulation study of fullerene translocation
through lipid membranes. Nature Nanotech. 2008;3(6):363-368.
44. Gupta R, Rai B. Effect of size and surface charge of gold
nanoparticles on their skin permeability: A molecular dynamics study.Sci. Rep. 2017;7(1):45292.
45. Dallavalle M, Calvaresi M, Bottoni A, Melle-Franco M, Zerbetto F.
Graphene can wreak havoc with cell membranes. ACS Appl. Mater.
Interfaces. 2015;7(7):4406-4414.
46. Mao J, Guo R, Yan L-T. Simulation and analysis of cellular
internalization pathways and membrane perturbation for graphene
nanosheets. Biomaterials. 2014;35(23):6069-6077.
47. Gao H, Shi W, Freund LB. Mechanics of receptor-mediated endocytosis.Proceedings of the National Academy of Sciences of the United
States of America. 2005;102(27):9469-9474.
48. Deserno M. Elastic deformation of a fluid membrane upon colloid
binding. Phys. Rev. E. 2004;69(3):031903.
49. Ding H-m, Ma Y-q. Interactions between Janus particles and
membranes. Nanoscale. 2012;4(4):1116-1122.
50. Gao X, Dong J, Zhang X. The effect of nanoparticle size on
endocytosis dynamics depends on membrane–nanoparticle interaction.Mol. Simulat. 2015;41(7):531-537.
51. Orsi M, Haubertin DY, Sanderson WE, Essex JW. A quantitative
coarse-grain model for lipid bilayers. J. Phys. Chem. B.2008;112(3):802-815.
52. Huang C, Zhang Y, Yuan H, Gao H, Zhang S. Role of nanoparticle
geometry in endocytosis: Laying down to stand up. Nano Lett.2013;13(9):4546-4550.
53. Chen P, Yue H, Zhai X, Huang Z, Ma G-H, Wei W, Yan L-T. Transport of
a graphene nanosheet sandwiched inside cell membranes. Sci. Adv.2019;5(6):eaaw3192.
54. Xu Z, Gao L, Chen P, Yan L-T. Diffusive transport of nanoscale
objects through cell membranes: a computational perspective. Soft
Matter. 2020;16(16):3869-3881.
55. Gu Y, Sun W, Wang G, Zimmermann MT, Jernigan RL, Fang N. Revealing
rotational modes of functionalized gold nanorods on live cell membranes.Small. 2013;9(5):785-792.
56. Li SX, Luo Z, Xu Y, Ren H, Deng L, Zhang XR, Huang F, Yue TT.
Interaction pathways between soft lipid nanodiscs and plasma membranes:
A molecular modeling study. Biochim. Biophys. Acta, Biomembr.2017;1859(10):2096-2105.
57. Lv K, Li Y. Indentation of graphene-covered atomic force microscopy
probe across a lipid bilayer membrane: Effect of tip shape, size, and
surface hydrophobicity. Langmuir. 2018;34(26):7681-7689.
58. Yi X, Shi X, Gao H. A universal law for cell uptake of
one-dimensional nanomaterials. Nano Lett. 2014;14(2):1049-1055.
59. Li Y, Kroger M, Liu WK. Shape effect in cellular uptake of PEGylated
nanoparticles: comparison between sphere, rod, cube and disk.Nanoscale. 2015;7(40):16631-16646.
60. Chen P, Huang Z, Liang J, Cui T, Zhang X, Miao B, Yan L-T. Diffusion
and directionality of charged nanoparticles on lipid bilayer membrane.ACS Nano. 2016;10(12):11541-11547.
61. Liu B, Goree J. Superdiffusion and non-gaussian statistics in a
driven-dissipative 2D dusty plasma. Phys. Rev. Lett.2008;100(5):055003.
62. Baskaran A, Marchetti MC. Enhanced diffusion and ordering of
self-propelled rods. Phys. Rev. Lett. 2008;101(26):268101.
63. Ji Q-J, Yuan B, Lu X-M, Yang K, Ma Y-Q. Controlling the nanoscale
rotational behaviors of nanoparticles on the cell membranes: A
computational model. Small. 2016;12(9):1140-1146.
64. Zhang LY, Zhao YP, Wang XQ. Nanoparticle-mediated mechanical
destruction of cell membranes: A coarse-grained molecular dynamics
study. ACS Appl. Mater. Interfaces. 2017;9(32):26665-26673.
65. Li Y, Chen X, Gu N. Computational investigation of interaction
between nanoparticles and membranes: Hydrophobic/hydrophilic effect.J. Phys. Chem. B. 2008;112(51):16647-16653.
66. Liang Q. Penetration of polymer-grafted nanoparticles through a
lipid bilayer. Soft Matter. 2013;9(23):5594-5601.
67. Zhang HZ, Ji QJ, Huang CJ, Zhang SL, Yuan B, Yang K, Ma YQ.
Cooperative transmembrane penetration of nanoparticles. Sci. Rep.2015;5:10525.
68. Chen P, Yan L-T. Physical principles of graphene cellular
interactions: computational and theoretical accounts. J. Mater.
Chem. B. 2017;5(23):4290-4306.
69. Pogodin S, Slater NKH, Baulin VA. Surface patterning of carbon
nanotubes can enhance their penetration through a phospholipid bilayer.ACS Nano. 2011;5(2):1141-1146.
70. Lin X, Gu N. Surface properties of encapsulating hydrophobic
nanoparticles regulate the main phase transition temperature of lipid
bilayers: A simulation study. Nano Res. 2014;7(8):1195-1204.
71. Ding H-m, Ma Y-q. Controlling cellular uptake of nanoparticles with
pH-sensitive polymers. Sci. Rep. 2013;3(1):2804.
72. Hao LX, Lin L, Zhou J. pH-responsive zwitterionic copolymer
dha-pblg-pcb for targeted drug delivery: A computer simulation study.Langmuir. 2019;35(5):1944-1953.
73. Shen ZQ, Ye HL, Kroger M, Li Y. Aggregation of polyethylene glycol
polymers suppresses receptor-mediated endocytosis of PEGylated
liposomes. Nanoscale. 2018;10(9):4545-4560.
74. Hu J-m, Tian W-d, Ma Y-q. Computational investigations of
arginine-rich peptides interacting with lipid membranes. Macromol.
Theory Simul. 2015;24(4):399-406.
75. Albanese A, Chan WCW. Effect of gold nanoparticle aggregation on
cell uptake and toxicity. ACS Nano. 2011;5(7):5478-5489.
76. Li Y, Yuan B, Yang K, Zhang X, Yan B, Cao D. Counterintuitive
cooperative endocytosis of like-charged nanoparticles in cellular
internalization: computer simulation and experiment.Nanotechnology. 2017;28(8):085102.
77. Ni S-d, Yin Y-w, Li X-l, Ding H-m, Ma Y-q. Controlling the
interaction of nanoparticles with cell membranes by the polymeric
tether. Langmuir. 2019;35(39):12851-12857.
78. Wang S, Li X, Gong X, Liang H. Mechanistic modeling of spontaneous
penetration of carbon nanocones into membrane vesicles.Nanoscale. 2020;12(4):2686-2694.
79. Yi X, Shi X, Gao H. Cellular uptake of elastic nanoparticles.Phys. Rev. Lett. 2011;107(9):098101.
80. Li Y, Feng DW, Zhang XR, Cao DP. Design strategy of cell-penetrating
copolymers for high efficient drug delivery. Biomaterials.2015;52:171-179.
81. Li JW, Wang JF, Yao Q, Yu K, Yan YG, Zhang J. Cooperative assembly
of Janus particles and amphiphilic oligomers: the role of Janus balance.Nanoscale. 2019;11(15):7221-7228.
82. Guo XD, Zhang LJ, Qian Y. Systematic multiscale method for studying
the structure–performance relationship of drug-delivery systems.Ind. Eng. Chem. Res. 2012;51(12):4719-4730.
83. Xia QS, Ding HM, Ma YQ. Can dual-ligand targeting enhance cellular
uptake of nanoparticles? Nanoscale. 2017;9(26):8982-8989.
84. Guo XD, Zhang LJ, Wu ZM, Qian Y. Dissipative particle dynamics
studies on microstructure of pH-sensitive micelles for sustained drug
delivery. Macromolecules. 2010;43(18):7839-7844.
Figure. 1. Main content of this review. (Some details of this
figure are reused from Reference81 with permission
from The Royal Society of Chemistry, Reference82 with
permission from Copyright © 2012, American Chemical Society,
Reference33 with permission from Copyright © 2016,
American Chemical Society, Reference26 with permission
from The Royal Society of Chemistry, Reference83 with
permission from The Royal Society of Chemistry,
Reference28 with permission from The Royal Society of
Chemistry, Reference64 with permission from Copyright
© 2017, American Chemical Society.)