Spontaneous self-assembly of diblock copolymers in nanoconfined geometries by dissipative particle dynamics

We performed dissipative particle dynamics (DPD) simulations to reproduce phase separation morphologies of diblock copolymers for directed self-assembly (DSA) lithography. DSA is a promising technique to overcome the current photolithography resolution limit. The Flory–Huggins χ parameter estimated from a small-angle X-ray scattering experiment was used for the DPD simulations owing to the multiple degrees of coarse-graining. The degree of coarse-graining and the bond parameter for the spring force were optimised to represent the experimental result of the number of lamellar layers formed in a trench guide. The DPD simulations using these parameters can also represent the diameter of the central cylinder domain that is formed by phase separation in the cylindrical hole. It was found that the bond parameter considering the spreading of polymer segments in a coarse-grained particle gives good quantitative agreement between the results of the simulations and the experimental data.     

Synthesis and characterization of the biodegradable polycaprolactone-graft-chitosan amphiphilic copolymers

A novel synthetic approach to biodegradable amphiphilic copolymers based on poly (epsilon-caprolactone) (PCL) and chitosan was presented, and the prepared copolymers were used to prepare nanoparticles successfully. The PCL-graft-chitosan copolymers were synthesized by coupling the hydroxyl end-groups on preformed PCL chains and the amino groups present on 6-O-triphenylmethyl chitosan and by removing the protective 6-O-triphenylmethyl groups in acidic aqueous solution. The PCL content in the copolymers can be controlled in the range of 10-90 wt %. The graft copolymers were thoroughly characterized by 1H NMR, 13C NMR, FT-IR and DSC. The nanoparticles made from the graft copolymers were investigated by 1H NMR, DLS, AFM and SEM measurements. It was found that the copolymers could form spherical or elliptic nanoparticles in water. The amount of available primary amines on the surface of the prepared nanoparticles was evaluated by ninhydrin assay, and it can be controlled by the grafting degree of PCL.     

Advancing simulations of biological materials: applications of coarse-grained models on graphics processing unit hardware

The timescales of biological processes, primarily those inherent to the molecular mechanisms of disease, are long (>μs) and involve complex interactions of systems consisting of many atoms (>10⁶). Simulating these systems requires an advanced computational approach, and as such, coarse-grained (CG) models have been developed and highly optimised for accelerator hardware, primarily graphics processing units (GPUs). In this review, I discuss the implementation of CG models for biologically relevant systems, and show how such models can be optimised and perform well on GPU-accelerated hardware. Several examples of GPU implementations of CG models for both molecular dynamics and Monte Carlo simulations on purely GPU and hybrid CPU/GPU architectures are presented. Both the hardware and algorithmic limitations of various models, which depend greatly on the application of interest, are discussed.     

Coarse-grained molecular simulation of self-assembly nanostructures of CTAB on nanoscale graphene

Coarse-grained molecular dynamics simulation has been performed to study the aggregated morphology of the cationic surfactant, cetyltrimethylammonium bromide (CTAB), adsorbed on nanoscale graphene surfaces. The CTAB surfactants can self-assemble on graphene to form various supramolecular morphologies and structures. The effect of packing density, thickness of graphene sheet and width of graphene nanoribbon on the CTAB–graphene self-assembly has been investigated. The buoyant densities of various graphene–CTAB assemblies were calculated, which increase with surfactant coverage and number of graphene layers. This result demonstrates that density gradient can be used to isolate graphenes with various layers. This simulation provides larger-scale microscopic insight into the supramolecular self-assembly nanostructures for the CTAB surfactants aggregated on graphene, which could be valuable to guide fabrication of graphene-based hybrid nanocomposites.     

Development of a simple coarse-grained DNA model for analysis of oligonucleotide complex formation

In this paper, we develop a coarse-grained nucleotide model for the purpose of simulating large-scale aptamer-based hydrogel network formation in future research. In the model, each nucleotide is represented by a single interaction site containing sugar, phosphate and base. Discontinuous molecular dynamics (DMD) simulations are performed to simulate formation and denaturation of oligonucleotide duplexes as a function of temperature. The simulated melting temperatures of oligonucleotide duplexes are calculated in simulations of systems with different sequences, lengths and concentrations of oligonucleotides, and compared to data from the OligoAnalyzer tool. The denaturation of oligonucleotide triplexes containing a hybridised structure of three different oligonucleotides is analysed using both simulations and experiments. The nucleotide model is found to be a good predictor of the oligonucleotide’s hybridised state for both duplexes and triplexes. This coarse-grained model has wide ranging applications in the development or optimisation of DNA-based technologies including DNA origami, DNA-enabled hydrogels and DNA-based biosensors.     

Cationic amphiphilic star and linear block copolymers: synthesis, self-assembly, and in vitro gene transfection

A series of amphiphilic star and linear block copolymers were synthesized using ATRP. The core consisted of either polystyrene (PS) or poly(n-butyl acrylate) (PBuA), having different glass-transition (T(g)) values. These polymers were used as macroinitiators in the polymerization of the cationic 2-(dimethylamino)ethyl methacrylate (DMAEMA). The polymers were used to study the effects of polymer architecture and flexibility on the self-assembling properties, DNA complexation, and transfection. All polymers formed core-shell micelles in aqueous solutions and condensed plasmid DNA. Linear PDMAEMA-PBuA-PDMAEMA has transfection efficiency comparable to PEI25K in ARPE19 cell line. Glassy state of the micellar core and star-shaped architecture decreased the DNA transfection compared with the rubbery and linear polymer structures. The polymers showed low cellular toxicity at low nitrogen/phosphate (n/p) ratios.     

Linking two worlds in polymer chemistry: The influence of block uniformity and dispersity in amphiphilic block copolypeptoids on their self-assembly

The self-assembly of block copolymers has captured the interest of scientists for many decades because it can induce ordered structures and help to imitate complex structures found in nature. In contrast to proteins, nature's most functional hierarchical structures, conventional polymers are disperse in their length distribution. Here, we synthesized hydrophilic and hydrophobic polypeptoids via solid-phase synthesis (uniform) and ring-opening polymerization (disperse). Differential scanning calorimetry measurements showed that the uniform hydrophobic peptoids converge to a maximum of the melting temperature at a much lower chain length than their disperse analogs, showing that not only the chain length but also the dispersity has a considerable impact on the thermal properties of those homopolymers. These homopolymers were then coupled to yield amphiphilic block copolypeptoids. SAXS and AFM measurements confirm that the dispersity plays a major role in microphase separation of these macromolecules, and it appears that uniform hydrophobic blocks form more ordered structures.     

Xyloglucan-based diblock co-oligomer: Synthesis,self-assembly and steric stabilization of proteins

We propose a novel plant-based amphiphilic diblock co-oligomers (BCO) surfactant containing only carbohydrate segments and examine its potential as a biosourced stabilizer. The synthesis of an amphiphilic xyloglucan-based BCO, composed of a hydrophilic xyloglucan oligosaccharide (XGO) block “clicked” to a hydrophobic peracetylated XGO is described. Dynamic light scattering experiments correlated with transmission electron microscopy observations showed that this new class of amphiphilic BCO self-assembles in water to form spherical micelles with a hydrodynamic diameter of 22 nm. Preliminary studies indicate that the XGO-based BCO sterically stabilizes gliadin and zein nanoparticle suspensions. The stabilization results were compared to those using pluronic F-68, a commercial surfactant. For gliadin nanoparticles, both surfactants result in essentially the same morphology and polydispersity. However, for the zein nanoparticles, the XGO-based BCO stabilizer gave lower polydispersity.     

Modelling and simulation of DNA-mediated self-assembly for superlattice design

ABSTRACT

Functionalisation of colloidal particles with DNA provides a powerful and flexible path towards self-assembly of ordered materials. Given the nearly limitless possibilities for constructing DNA-functionalised particles, and the wide range of conditions under which they can be assembled, it is crucial to gain an understanding of the principles governing self-assembly of these particles and how their properties affect the structures produced. A number of computational models for DNA-functionalised systems have successfully described their properties, and molecular simulation techniques have provided a unique insight into the factors underlying their assembly. Here, we discuss a variety of efforts using simulations to solve an important design problem in DNA-mediated assembly: how the properties of individual DNA-functionalised particles affect their interactions with each other, and ultimately how these interactions determine what structures can be produced.     

Spectroscopic study of porphyrin self-assembly: Role of pH,time, and chiral template

In this study, we performed an ultraviolet-visible (UV-Vis) and circular dichroism (CD) spectroscopic analysis of the binary and ternary supramolecular structures formed by self-assembling the following three water-soluble porphyrins with and without a chiral template: the negatively charged, meso-Tetra(4-sulfonatophenyl) porphine (H₂TPPS⁴⁻); the positively charged meso-trans-(di(N-methyl-4-pyridyl)diphenyl) porphine (trans-DmPyDPP) and meso-cis-(di(N-methyl-4-pyridyl)diphenyl) porphine (cis-DmPyDPP). Polyglutamic acid (both L and D enantiomers) was selected as the chiral template due to its ability to change secondary structure with pH. The propensity for the porphyrins to show an induced CD in the presence of polyglutamic acid is demonstrated. The induced chirality of all supramolecular structures was found to depend on the pH of the solution, the chirality of the polymer, and the order of addition of the positively and negatively charged porphyrins (for ternary complexes). Of particular interest is that the interaction of H₂TPPS⁴⁻ with the chiral scaffold seems to undergo a dynamic rearrangement of the supramolecular structure as evident from the change in the CD spectrum over time. Moreover, experiments with ternary complexes suggest that the preferential interaction of trans-DmPyDPP with the random coil of the polymer shows promise as a sensor of protein secondary structure.     

A kinetic model for an autopoietic synthesis of micelles

An improved solvable kinetic model for the autocatalytic production of micelles via the basic hydrolysis of ethyl caprylic ester is presented. A good agreement with the experimental results is obtained, in particular a second observable of the system, the micellar concentration is correctly forseen by the improved model.     

Membrane partitioning of peptide aggregates: coarse-grained molecular dynamics simulations

Abstract

Coarse-grained molecular dynamics (CGMD) simulation technique (MARTINI force field) is applied to monitor the aggregation of helical peptides representing the transmembrane sequence and its extension of bone marrow stromal cell antigen 2 (BST-2). One of the peptides is coupled with a protein transducing domain (PTD) of nine arginine residues (R9) at its N-terminal side as well as a peptide, pep11**, which has been shown to bind to human papilloma virus 16 (HPV16) E6 oncoprotein. A short hydrophobic stretch of the transmembrane domain (TMD) of BST-2 aggregates the fastest and inserts into a lipid membrane. An aggregate of R9-pep11** attaches to the membrane via simultaneous contact of many arginine residues. Monomers from the aggregates of the shortest of the hydrophobic TMDs dissolve into the opposing leaflet when the aggregate spans the bilayer. A ‘flipping’ of the individual monomeric peptides is not observed.

Communicated by Ramaswamy H. Sarma     

A predictive coarse-grained model for position-specific effects of post-translational modifications

Biomolecules undergo liquid-liquid phase separation (LLPS), resulting in the formation of multicomponent protein-RNA membraneless organelles in cells. However, the physiological and pathological role of post-translational modifications (PTMs) on the biophysics of phase behavior is only beginning to be probed. To study the effect of PTMs on LLPS in silico, we extend our transferable coarse-grained model of intrinsically disordered proteins to include phosphorylated and acetylated amino acids. Using the parameters for modified amino acids available for fixed-charge atomistic force fields, we parameterize the size and atomistic hydropathy of the coarse-grained-modified amino acid beads and, hence, the interactions between the modified and natural amino acids. We then elucidate how the number and position of phosphorylated and acetylated residues alter the protein’s single-chain compactness and its propensity to phase separate. We show that both the number and the position of phosphorylated threonines/serines or acetylated lysines can serve as a molecular on/off switch for phase separation in the well-studied disordered regions of Fused in Sarcoma (FUS) and DDX3X, respectively. We also compare modified residues to their commonly used PTM mimics for their impact on chain properties. Importantly, we show that the model can predict and capture experimentally measured differences in the phase behavior for position-specific modifications, showing that the position of modifications can dictate phase separation. In sum, this model will be useful for studying LLPS of post-translationally modified intrinsically disordered proteins and predicting how modifications control phase behavior with position-specific resolution.     

Bioaugmentation of carbofuran residues in soil by Burkholderia cepacia PCL3: A small-scale field study

A small-scale field study was conducted in 1 m × 1.25 m × 20 cm plots. In the soil with only indigenous microorganisms, carbofuran degradation was slow with a long half-life (t_1/2) of 127 d. Bioaugmenting the soil with the immobilized PCL3 could shorten the t_1/2 of carbofuran to 16 d. The t_1/2 rose to a significantly longer 28 d when the free cells of PCL3 were used instead of the immobilized cells. Viable cell counting of carbofuran degraders in soil indicated that the carbofuran degradation efficiency directly correlated to the number of introduced carbofuran degraders that survived in the system. PCL3 in free-cell form did not survive in the soil during the field operation; this suggested that the immobilization of PCL3 is needed in order to implement the bioaugmentation technique in a real environment.     

Refinement of a coarse-grained model of poly(2,6-dimethyl-1,4-phenylene ether) and its application to blends of PPE and PS

A coarse-grained (CG) molecular simulation model has been refined for poly(2,6-dimethyl-1,4-phenylene ether) (PPE). This was successfully validated against atomistic simulation and experimental data. Particularly, the glass transition temperature (T_g) of PPE was studied using both atomistic and CG models and compared favourably to experimental data. In addition, we used the CG model together with an existing Martini CG model of polystyrene (PS) to study the blending behaviour of these two polymers. We solved the problem to mix the different potentials and molecular dynamics of high-molecular-weight blends of PPE/PS was performed in detail.     

Mixed self-assembly of polydiacetylenes for highly specific and sensitive strip biosensors

Polydiacetylenes (PDAs), which possess unique properties that allow them to change color in response to environmental changes such as variations in pH, temperature, and molecular binding, have been widely investigated as signal transducers in biosensor applications. Most PDA-based sensors reported to date have been evaluated largely on the basis of their ability to detect purified samples, however, and their specificity has rarely been tested. In this study, novel PDAs fabricated on polyvinylidene fluoride (PVDF) strips by photoreaction of composite diacetylene self-assemblies were developed as biosensors, and nonspecific binding to off-target biomolecules was assessed. A mixed PDA surface containing biotin and ethanolamide bound the target, i.e., streptavidin, more specifically than did biotin alone. The optimized PDA biosensor exhibited approximately 2850-fold higher selectivity for streptavidin relative to bovine serum albumin controls. A PDA biosensor that was further prepared showed distinctive signals for the urine of diabetic patients compared to urine samples from healthy/non-diabetic person due to the concentration of microalbuminuria. To our knowledge, this is the first strip-type biosensor fabricated with PDAs and the first PDA-based biosensor that can effectively overcome the problem of nonspecific binding.     

Preparation, stability, and in vitro performance of vesicles made with diblock copolymers

Vesicles made completely from diblock copolymers-polymersomes-can be stably prepared by a wide range of techniques common to liposomes. Processes such as film rehydration, sonication, and extrusion can generate many-micron giants as well as monodisperse, approximately 100 nm vesicles of PEO-PEE (polyethyleneoxide-polyethylethylene) or PEO-PBD (polyethyleneoxide-polybutadiene). These thick-walled vesicles of polymer can encapsulate macromolecules just as liposomes can but, unlike many pure liposome systems, these polymersomes exhibit no in-surface thermal transitions and a subpopulation even survive autoclaving. Suspension in blood plasma has no immediate ill-effect on vesicle stability, and neither adhesion nor stimulation of phagocytes are apparent when giant polymersomes are held in direct, protracted contact. Proliferating cells, in addition, are unaffected when cultured for an extended time with an excess of polymersomes. The effects are consistent with the steric stabilization that PEG-lipid can impart to liposomes, but the present single-component polymersomes are far more stable mechanically and are not limited by PEG-driven micellization. The results potentiate a broad new class of technologically useful, polymer-based vesicles.