Computational Soft Nanotechnology with Mesodyn

The simulation of microstructures on a scale 1–1000?nm is a typical problem in colloid and polymer science, and this is also the realm of modern computational “soft nanotechnology”. Accordingly, computational methods rely heavily on time-honoured approaches for calculating the thermodynamical stability of complex mixtures. We describe such approaches in the framework of MesoDyn, a general purpose software package for field-based simulations methods, such as the polymer mean-field model for microphase formation and the Poisson–Boltzmann model for electrostatic interactions. The paper concludes with a small review of examples of application: the formation of microscopic structures in block copolymer bulk solutions, block copolymer melt structures on surfaces (thin films) and structure formation in tiny polymer surfactant droplets (polymersomes). The method works quite well in all cases where a mean-field model is appropriate, but it is a challenge to extend the simulations to systems in which specific correlations are important.     

Ecosystem spatial self-organization: Free order for nothing?

Ecosystems are complex adaptive systems (CAS) by nature, which means that macroscopic patterns and properties emerge from, and feed back to affect, the interactions among adaptive individual ecological agents. These agents then further adapt (genetically) to the outcomes of those interactions. The concept of self-organization has become increasingly important for understanding ecosystem spatial heterogeneity and its consequences. It is well accepted that ecosystems can self-organize, and that resulting spatial structures carry functional consequences. Feedbacks from the outcome of spatial pattern to the individual agents from which patterns emerge, are an essential component of the definition of CAS but have been rarely examined for ecosystems. We explore whether spatial self-organization provides a mechanism for such feedback for ecosystems as CAS, that is, whether ecosystem-level outcomes of self-organized patterning could feed back to affect or even reinforce local pattern-forming processes at the agent level. Diffuse feedbacks of ecological and evolutionary significance ensue as a result of spatial heterogeneity and regular patterning, whether this spatial heterogeneity results from an underlying template effect or from self-organization. However, feedbacks directed specifically at pattern-forming agents to enhance pattern formation—reinforcing feedback—depend upon the level of organization of agents. Reinforcing evolutionary feedbacks occur at the individual level or below. At the ecosystem level, evidence for mechanisms of feedback from outcomes to patterning to agents forming the patterning remain tenuous. Spatial self-organization is a powerful dynamic in ecosystem and landscape science but feedbacks have been only loosely integrated so far. Self-organized patterns influencing dynamics at the ecosystem level represent “order for free”. Whether or not this free order generated at the ecosystem level carries evolutionary function or is merely epiphenomenal is a fundamental question that we address here.     

Mesoscale Modelling

Abstract

Increasingly, industrial materials are being designed to have structure on length scales of tens to thousands of nanometers. These structures are crucial to achieving a particular desired material property. Such structures, however, may depend on the underlying chemistry of the material for their existence. For example, a thousandfold increase in the ionic conductivity of a polymer blend may only occur in a narrow region of a hugely complex phase diagram, the location' of which region can be expected to depend on the molecular chemistry and physics from the monomer scale to the coil size.

Traditional Computational Chemistry has proved incapable of dealing with the length and time scales involved in the formation of these ‘Mesoscale’ structures. On the other hand, traditional Computational Physics has proved incapable of consistently incorporating the necessary chemical detail for modelling real industrial materials. In this paper we present two novel methods which successfully address both the chemistry and the physics of mesophase formation. The methods, described in detail, are MesoDyn and Dissipative Particle Dynamics (DPD).

Unlike phenomenological theories of materials, such as the Landau models which one finds in much of the computational physics literature, the two models mentioned incorporate molecular geometry and connectivity explicitly. We discuss each of the methods briefly.

We then give an overview of how these methods are being used in industry to optimise materials and processes. We discuss previous simulation results for triblock Pluronic surfactants in solution studied with MesoDyn, and for diblock copolymers studied with DPD, where the known experimental changes in morphology from micellar to hexagonal to bicontinuous to lamellar have been successfully reproduced. We also present new results for several systems, including binary and ternary blends, where the third component in the latter system is a diblock copolymer, which acts as a compatibiliser. We discuss the effects of changing solvent character on the material properties of these systems, as well as the effects of an externally imposed shear flow.     

Development of Direct Grafting on Cyclic Olefin Copolymers to Improve Hydrophilicity by Using Bioactive Polymers

ObjectivesTo improve the hydrophilicity of cyclic olefin copolymer, a simple and rapid method using two-stage with ultraviolet irradiation was developed in order to graft a bioactive polymer on the surface of these polymers.Materials and MethodsA bioactive polymer, poly(sodium styrene sulfonate) was grafting in two steps on the cyclic olefin copolymer surface. The process consists to activate the surface with ozone and grafting to under UV irradiation in presence of sodium styrene sulfonate. The presence of polymer on the surfaces was characterized by water contact angle, Fourier transform infrared spectroscopy, scanning electron microscopy with energy dispersive spectroscopy and the quantity of polymer grafted was determined by a colorimetric method.ResultsFirst, the time of UV irradiation for the grafting was studied. The results showed that the maximum grafting rate is reached after 60 minutes of reaction. Second, the influence of the presence of additive on the grafting was investigated. The degree of grafting is significantly reduced compared to a sample without additive.ConclusionWe have developed a simple and fast method to graft a hydrophilic and bioactive polymer covalently to a COC surface.     

Development of Spatial Distribution Patterns by Biofilm Cells

Confined spatial patterns of microbial distribution are prevalent in nature, such as in microbial mats, soil communities, and water stream biofilms. The symbiotic two-species consortium of Pseudomonas putida and Acinetobacter sp. strain C6, originally isolated from a creosote-polluted aquifer, has evolved a distinct spatial organization in the laboratory that is characterized by an increased fitness and productivity. In this consortium, P. putida is reliant on microcolonies formed by Acinetobacter sp. C6, to which it attaches. Here we describe the processes that lead to the microcolony pattern by Acinetobacter sp. C6. Ecological spatial pattern analyses revealed that the microcolonies were not entirely randomly distributed and instead were arranged in a uniform pattern. Detailed time-lapse confocal microscopy at the single-cell level demonstrated that the spatial pattern was the result of an intriguing self-organization: small multicellular clusters moved along the surface to fuse with one another to form microcolonies. This active distribution capability was dependent on environmental factors (carbon source and oxygen) and historical contingency (formation of phenotypic variants). The findings of this study are discussed in the context of species distribution patterns observed in macroecology, and we summarize observations about the processes involved in coadaptation between P. putida and Acinetobacter sp. C6. Our results contribute to an understanding of spatial species distribution patterns as they are observed in nature, as well as the ecology of engineered communities that have the potential for enhanced and sustainable bioprocessing capacity.     

Incorporation of Sulfonylurea into N-Isopropylacrylamide as an Extracellular Matrix for an Artificial Pancreas

High-molecular-weight N-isopropylacrylamide copolymers with small amounts of sulfonylurea (SU, typically 2-4 mol% in the feed) were synthesized by free radical polymerization in benzene. SU-incorporated polymer solutions (5, 6, 8, and 10% w/v) in a culture medium (pH 7.4, 0.15 M ionic strength) with islet cells were mixed and poured into Millicells which supported gel formation. In order to increase the gelation temperature, the SU-incorporated copolymer gel, p(NiPAAm-co-SU), was blended with the p(NiPAAm-co-AAc) polymer at a ratio of 4 to 96. Interaction between the islet cells and the synthetic matrix of SU-incorporated copolymer gel resulted in effective cell viability and such cell functions as insulin secretion. To verify the specific interaction between the SU (K⁺ channel closer)-incorporated copolymer and islet cells, the cells were pretreated with diazoxide, an agonist of the ATP-sensitive K⁺ channel (K⁺ channel opener), before interaction between the polymer and islet cells. This treatment suppressed the action of SU on the islet cells. The results from this study provide evidence that the SU-incorporated copolymer stimulated insulin secretion by specific interaction between SU moieties in the polymer and the islet cells.     

Modeling of Selforganizing Systems

The concept of self-assembly developed for the construction of topologically complex molecules such as [2]-catenanes and rotaxanes is based on non-covalent interactions between constituent parts. High product yields are explained by favourable orientations of intermediates. These intermediates are found to be 2 - 9 kcal/mol lower in energy than the reactand ground states and the recognition process could be reproduced by semiempirical calculations using the PM3 Hamiltonian. Cyclobis(paraquat-p-phenylene) (1 ⁴⁺), which is known for its extraordinary capability to form charge-transfer complexes, plays an important role. The conformational analysis of the hypersurface of (1 ⁴⁺) and other compounds was performed using the MM2 force field. The concept of self-organization uses electron accepting hosts like 1 ⁴⁺ as well as donating hosts like crown ethers. Therefore the study was extended on donating hosts and on their capability to form catenanes. These very interesting compounds show stabilization energies of about 36 kcal/mol. Electronic Supplementary Material available.     

Dissipative particle dynamics simulation of the soft micro actuator using polymer chain displacement in electro-osmotic flow

ABSTRACT

In this research, the numerical simulation of a soft polymer micro actuator performance has been investigated using the dissipative particle dynamics method in electro-osmotic flow. Effective factors including electro-osmotic flow and polymer chain parameters have been studied. First of all, considering a wide range of electro-osmotic parameters, the validation of analytical results is carried out in a simple micro channel. The electric field and zeta potential changes are linearly related to the flow rate, and the kh parameter behaves nonlinearly to around the kh?=?10. In the following, a convergent–divergent channel is used for the soft micro actuator simulation in which a polymer chain as a heart of actuation is embedded in the middle. As the main control parameter, the direction of the electric field is changed every 4?s, and it leads to a reciprocating motion. The numerical results indicate that the displacement of the soft polymer chain will be increased by enhancing the electric field, the number of beads, decreasing the harmonic bond coefficient and also exposing more length of a polymer chain in front of fluid flow. The results of this study may be useful for some future applications such as artificial fibres and muscles.     

Comb-Type Copolymers for Controlled DNA Delivery

Abstract

Various comb-type copolymer containing a polycation as a main chain was design to construct delivery systems of DNAs. The comb-type copolymers having cell-specific polysaccharides were proved to be useful to deliver DNA to the target cells in vivo. Of interest, the copolymers with abundant side chains of hydrophilic polymers are capable of stabilizing DNA triplex. Further, injectable nanoparticles for controlled releases of DNAs were fabricated from the copolymer and a biodegradable polymer.     

Nanostructuring of Continuous Gold Film by Laser Radiation Under Surface Plasmon Polariton Resonance Conditions

The physical mechanisms of metallic nanoparticles formation by laser technology were studied. The system air/Au film/glass was irradiated by laser at the conditions of surface plasmon resonance. A surface electromagnetic wave was excited in Kretchmann configuration by the fundamental and second harmonics of the Q-switched YAG/Nd⁺³ laser with pulse power density close to the threshold of melting. Nanostructuring of Au film was observed only for the second harmonic (λ = 0.532 μm) irradiation at the surface plasmon polariton resonance (SPR) conditions. Estimations were done using the interference model of the differently directed plasmon polariton waves excited by a surface electromagnetic wave on the metal surface. It was shown that a regular pattern of locally heated spots can be formed in a metallic film by pulsed laser irradiation. The spatial distribution of this pattern is close to the period of interference. The observed effect of laser nanofragmentation is explained by the self-organization of plasmon polariton subsystem in the process of Au nanoparticles formation at high laser intensity levels. These methods open new possibilities for nanostructured surfaces formation utilizing simple self-organization processes.     

Chondrogenic properties of human periosteum-derived progenitor cells (PDPCs) embedded in a thermoreversible gelation polymer (TGP)

Periosteum-derived progenitor cells (PDPCs) were isolated using a fluorescence-activated cell sorter and their chondrogenic potential in biomaterials was investigated for the treatment of defective articular cartilage as a cell therapy. The chondrogenesis of PDPCs was conducted in a thermoreversible gelation polymer (TGP), which is a block copolymer composed of temperature-responsive polymer blocks such as poly(N-isopropylacrylamide) and of hydrophilic polymer blocks such as polyethylene oxide, and a defined medium that contained transforming growth factor-β3 (TGF-β3). The PDPCs exhibited chondrogenic potential when cultured in TGP. As the PDPCs-TGP is an acceptable biocompatible complex appropriate for injection into humans, this product might be readily applied to minimize invasion in a defected knee.     

Synthesis of 3-hydroxybutyrate-CO-4-hydroxybutyrate copolymers by hydrogen-oxidizing bacteria

Synthesis of 3- and 4-hydroxybutyrate copolymer (3HB-co-4HB), the most promising member of the biodegradable polyhydroxyalkanoate (PHA) family, has been studied. Cultivation conditions of naturally occurring strains of hydrogen-oxidizing bacteria Ralstonia eutropha B5786 and Cupriavidus eutrophus B10646 have been optimized to ensure efficient synthesis of the 3HB-co-4HB copolymer. A set of highly pure samples of the 3HB-co-4HB copolymer with 4HB content varying from 8.7 to 24.3 mol% has been obtained. Incorporation of 4HB into the copolymer was shown to cause a more pronounced decrease in polymer crystallinity than the incorporation of 3-hydroxyvalerate or 3-hydroxyhexanoate; samples with a degree of crystallinity below 30% have been obtained. The weight average molecular mass of the 3HB-co-4HB copolymers was shown to be independent on the monomer ratio and to vary broadly (from 540 to 1110 kDa).     

Quantum-Chemical Analysis of C-H…O and C-H…N Interactions in RNA Base Pairs—H-Bond Versus Anti-H-Bond Pattern

Abstract

Geometries and interaction energies of unusual UU and AA base pairs with one standard hydrogen bond (H-bond) and additional C-H…O or C-H…N contacts have been determined by quantum-chemical methods taking into account electron correlation. Whereas the C-H bond length in the UU C-H…O contact increases upon complex formation (H-bond pattern), the C-H bond of the AA C-H….N interaction is shortened (anti-H-bond pattern). The same properties are found for model complexes between U or A and formaldehyde that have intermolecular C-H…acceptor contacts but no standard H-bonds. Both the C-H…acceptor H-bond and anti-H-bond interactions are attractive. A possible influence of the donor CH group charge distribution on the interaction pattern is discussed.     

Enzymatic Degradation of GlycosaminogIycans

Abstract

Glycosarninoglycans (GAGs) play an intricate role in the extracellular matrix (ECM), not only as soluble components and polyelectrolytes, but also by specific interactions with growth factors and other transient components of the ECM. Modifications of GAG chains, such as isomerization, sulfation, and acetylation, generate the chemical specificity of GAGs. GAGS can be depolymerized enzymatically either by eliminative cleavage with lyases (EC 4.2.2.-) or by hydrolytic cleavage with hydrolases (EC 3.2.1.-). Often, these enzymes are specific for residues in the polysaccharide chain with certain modifications. As such, the enzymes can serve as tools for studying the physiological effect of residue modifications and as models at the molecular level of protein-GAG recognition. This review examines the structure of the substrates, the properties of enzymatic degradation, and the enzyme substrate-interactions at a molecular level. The primary structure of several GAGS is organized macro-scopicallyby segregation into alternating blocks of specific sulfation patterns and microscopicallyby formation of oligosaccharide sequences with specific binding functions. Among GAGs, considerable dermatan sulfate, heparin and heparan sulfate show conformational flexibility in solution. They elicit sequence-specific interactions with enzymes that degrade them, as well as with other proteins, however, the effect of conformational flexibility on protein-GAG interactions is not clear. Recent findings have established empirical rules of substrate specificity and elucidated molecular mechanisms of enzyme-substrate interactions for enzymes that degrade GAGs. Here we propose that local formation of polysaccharide secondary structure is determined by the immediate sequence environment within the GAG polymer, and that this secondary structure, in turn, governs the binding and catalytic interactions between proteins and GAGs.     

Deep Energetic Trap States in Organic Photovoltaic Devices

The nature of energetic disorder in organic semiconductors is poorly understood. In photovoltaics, energetic disorder leads to reductions in the open circuit voltage and contributes to other loss processes. In this work, three independent optoelectronic methods were used to determine the long‐lived carrier populations in a high efficiency N‐alkylthieno[3,4‐c]pyrrole‐4,6‐dione (TPD) based polymer: fullerene solar cell. In the TPD co‐polymer, all methods indicate the presence of a long‐lived carrier population of ～ 10¹⁵ cm^?3 on timescales ≥ 100 μs. Additionally, the behavior of these photovoltaic devices under optical bias is consistent with deep energetic lying trap states. Comparative measurements were also performed on high efficiency poly‐3‐hexylthiophene (P3HT): fullerene solar cells; however a similar long‐lived carrier population was not observed. This observation is consistent with a higher acceptor concentration (doping) in P3HT than in the TPD‐based copolymer.     

The use of Hydrophobic Dye Molecules in Monitoring the Liposome Bilayer Microenvironment and Locating Block Copolymers Added to Enhance Liposome Steric Stability

Abstract

The dispersion of soybean lecithin in water leads to the formation of multilamellar vesicles (MLVs), which on sonication (4hrs approx.) break down to small unilamellar vesicles of ～ 50nm diameter. The addition of polymeric molecules in the liposomal system provides increased steric stabilization. The molecules used were (tri-)block copolymers (Synperonics) containing a central hydrophobic part (polypropylene oxide-PPO) and two hydrophillic chains (polyethylene oxide-PEO) extending from either side. The interaction of these molecules with the vesicle bilayer is thought to be of upmost importance to the mechanical stress, thermodynamic restrictions and steric stability that may be induced. The exact localisation of the copolymer molecules was attempted using a multiprobe technique. The full spectrum of two hydrophobic dyes, namely Nile red (NIL) and Pinacyanol chloride (PCYN), were compared while solubilized inside the liposome bilayer. The sensitivity of their spectral characteristics to polarity and molecular mobility produced a monitor of the bilayer micropolarity and fluidity. The relatively high hydrophobicity of Nile red (NIL) provides an accurate polarity sensor of the bilayer microenvironment. The formation of Pinacyanol chloride (PCYN) dimers (and their respective peak) was directly related to the distance between the dye molecules. Shifts of the maximum absorbance (X_max) for both dyes showed that the bilayer environment was becoming more apolar with increasing copolymer concentration. The absorbance intensity decreased with increasing copolymer concentration, denoting a reduction in the solubilization of both dyes and therefore of the bilayer population. The absorbance peak of Pinacyanol chloride (PCYN) due to dimer formation increased at moderate copolymer concentrations, showing signs of possible incorporation inside the bilayer. These experiments provided information about the bilayer structure. Adding block copolymers at an optimum concentration may increase the stability of the liposome by incorporation, following various models proposed. However, at high content of copolymer some bilayer solubilization and mixed micelle formation may occur.     

空间组织模式：微生物群落组装的“游戏”规则

在生物膜形成过程中,微生物种群之间通过主动或者被动的生物过程所形成的独特空间结构被称为空间组织模式。微生物空间组织模式广泛存在于自然和人工环境中,比如医疗、工业和生态系统等,是微生物形成和维持特定群落结构并发挥功能的主要方式,也是形成和维持微生物群落多样性的关键机制。然而,由于微生物群落的复杂性及相关研究方法的局限性,微生物空间组织模式方面的研究目前仍然处于起始阶段。本文梳理了微生物空间组织模式领域的研究进展,系统总结了空间组织模式初始阶段（微生物界面附着）和成熟阶段（空间自组织）的形成过程与协同机制,以及其对微生物养分利用和元素循环、微生物多样性维持和种群进化及功能的影响和调控机制,并分析了影响微生物空间组织模式的关键环境因素。     

Extraction of lipase from Aspergillus niger by insoluble complex formation with anionic and cationic polyelectrolytes

The insoluble complex formation between lipase from Aspergillus niger and the electrically charged polymers, polyacrylic acid (PAA), poly-vinil sulfonate (PVS) and chitosan (CHI), was studied by using turbidimetric and enzymatic methods on a commercial lyophilized (Ly) and a filtrate of solid culture medium (SCM). It could be shown that both electrostatic interactions as hydrophobic are involved in the formation of insoluble complexes. The kinetics of the complex formation were determined. Lipase enzymatic activity is maintained through time in the presence of polyelectrolytes.On the Ly the three polymers produced insoluble complex, with a stoichiometric ratio (polymer mass per mass of Ly from Aspergillus niger) of PAA/Ly: 0.035, PVS/Ly: 0.099 and CHI/Ly: 0.071 mg/mg Ly. For the anionic polyelectrolytes, the PAA presents slightly better results than PVS to be used when the protein concentration is similar to the lyophilized.The filtrate of the SCM has a total protein concentration much lower than commercial lyophilized. Working with CHI as cationic polymer a recovery of the activity in the re-dissolved precipitate higher than 80%, with purification factors greater than 3 were achieved, both at 8 and 20 °C. Therefore, this methodology could be used as a first step of purification.