Generic Polymer Research Articles

Recovering the reptation dynamics of polymer melts in dissipative particle dynamics simulations via slip-springs

We report a multi-chain approach for dissipative particle dynamics where the uncrossability constraints of polymer chains are mimicked by temporary cross-links, so-called slip-springs. The conformational statistics of the chains are not affected by the introduction of slip-springs. Dynamical properties such as mean square displacements, diffusion coefficient, and longest relaxation time are in good agreement with the results of reptation theory. According to our analysis, the present formalism is 500 times faster and requires 7 times fewer beads than conventional generic polymer models employing Newtonian dynamics and excluded-volume potentials.

From Flexible to Stiff: Systematic Analysis of Structural Phases for Single Semiflexible Polymers

Inspired by recent studies revealing unexpected pliability of semiflexible biomolecules like RNA and DNA, we systematically investigate the range of structural phases by means of a simple generic polymer model. Using a two-dimensional variant of Wang-Landau sampling to explore the conformational space in energy and stiffness within a single simulation, we identify the entire diversity of structures existing from the well-studied limit of flexible polymers to that of wormlike chains. We also discuss, in detail, the influence of finite-size effects in the formation of crystalline structures that are virtually inaccessible via conventional computational approaches.

Determination of the interfacial properties of carbon nanotube reinforced polymer composites using atomistic-based continuum model

The present study investigates the interfacial properties of carbon nanotube (CNT) reinforced polymer composites by simulating a nanotube pull-out experiment. An atomistic description of the problem is achieved by implementing constitutive relations that are derived solely from interatomic potentials. Specifically, we adopt the Lennard-Jones (LJ) interatomic potential to simulate a non-bonded interface, where only the van der Waals (vdW) interactions between the CNT and surrounding polymer matrix are assumed to exist. The effects of such parameters as the CNT embedded length, the number of vdW interactions, the thickness of the interface, the CNT diameter and the cut-off distance of the LJ potential on the interfacial shear strength (ISS) are investigated and discussed. The problem is formulated for both a generic thermoset polymer and a specific two-component epoxy based on a diglycidyl ether of bisphenol A (DGEBA) and triethylene tetramine (TETA) formulation. The study further illustrates that by accounting for different CNT capping scenarios and polymer morphologies around the embedded end of the CNT, the qualitative correlation between simulation and experimental pull-out profiles can be improved.

Aggregated yet Disordered: A Molecular Simulation Study of the Self-Aggregation of Elastin

Elastin is the protein responsible for the elastic recoil of skin, arteries, and lungs. Elastin exhibits high resilience and remarkable durability; it also undergoes phase separation and self-organization into a fibrillar structure upon increasing temperature. These properties make elastin ideal for biomaterials applications. In order to investigate the molecular basis for elastin self-aggregation, we performed extensive atomistic molecular dynamics simulations of a monomer and an aggregate of eight elastin-like peptides in explicit water. These simulations required a total time of nearly 0.5 ms, and utilized simulated tempering distributed replica sampling, a method that relies on a random walk in temperature to enhance conformational sampling. We obtain a configurational ensemble of the elastin-like aggregate that resembles a “polymer melt” in which the chains are completely entangled with each other, but retain significant hydration and do not form a water-excluding hydrophobic core. Within the aggregate, the chains act to “solvate” each other: intramolecular interactions present in the monomer in aqueous solution are largely replaced by intermolecular interactions in the aggregate. As a result, the overall chain dimensions are similar to the expected dimensions of chains in an ideal solvent, a state in which chain entropy is maximized. This is the prediction of the Flory theorem for generic polymer chains within a polymer melt, but has never, to our knowledge, been observed before for an aggregate of polypeptide chains in atomistic detail. Finally, we note that our results are not consistent with the current model of elastin self-aggregation, which involves a conformational transition of a monomer towards a more “ordered” aggregation-prone state. Instead, we propose a model in which both the hydrophobic effect and the enhanced chain entropy afforded by the interactions with other peptides within the aggregate favour elastin self-aggregation.

Statistical Thermodynamics of Polymer Quantum Systems

Polymer quantum systems are mechanical models quantized similarly as loop quantum gravity. It is actually in quantizing gravity that the polymer term holds proper as the quantum geometry excitations yield a reminiscent of a polymer material. In such an approach both non-singular cosmological models and a microscopic basis for the entropy of some black holes have arisen. Also important physical questions for these systems involve thermodynamics. With this motivation, in this work, we study the statistical thermodynamics of two one dimensional {\em polymer} quantum systems: an ensemble of oscillators that describe a solid and a bunch of non-interacting particles in a box, which thus form an ideal gas. We first study the spectra of these polymer systems. It turns out useful for the analysis to consider the length scale required by the quantization and which we shall refer to as polymer length. The dynamics of the polymer oscillator can be given the form of that for the standard quantum pendulum. Depending on the dominance of the polymer length we can distinguish two regimes: vibrational and rotational. The first occur for small polymer length and here the standard oscillator in Schr\"odinger quantization is recovered at leading order. The second one, for large polymer length, features dominant polymer effects. In the case of the polymer particles in the box, a bounded and oscillating spectrum that presents a band structure and a Brillouin zone is found. The thermodynamical quantities calculated with these spectra have corrections with respect to standard ones and they depend on the polymer length. For generic polymer length, thermodynamics of both systems present an anomalous peak in their heat capacity $C_V$.

Density profile and polymer configurations for a polymer melt in a regular array of nanotubes

By using two generic polymer models, namely self-consistent field theory and bond-fluctuation Monte-Carlo simulations, we investigate numerically the properties of a polymer melt in a hexagonal array of nanotubes as a function of the polymer length, the interaction with the nanotubes and the compressibility or average density. The combined effect of the attractive interaction with the nanotube walls, the entropy decrease due to the impenetrability of the walls and the hexagonal arrangement of the nanotubes with varying gap size in between them leads to a wide array of possible density profiles and polymer configurations as a function of the model parameters. Even in the case of the Monte-Carlo simulations, where the contact interaction affects only the first layer of monomers, the effect of the wall can nevertheless be felt throughout the entire melt at intermediate temperatures.

Design and integration of a generic disposable array-compatible sensor housing into an integrated disposable indirect microfluidic flow injection analysis system

We describe an integration strategy for arbitrary sensors intended to be used as biosensors in biomedical or bioanalytical applications. For such devices ease of handling (by a potential end user) as well as strict disposable usage are of importance. Firstly we describe a generic array compatible polymer sensor housing with an effective sample volume of 1.55 μl. This housing leaves the sensitive surface of the sensor accessible for the application of biosensing layers even after the embedding. In a second step we show how this sensor housing can be used in combination with a passive disposable microfluidic chip to set up arbitrary 8-fold sensor arrays and how such a system can be complemented with an indirect microfluidic flow injection analysis (FIA) system. This system is designed in a way that it strictly separates between disposable and reusable components- by introducing tetradecane as an intermediate liquid. This results in a sensor system compatible with the demands of most biomedical applications. Comparative measurements between a classical macroscopic FIA system and this integrated indirect microfluidic system are presented. We use a surface acoustic wave (SAW) sensor as an exemplary detector in this work.

Study of PEGylated Lipid Layers as a Model for PEGylated Liposome Surfaces: Molecular Dynamics Simulation and Langmuir Monolayer Studies

We have combined Langmuir monolayer film experiments and all-atom molecular dynamics (MD) simulation of a bilayer to study the surface structure of a PEGylated liposome and its interaction with the ionic environment present under physiological conditions. Lipids that form both gel and liquid-crystalline membranes have been used in our study. By varying the salt concentration in the Langmuir film experiment and including salt at the physiological level in the simulation, we have studied the effect of salt ions present in the blood plasma on the structure of the poly(ethylene glycol) (PEG) layer. We have also studied the interaction between the PEG layer and the lipid bilayer in both the liquid-crystalline and gel states. The MD simulation shows two clear results: (a) The Na(+) ions form close interactions with the PEG oxygens, with the PEG chains forming loops around them and (b) PEG penetrates the lipid core of the membrane for the case of a liquid-crystalline membrane but is excluded from the tighter structure of the gel membrane. The Langmuir monolayer results indicate that the salt concentration affects the PEGylated lipid system, and these results can be interpreted in a fashion that is in agreement with the results of our MD simulation. We conclude that the currently accepted picture of the PEG surface layer acting as a generic neutral hydrophilic polymer entirely outside the membrane, with its effect explained through steric interactions, is not sufficient. The phenomena we have observed may affect both the interaction between the liposome and bloodstream proteins and the liquid-crystalline-gel transition and is thus relevant to nanotechnological drug delivery device design.

Morphology of printed lines and droplet deposits using hydrophilic nanoparticle suspensions

This paper focuses on the morphology of continuous mode printed lines of a generic polymer suspension. The suspension consists of carboxylate nanoparticles. The printing is performed by forming a stable capillary-bridge of the suspension between the print-nozzle and glass substrate. The printed deposits are examined microscopically. The printing technique used here is easy to implement and allows a wider property window for the fluids that can be printed compared to drop on demand mode printing. The morphology of these printed lines is found to be dependent on the number of layers of the nanoparticles present. To further understand the fundamental mechanism of printed nanoparticle deposit morphology development, droplet deposits of the suspension are also prepared and analyzed.

Use of Wireless Capsule Endoscopy for Evaluation of Sustained Gastric Presence of a Polymer Medication Delivery System

Purpose: Wireless capsule endoscopy (CE) has been demonstrated to be superior to traditional imaging for the diagnosis of small bowel disorders, but has not been utilized for investigation of gastric abnormalities. CE offers the potential opportunity to provide quantitative data regarding gastric emptying. The dosing and efficacy of drugs released via an extended release polymer delivery system is dependent on the retention of the device in the gastric lumen. The purpose of this study is to assess the utility of CE for the evaluation of the presence of a generic drug polymer delivery system in the stomach at specified time periods after ingestion. Methods: Eleven subjects taking daily metformin ER 500 mg (study tablet) were recruited to participate. Subjects ingested a standardized breakfast meal and the study tablet followed by an eight hour fasting period. Subjects underwent a CE study for a three hour period of time starting five hours after ingestion of the study tablet. Results: Ten subjects completed the study protocol. Photographs of the swollen study tablet after being immersed in simulated gastric fluid for several hours in a laboratory setting were used for comparison purposes. The images obtained from the remaining ten subjects showed the study tablet in the gastric lumen mixed with food debris. The study tablet could be identified on the basis of the tablet's smooth contour and uniform color. Conclusion: CE imaging was able to identify the study tablet in all 10 subjects despite the presence of retained food debris. CE offers the potential for the evaluation of gastric retention of drugs utilizing a polymer medication delivery system in a fed state.

Structure and dynamics of interphase chromosomes.

During interphase chromosomes decondense, but fluorescent in situ hybridization experiments reveal the existence of distinct territories occupied by individual chromosomes inside the nuclei of most eukaryotic cells. We use computer simulations to show that the existence and stability of territories is a kinetic effect that can be explained without invoking an underlying nuclear scaffold or protein-mediated interactions between DNA sequences. In particular, we show that the experimentally observed territory shapes and spatial distances between marked chromosome sites for human, Drosophila, and budding yeast chromosomes can be reproduced by a parameter-free minimal model of decondensing chromosomes. Our results suggest that the observed interphase structure and dynamics are due to generic polymer effects: confined Brownian motion conserving the local topological state of long chain molecules and segregation of mutually unentangled chains due to topological constraints.

Connectivity and Entanglement Stress Contributions in Strained Polymer Networks

Using molecular dynamics simulations and a variant of our primitive path analysis algorithm, we have measured the total stress as well as the connectivity stress contribution for a large variety of generic bead-spring model polymer networks. For randomly cross- and end-linked networks the inferred entanglement stress contribution is excellent agreement with the predictions of the Rubinstein–Panyukov slip-tube model (Macromolecules 2002, 35, 6670). For networks undergoing further cross-linking and bond-breaking in the strained state (chemical aging), the observed stress−strain behavior can be described by a generalization of the slip-tube model in the spirit of Tobolsky’s independent network hypothesis. The stress-transfer between independent networks during postcuring appears to obey unexpectedly simple relations.

Effect of Filler Particle Size on the Properties of Model Nanocomposites

Molecular dynamics simulations have been used to examine the effect of the size of a spherical inclusion in generic model polymer nanocomposite systems. Results are presented concerning the effect of the increasing particle size on the thickness of the interphase, i.e., the perturbed zone of polymer surrounding the inclusion. The behavior of the mass density, molecular orientation, fraction of trans conformers, as well as dynamic properties are presented as a function of the distance from the nanoparticle surface. The effect of temperature on these distributions is also discussed. Long simulations have been carried out to determine the variation in the glass transition of the filled polymers as compared to the pure systems. It is established that, within errors, the interphase thickness is independent of the size of the nanoparticle for the range of particle sizes analyzed. This information is particularly important for the second stage of the project where it is used in continuum micromechanical calculat...

Parallel Multiscale Modeling of Biopolymer Dynamics with Hydrodynamic Correlations

We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Molecular Dynamics (MD) with a mesoscopic Lattice Boltzmann (LB) method for the solvent dynamics, explicitly taking into account the interactions of the molecule with the surrounding fluid. We describe an efficient parallel implementation of the method which exhibits excellent scalability on the Blue Gene platform. We investigate both dynamical and statistical aspects of the translocation process by simulating polymers of various initial configurations and lengths. For a representative molecule size, we explore the effects of important parameters that enter in the simulation, paying particular attention to the strength of the molecule-solvent coupling and of the external electric field which drives the translocation process. Finally, we explore the connection between the generic polymers modeled in the simulation and DNA, for which interesting recent experimental results are available.

A Comparison of Toxic Product Yields Obtained From Five Laboratories Using the Steady State Tube Furnace (ISO TS 19700)

The steady state tube furnace has been developed from BS 7990 into the first internationally recognized standard for assessment of fire gas toxicity, ISO TS 19700. The apparatus has been shown to reliably replicate different fire stages, and is capable of generating toxic product yields as a function of the equivalence ratio ?. Work is reported from 5 laboratories currently using the steady state tube furnace where it has been used to assess the toxic product yields from a range of generic polymer materials, as a function of equivalence ratio. For the polymers tested, (LDPE, PP, PVC, Nylon, and PS) a high degree of reproducibility is observed across the range of ventilation conditions. In particular, the carbon monoxide yield, which is most susceptible to fire conditions shows consistent behaviour, which is independent of a particular laboratory.

Viscosity and Structural Alteration of a Coarse-Grained Model of Polystyrene under Steady Shear Flow Studied by Reverse Nonequilibrium Molecular Dynamics

The reverse nonequilibrium molecular dynamics (RNEMD) method is implemented to predict the viscosity of a coarse-grained model of short-chain polystyrene. The coarse-grained model has been derived to reproduce the structure of polystyrene. It is therefore not a generic model, but polymer-specific. Here, its performance for dynamical quantities is tested. The zero-shear viscosity is compared with experimental data. The pronounced difference can be mainly attributed to the inherent dynamic properties of the coarse-grained model. The qualitative results are compared to previous results calculated via conventional nonequilibrium molecular dynamics (NEMD) and more generic polymer models, and the agreement is reasonable. The structural alterations under shear are investigated by characterizing the molecular deformation and birefringence extinction angle.

One-dimensional thermal model of cold-start in a polymer electrolyte fuel cell stack

A transient, one-dimensional thermal model for a generic polymer electrolyte fuel cell (PEFC) stack is developed to investigate the cold-start ability and the corresponding energy requirement over different operating and ambient conditions. The model is constructed by applying the conservation of energy on each stack component and connecting the component's relevant boundaries to form a continuous thermal model. The phase change of ice and re-circulation of coolant flow are included in the analytical framework and their contribution to the stack thermal mass and temperature distribution of the components is also explored. A parametric study was conducted to determine the governing parameters, relative impact of the thermal mass of each stack component and ice, and anticipated temperature distribution in the stack at start-up for various operating conditions. Results indicate that 20 cells were sufficient to accurately experimentally and computationally simulate the full size stack behavior. It was observed that an optimum range of operating current density exists for a chosen stack design, in which rapid start-up of the stack from sub-zero condition can be achieved. Thermal isolation of the stack at the end plates is recommended to reduce the start-up time. Additionally, an end plate thickness exceeding a threshold value has no added effect on the stack cold-start ability. Effect of various internal and external heating mechanisms on the stack start-up were also investigated, and flow of heated coolant above 0 °C was found to be the most effective way to achieve the rapid start-up.

Toward an Accurate Theoretical Framework for Describing Ensembles for Proteins under Strongly Denaturing Conditions

Our focus is on an appropriate theoretical framework for describing highly denatured proteins. In high concentrations of denaturants, proteins behave like polymers in a good solvent and ensembles for denatured proteins can be modeled by ignoring all interactions except excluded volume (EV) effects. To assay conformational preferences of highly denatured proteins, we quantify a variety of properties for EV-limit ensembles of 23 two-state proteins. We find that modeled denatured proteins can be best described as follows. Average shapes are consistent with prolate ellipsoids. Ensembles are characterized by large correlated fluctuations. Sequence-specific conformational preferences are restricted to local length scales that span five to nine residues. Beyond local length scales, chain properties follow well-defined power laws that are expected for generic polymers in the EV limit. The average available volume is filled inefficiently, and cavities of all sizes are found within the interiors of denatured proteins. All properties characterized from simulated ensembles match predictions from rigorous field theories. We use our results to resolve between conflicting proposals for structure in ensembles for highly denatured states.

Hydrogel polymer appears to mimic the performance of the GroEL/GroES molecular chaperone machine

Controlled protein folding/refolding remains a substantial challenge to the biotechnology industry. Robust and adaptable artificial polymer molecular chaperones could make important contributions towards solving this problem. Taking inspiration from the mechanism of the GroEL/GroES molecular chaperone machine, we report the preparation and testing of a selection of cross-linked thermo-responsive hydrogels, one of which is shown to assist quantitative refolding of a stringent unfolded protein substrate (mitochondrial malate dehydrogenase [mMDH]) during temperature cycling between hydrophobic and hydrophilic states. To our knowledge, this is the first hydrogel-only artificial polymer molecular chaperone to be derived, which is also potentially a generic artificial polymer molecular chaperone for use in a folding bioreactor.

Aqueous Based Single Wafer Cleaning Process Development and Integration into 65nm Process Flow using Metal Hard Mask

AbstractAs the industry develops processes for the 65 and 45 nm technology nodes, post etch/ash cleaning faces new challenges with far more stringent requirements on surface cleanliness and materials loss. The introduction and integration of new materials, such as metal hard mask, creates additional requirements for wafer cleaning due to the occurrence of new defect modes related to metal hard mask. These include organometallic residue and metal fluorite compounds precipitating with time. We have developed a novel aqueous solution (AQ) based single wafer cleaning process to address these new defect modes. Physical characterization results and process integration electrical data and reliability data (TEM cross section review of the vias) are presented in this paper.The main conclusions can be summarized as follows: (1) In the dual damascene Cu/low-k process flow with hard mask, there are three typical residues after etch/ash: generic polymer residue, organometallic residue strongly bonded to metal maks, and time-dependent metal fluoride residue. (2) Generic polymer residue is very well characterized [1,2] and is usually easy to remove with solvent or aqueous solution [2,3]. (3)We developed an oxidizing chemistry based process to undercut the hard mask for the organometallic residue removal, which proved highly effective. (4)The time-dependent metal fluoride reside makes queue time control after etch/ash very critical (<1 hour). We developed a process with a fluorine based aqueous chemistry to address the metal fluoride residue, which proved highly effective. With this new process, queue time control is not required. (5) The post etch/ash cleaning for the Cu/low-k structure with metal hard mask typically employs the solvent/dry plasma ash multi-step procedure [4]. The new process developed in this research reduced the multi-step process to one wet clean step with two different aqueous chemistries in sequence. (6) The integration electrical data shows that the new single step aqueous cleaning process performance is comparable to, or even better than that from the solvent/dry plasma ash multi cleaning process. (7) Blanket Cu loss with the new process is about 23A/min, however TEM analysis of the vias after full integration shows Cu loss, we are working to improve the integration related Cu loss.