Zilu Wang

Dynamics of vesicle formation from lipid droplets: Mechanism and controllability

A coarse-grained model developed by Marrink et al. [J. Phys. Chem. B 111, 7812 (2007)] is applied to investigate vesiculation of lipid [dipalmitoylphosphatidylcholine (DPPC)] droplets in water. Three kinds of morphologies of micelles are found with increasing lipid droplet size. When the initial lipid droplet is smaller, the equilibrium structure of the droplet is a spherical micelle. When the initial lipid droplet is larger, the lipid ball starts to transform into a disk micelle or vesicle. The mechanism of vesicle formation from a lipid ball is analyzed from the self-assembly of DPPC on the molecular level, and the morphological transition from disk to vesicle with increasing droplet size is demonstrated. Importantly, we discover that the transition point is not very sharp, and for a fixed-size lipid ball, the disk and vesicle appear with certain probabilities. The splitting phenomenon, i.e., the formation of a disk/vesicle structure from a lipid droplet, is explained by applying a hybrid model of the Helfrich membrane theory. The elastic module of the DPPC bilayer and the smallest size of a lipid droplet for certain formation of a vesicle are successfully predicted.

Kinetics of multicompartment micelle formation by self-assembly of ABC miktoarm star terpolymer in dilute solution

Multicompartment micelles, as novel nanoscopic structures, have great potentialities in the fields of multifunctional nanoreactors and carriers. In this work, multicompartment micelle formation in an initially homogeneous dilute solution of ABC miktoarm star terpolymer is investigated with polymeric external potential dynamics. Apart from the hamburger micelle, toroidal micelle, raspberry micelle, worm micelle and laterally structured vesicle, which have been reported before, three novel morphologies are observed, including laterally structured vesicle with a core, spotted vesicle with a core and segmented cage-like micelle, by varying the concentration of copolymers, the volume fractions of three blocks, the solvophobicity of the solvophobic A and C blocks, and the solvophilicity of the solvophilic B block. The structural stability of the prolate vesicle with alternating ring-shape AC strips is demonstrated using Helfrichs membrane model combining with the strong segregation theory of block copolymers. In the dynamics of vesicle formation, two formation pathways of multicompartment vesicles are found: when the volume fraction of B block is smaller, the formation pathway of vesicles includes nucleation, coalescence and growth; when the volume fraction of B block is larger, the formation process of vesicles only includes nucleation and growth. The formation mechanisms of toroidal and cage-like micelles are also studied in this work. Our simulation results enrich the knowledge of the morphologies of multicompartment micelles and reveal the formation mechanism of complex multicompartment micelles of miktoarm star terpolymer in solution.

Phase transition of a single star polymer: A Wang-Landau sampling study

Star polymers, as an important class of nonlinear macromolecules, process special thermodynamic properties for the existence of a common connecting point. The thermodynamic transitions of a single star polymer are systematically studied with the bond fluctuation model using Wang-Landau sampling techniques. A new analysis method employing the shape factor is proposed to locate the coil-globule (CG) and liquid-crystal (LC) transitions, which shows a higher efficiency and accuracy than the canonical specific heat function. The LC transition temperature is found to obey the identical scaling law as the linear polymers. However, the CG transition temperature shifts towards the LC transition with the increasing of the arm number. The reason is that for the star polymer a lower temperature is needed for the attractive force to overcome the excluded volume effect of the polymer chain because of its high arm density. This work clearly proves the structural distinction of the linear and star polymers can only affect the CG transition while has no influence on the LC transition.

A coarse-grained molecular dynamics – reactive Monte Carlo approach to simulate hyperbranched polycondensation

A coarse-grained molecular dynamics (CG-MD) and reactive Monte Carlo (RMC) hybrid method (CG-MD + RMC) has been developed to investigate the hyperbranched polycondensation of 3,5-bis(trimethylsiloxy)benzoyl chloride to poly(3,5-dihydroxybenzoic acid). The CG force field to describe the formation of the hyperbranched macromolecules has been extracted from all-atom molecular dynamics simulations by the mapping technology of iterative Boltzmann inversion. In the mapping process branched poly(3,5-dihydroxybenzoic acid) in an all-atom description has been employed as a target object to derive the CG force field for hyperbranched polymers. In the RMC simulations, the reactivity ratio of the functional groups has been optimized by fitting experimental data with the iterative dichotomy method (Macromolecules, 2003, 36, 97). Using such a simulation framework, detailed information including the molecular weight, the molecular weight distribution and the branching degree of a specific polymerization process has been derived. Radial distribution functions of the atomistic and coarse-grained systems are in excellent agreement. A good agreement between the present simulations and experiment has been demonstrated, too. Especially, the intramolecular cyclization fraction has been reproduced quantitatively. This work illustrates that the present reactive CG-MD + RMC model can be used for quantitative studies of specific hyperbranched polymerizations.

Phase transition of a single protein-like copolymer chain

Protein-like copolymers (PLCs) are a kind of artificial macromolecule owning protein characteristics. We investigate the general phase transition of a single PLC chain with uniform block structure using a parallel Wang–Landau sampling method. Two typical PLC models, i.e. HP and AB models, are employed to reveal the hydrophobic effect and the phase separation effect for a PLC chain folding in aqueous environments. It is found that the block length m greatly influences the phase transition of PLC. With increasing m, the low energy stable structures for the HP model change from a tube-like aggregation to a tadpole-shape structure, and for the AB model they evolve from a multilayer structure to two separated spheres. When m is very small, the liquid–crystal transition disappears. When m is larger, the AB-PLC shows two first order transitions corresponding to the A and B phase separation transition and the liquid–crystal transition, respectively, while the HP model only shows one first order liquid–crystal transition. We further found that during the freezing of the AB-PLC, the whole chain experiences a special intermediate state where one component is embedded by another component. The result is valuable to design the functional single-molecule devices and next generation nano building blocks using PLCs.

Denaturation and renaturation behaviors of short DNA in a confined space

A deep understanding to the denaturation and renaturation behaviors of DNA in a confined state is fundamentally important to control the self-assembly of DNA in a chamber or channel for various applications. In this report, we study the denaturation and renaturation behaviors of short DNA confined in cylindrical and spherical spaces with the 3-Site-Per-Nucleotide coarse-grained DNA model applying the replica exchange molecular dynamics technology. It is found that as the confinement size decreases, the melting temperature Tm increases and the transition becomes broad. The analysis of the potential of mean force shows that the confinement increases the relative free energy of the denatured state of DNA and decreases the renaturation energy barrier. Besides the denatured and native states, the metastable parallel-stranded structure is also found. The simulation results show that the shapes of the confinement spaces and the short DNA sequences remarkably affect the renaturation behavior. In the cylindrical space, the DNA renaturation changes from random-binding to slithering-binding with the size of the confinement space decreasing. In contrast, the DNA renaturation in the spherical and symmetrical confinement space proceeds through strand binding and rolling. The relationship between the melting temperature and the confinement size, ΔTm/Tm ∼ Rc (-υ), is estimated and the exponential index υ equals about 1.32 and 1.75 in the cylindrical and spherical confinements, respectively. It is further compared with the theoretical result of the rigid rod model and a qualitative agreement with the simulation is achieved.

Dynamics of Micelle Formation from Mixed Lipid Droplets

Amphiphilic lipid molecules can form various micelles depending on not only their molecular composition but also their self‐assembly pathway. In this work, coarse‐grained molecular dynamics simulations have been applied to study the micellization behaviors of mixed dipalmitoylphosphatidylcholine (DPPC)/hexadecylphosphocholine (HPC) droplets. By varying DPPC/HPC composition and the size of lipid droplets, various micelles such as spherical and nonspherical (oblate or prolate) vesicles, disk‐like micelles, double or single ring‐like and worm‐like micelles were observed. It is found that the lipid droplet as an initial state favors forming vesicles and ring‐like micelles due to in situ micellization. Our simulation results demonstrate that using special initial conditions combined with various molecular compositions is an effective way to tune lipid micellar structure.

Mesoscale Simulation of Vesiculation of Lipid Droplets

An implicit solvent coarse-grained (CG) lipid model using three beads to reflect the basically molecular structure of two-tailed lipid is developed. In this model, the nonbonded interaction employs a variant MIE potential and the bonded interaction utilizes a Harmonic potential form. The CG force field parameters are achieved by matching the structural and mechanical properties of dipalmitoylphosphatidylcholine (DPPC) bilayers. The model successfully reproduces the formation of lipid bilayer from a random initial state and the spontaneous vesiculation of lipid bilayer from a disk-like structure. After that, the model is used to systematically study the vesiculation processes of spherical and cylindrical lipid droplets. The results show that the present CG model can effectively simulate the formation and evolution of mesoscale complex vesicles.

Net motion of a charged macromolecule in a ratchet-slit

Hydrodynamic effects in a ratchet channel may produce counterintuitive phenomena. We report herein a net motion investigation of a charged macromolecule in a ratchet-slit under an AC electric field using explicit solvent molecular dynamics. A negative net motion was discovered and complex responses to the slit structure, external electric field and charge distribution were explored. It has been demonstrated that the complex responses originate from the competition among three ratchet forces in the diffusion of macromolecules, i.e. the entropy force, solvent dissipative force and conformation inversion resistance (the first force produces positive net motion, while the other two contribute to the negative net motion together). This new transport mechanism can be applied to developing novel effective techniques for the separation of bio-macromolecules with different charge sequences.

Computer Simulation of Self-Assembly of Disc-Shaped Nanoparticles

Understanding how nanoparticles self-assemble into specific structures is important in biology. The self-assembly structures of disc-shaped nanoparticles are investigated using Gay Berne potential. Through the simulated annealing Monte Carlo simulation under NVT condition, we found that various nanostructures such as nematic phase and isotropic phase are discovered. The formation mechanism of these novel nanostructures is discussed.