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.     

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.     

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.     

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     

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.     

Study of the stability of long-range-ordered lamellar structures for directed self-assembly lithography,performed using dissipative particle dynamics

We performed dissipative particle dynamics (DPD) simulations to obtain long-range-ordered lamellar structures for directed self-assembly lithography. The self-assembled structure of diblock copolymers (DBCs) depends on the length of the different blocks and the difference in their solubility parameters. In the DPD simulations, the DBCs were formed from coarse-grained particles, and the difference between the solubility parameters was represented by a repulsion parameter. We examined the phase separation morphology of the DBCs, which were confined using a trench model system. The repulsion parameter for the assembly of the lamellar structures from the DBC particles was chosen from six types of parameters. The orientation of the lamellar structure was controlled by the repulsion parameter that described the repulsion between the particles and the wall of the system. We changed the width of the trench, and examined the probability for the formation of the lamellar structure. The lamellar structure could not be obtained by increasing the width. To increase the probability, we placed a ridge at the centre of the bottom wall. It was found that the presence of the ridge increased the probability for the formation of the long-range-ordered lamellar structures.     

Nanoscale amphiphilic macromolecules as lipoprotein inhibitors: the role of charge and architecture

A series of novel amphiphilic macromolecules composed of alkyl chains as the hydrophobic block and poly(ethylene glycol) as the hydrophilic block were designed to inhibit highly oxidized low density lipoprotein (hoxLDL) uptake by synthesizing macromolecules with negatively charged moieties (ie, carboxylic acids) located in the two different blocks. The macromolecules have molecular weights around 5,500 g/mol, form micelles in aqueous solution with an average size of 20-35 nm, and display critical micelle concentration values as low as 10(-7) M. Their charge densities and hydrodynamic size in physiological buffer solutions correlated with the hydrophobic/ hydrophilic block location and quantity of the carboxylate groups. Generally, carboxylate groups located in the hydrophobic block destabilize micelle formation more than carboxylate groups in the hydrophilic block. Although all amphiphilic macromolecules inhibited unregulated uptake of hoxLDL by macrophages, inhibition efficiency was influenced by the quantity and location of the negatively charged-carboxylate on the macromolecules. Notably, negative charge is not the sole factor in reducing hoxLDL uptake. The combination of smaller size, micellar stability and charge density is critical for inhibiting hoxLDL uptake by macrophages.     

Merging concepts: The role of self-assembly in the development of pollen wall structure

In this article, we analyse established details of exine development from a perspective that favours the integration of self-assembly. We isolate those intervals in development in which genomic control is exercised and offer a number of scenarios, which show how self-assembly can build upon a genetic basis to give rise to the fundamental pollen exine structure. This paper is a synthesis of a new concept and a detailed review of achievements in the field of developmental palynology. It seeks to link what is known regarding development with the liquid crystal realm of colloid chemistry.     

Exine development: the importance of looking through a colloid chemistry ``window'

Most biological construction systems operate within the colloidal dimension. In view of this, it seems reasonable to reassess what is known of the early stages of exine development in the light of a brief excursion into colloid and micelle behaviour. The results of this analysis show remarkable similarity of structures and suggest that almost all of the features seen during early pollen wall development can be easily interpreted using simple, established colloidal principles. This study of exine framework and endexine development offers the possibility that growth of the early exine progresses by successive transitory mesophases of a constrained micellar system. The self-assembling micelle mesophases will all be clearly recognized as constituents of the developing exine. They include spherical, cylindrical, continuous layers of hexagonally-packed cylindrical units and lamellar mesophases which most probably correspond to future granules, columellae, complex columellar (and alveolar) microarchitecture and ``white-line-centred' lamellae. Furthermore, the various types of micelle involved have the potential to perform the functions previously loosely assigned to the exine.     

Atomistic and coarse-grained analysis of double spectrin repeat units: the molecular origins of flexibility

Spectrin is an ubiquitous protein in metazoan cells, and its flexibility is one of the keys to maintaining cellular structure and organization. Both alpha-spectrin and beta-spectrin polypeptides consist primarily of triple coiled-coil modular repeat units, and two important factors that determine spectrin flexibility are the bending flexibility between two consecutive repeat units and the conformational flexibility of individual repeat units. Atomistic molecular dynamics (MD) simulations are used here to study double spectrin repeat units (DSRUs) from the human erythrocyte beta-spectrin (HEbeta89) and the chicken brain alpha-spectrin (CBalpha1617). From the results of MD simulations, a highly conserved Trp residue in the A-helix of most repeat units that has been suggested to be important in conferring stability to the coiled-coil structures is found not to have a significant effect on the conformational flexibility of individual repeat units. Characterization of the bending flexibility for two consecutive repeats of spectrin via atomistic simulations and coarse-grained (CG) modeling indicate that the bending flexibility is governed by the interactions between the AB-loop of the first repeat unit, the BC-loop of the second repeat unit and the linker region. Specifically, interactions between residues in these regions can lead to a strong directionality in the bending behavior of two repeat units. The biological implications of these finding are discussed.     

A theoretical model for the association of amphiphilic transmembrane peptides in lipid bilayers

A theoretical model is proposed for the association of trans-bilayer peptides in lipid bilayers. The model is based on a lattice model for the pure lipid bilayer, which accounts accurately for the most important conformational states of the lipids and their mutual interactions and statistics. Within the lattice formulation the bilayer is formed by two independent monolayers, each represented by a triangular lattice, on which sites the lipid chains are arrayed. The peptides are represented by regular objects, with no internal flexibility, and with a projected area on the bilayer plane corresponding to a hexagon with seven lattice sites. In addition, it is assumed that each peptide surface at the interface with the lipid chains is partially hydrophilic, and therefore interacts with the surrounding lipid matrix via selective anisotropic forces. The peptides would therefore assemble in order to shield their hydrophilic residues from the hydrophobic surroundings. The model describes the self-association of peptides in lipid bilayers via lateral and rotational diffusion, anisotropic lipid-peptide interactions, and peptide-peptide interactions involving the peptide hydrophilic regions. The intent of this model study is to analyse the conditions under which the association of trans-bilayer and partially hydrophilic peptides (or their dispersion in the lipid matrix) is lipid-mediated, and to what extent it is induced by direct interactions between the hydrophilic regions of the peptides. The model properties are calculated by a Monte Carlo computer simulation technique within the canonical ensemble. The results from the model study indicate that direct interactions between the hydrophilic regions of the peptides are necessary to induce peptide association in the lipid bilayer in the fluid phase. Furthermore, peptides within each aggregate are oriented in such a way as to shield their hydrophilic regions from the hydrophobic environment. The average number of peptides present in the aggregates formed depends on the degree of mismatch between the peptide hydrophobic length and the lipid bilayer hydrophobic thickness: The lower the degree of mismatch is the higher this number is. Received: 30 December 1996 / Accepted: 9 May 1997     

Solution conformation of virginiamycin S. III. Patricin A: A further model for cooperative effects of the Pro ring conformation and backbone.

Although the main characteristics of the parent virginiamycin S conformation i.e. a bend of type VI (Lewis, P.N., Momamy, F.A. and Scheraga, H.A. (1973) Biochim. Biophys. Acta 303, 211--229) formed by the Pro-N-MePhe-X-PhGly sequence is still present in patricin A, the substitution of X = pipecolic acid by proline in the latter results in a destabilization of the tertiary structure of the depsipeptide, since two isomeric states of a peptidic bond appear in C2HC13 solution. Addition of +/- 30% (v:v) (C2H3)2SO totally shifts this equilibrium in favor of the major parent isomer. These results completely fit with what is known up to now on the occurrence and structure of turns (Chou and Fasman (1977) J. Mol. Biol. 115,135--175).     

A DNA assembly model of sentence generation

Recent results of corpus-based linguistics demonstrate that context-appropriate sentences can be generated by a stochastic constraint satisfaction process. Exploiting the similarity of constraint satisfaction and DNA self-assembly, we explore a DNA assembly model of sentence generation. The words and phrases in a language corpus are encoded as DNA molecules to build a language model of the corpus. Given a seed word, the new sentences are constructed by a parallel DNA assembly process based on the probability distribution of the word and phrase molecules. Here, we present our DNA code word design and report on successful demonstration of their feasibility in wet DNA experiments of a small scale.