Molecular Dynamics Simulation Of DNA-Directed Nanoparticle Self-Assembly And Self-Consistent Field Theory Simulation Of Block Copolymer

Assembly of nanoparticles(NPs)coated with complementary DNA strands leads to novel crystals with nanosized basic units rather than classic atoms,ions or molecules.The DNA-directed nanoparticle(DNA-NP)system provides various applications in medical diagnosis,sensing,data storage,plasmonics,and photovoltaics.The dynamics of DNA hybridization is very important in DNA-programmable nanoparticle crystallization.Here,coarse-grained molecular dynamics(MD)is utilized to explore the structural and dynamic properties of DNA hybridizations for a self-complementary DNA-directed nanoparticle self-assembly system.The hexagonal closepacked(HCP)and close-packed face-centered cubic(FCC)ordered structures are identified for the systems of different grafted DNA chains per nanoparticle,which are in good agreement with the experimental results.Most importantly,the dynamic crystallization processes of DNA hybridizations are elucidated by virtue of the mean square displacement,the percentage of hybridizations,and the lifetime of DNA bonds.The lifetime can be characterized by the DNA dehybridization,which has an exponential form.The lifetime of DNA bonds closely depends on the temperature.A suitable temperature for the DNA-nanoparticle crystallization is obtained in the work.Moreover,a too large volume fraction hinders the self-assembly process due to steric effects.This work provides some essential information for future design of nanomaterials.The assembly process of DNA-NP system is mediated by hybridization of DNA via specific base pairing interaction,and is kinetically linked to the disassociation of DNA duplexes.DNA-level physiochemical quantities,both thermodynamic and kinetic,are key to understanding this process and essential for the design of DNA-NP crystals.The melting transition properties are helpful to judge the thermostability and sensitivity of relative DNA probes or other applications.Three different cases are investigated by changing the linker length and the spacer length on which the melting properties depend using the molecular dynamics method.Melting temperature is determined by sigmoidal melting curves based on hybridization percentage versus temperature and the Lindemann melting rule simultaneously.We provide a computational strategy based on a coarse-grained model to estimate the hybridization enthalpy,entropy and free energy from percentages of hybridizations which are readily accessible in experiments.Importantly,the lifetime of DNA bond dehybridization based on temperature and the activation energy depending on DNA bond strength are also calculated.The simulation results are in good agreement with the theoretical analysis and the present experimental data.Our study provides a good strategy to predict the melting temperature which is important for the DNA-directed nanoparticle system,and bridges the dynamics and thermodynamics of DNA-directed nanoparticle systems by estimating the equilibrium constant from the hybridization of DNA bonds quantitatively.In addition,we studied the influence of chain rigidity on DNA-directed nanoparticle crystallization by molecular dynamics simulation.The results showed that the rigid and flexible chains grafted on nanoparticles can be used to design ordered supramolecular structure,but the mechanisms are different.The system with rigid DNA chains can induce nanoparticles'rearrangement into a body-centered cubic(BCC)lattice due to the DNA hybridization interactions.However,for the flexible chain system,the very low hybridization can even be ignored,yet the nanoparticles can still present BCC arrangement.For rigid chains,DNA binding interactions can induce BCC formation in a very narrow length range and are unfavorable to nanoparticle rearrangement for too long or short chains.The self-consistent field theory is used to explore the equilibrium phase behaviors of linear-dendritic triblock copolymer AB(2g+1-2)C2g+1(g is the generation number of the block B,and Gg is short for AB(2g+1-2)C2g+1)from G1 to G5.Eight phases are found:two-colored lamellar phase,three-colored lamellar phase,hexagonal phase,core shell hexagonal phase,tetragonal phase,core shell tetragonal phase,two interpenetrating tetragonal phase,lamellar phase with beads except disordered phase,by varying the interaction parameters between different blocks,the volume fractions of the blocks and the generation number.While investigating the effect of linear coil length on morphology,we find the longer linear length(fA=0.5)for G1,G2 can be beneficial to form the lamellar phase,however,tend to form hexagonal phase easily with generation number increasing from 3 to 5,and short linear length(fA=0.2)can be better for inducing hexagonal phase from G1 to G5.It becomes more and more difficult to phase separate with generation number increasing from 1 to 5 due to the architectural complexity.However,increasing the interaction parameters is helpful to facilitate phase separation.It is likely to offer new opportunity for designing nanomaterials and applying to template technology by finely controlling the dendron generations,length of the linear chain,interaction parameters of linear-dendritic triblock copolymers.