Monte Carlo simulations of densely-packed athermal polymers in the bulk and under confinement

We review the main results from extensive Monte Carlo (MC) simulations on athermal polymer packings in the bulk and under confinement. By employing the simplest possible model of excluded volume, macromolecules are represented as freely-jointed chains of hard spheres of uniform size. Simulations are carried out in a wide concentration range: from very dilute up to very high volume fractions, reaching the maximally random jammed (MRJ) state. We study how factors like chain length, volume fraction and flexibility of bond lengths affect the structure, shape and size of polymers, their packing efficiency and their phase behaviour (disorder–order transition). In addition, we observe how these properties are affected by confinement realized by flat, impenetrable walls in one dimension. Finally, by mapping the parent polymer chains to primitive paths through direct geometrical algorithms, we analyse the characteristics of the entanglement network as a function of packing density.

Technology transfer of renewable energy for rural development: historical evolution and lessons of experience from the model WWP

Technology transfer (TT) in the area of renewable energy (RE) throughout history has been an important tool for rural development (RD). Initially, the TT has been conceptualized as the purchase or donation of machinery from first world countries - without any consideration of staff training and contextual conditions for the adaptation of technology to the needs of the country. Various researches have revealed the existence of different approaches to planning the TT of RE, demonstrating the high complexity of projects from the social and contextual dimension. This paper addresses the conceptual evolution of the TT of RE for RD, examining its different periods considered for three criteria: historical events occurred, the role of stakeholders and changing objectives for the TT of RE for RD. For the conceptual analysis of changes the model Working With People (WWP) is used for planning and project management of high social complexity in RD. The analysis defines the existence of four historical periods in the TT of RE and synthesizes the lessons of experience from the three dimensions (ethical-social, technical-entrepreneurial, and political-contextual) of the WWP model.

Synergies and trade-offs between renewable energy expansion and biodiversity conservation - a cross-national multifactor analysis

Peer reviewed

Global change synergies and trade-offs between renewable energy and biodiversity

Funded by Kone Foundation ERC-StG. Grant Number: 260393 Academy of Finland Centre of Excellence Programme 2012–2017

Torsional directed walks, entropic elasticity, and DNA twist stiffness

DNA and other biopolymers differ from classical polymers because of their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the “torsional directed walk.” Motivated by a recent experiment on single lambda-DNA molecules [Strick, T. R., Allemand, J.-F., Bensimon, D., Bensimon, A. & Croquette, V. (1996) Science 271, 1835–1837], we formulate the torsional directed walk problem and solve it analytically in the appropriate force regime. Our technique affords a direct physical determination of the microscopic twist stiffness C and twist-stretch coupling D relevant for DNA functionality. The theory quantitatively fits existing experimental data for relative extension as a function of overtwist over a wide range of applied force; fitting to the experimental data yields the numerical values C = 120 nm and D = 50 nm. Future experiments will refine these values. We also predict that the phenomenon of reduction of effective twist stiffness by bend fluctuations should be testable in future single-molecule experiments, and we give its analytic form.

Solid-state synthesis and mechanical unfolding of polymers of T4 lysozyme

Recent advances in single molecule manipulation methods offer a novel approach to investigating the protein folding problem. These studies usually are done on molecules that are naturally organized as linear arrays of globular domains. To extend these techniques to study proteins that normally exist as monomers, we have developed a method of synthesizing polymers of protein molecules in the solid state. By introducing cysteines at locations where bacteriophage T4 lysozyme molecules contact each other in a crystal and taking advantage of the alignment provided by the lattice, we have obtained polymers of defined polarity up to 25 molecules long that retain enzymatic activity. These polymers then were manipulated mechanically by using a modified scanning force microscope to characterize the force-induced reversible unfolding of the individual lysozyme molecules. This approach should be general and adaptable to many other proteins with known crystal structures. For T4 lysozyme, the force required to unfold the monomers was 64 ± 16 pN at the pulling speed used. Refolding occurred within 1 sec of relaxation with an efficiency close to 100%. Analysis of the force versus extension curves suggests that the mechanical unfolding transition follows a two-state model. The unfolding forces determined in 1 M guanidine hydrochloride indicate that in these conditions the activation barrier for unfolding is reduced by 2 kcal/mol.

Branched co-polymers of histidine and lysine are efficient carriers of plasmids

We previously determined that a linear co-polymer of histidine and lysine (HK) in combination with liposomes enhanced the transfection efficiency of cationic liposomes. In the current study, we designed a series of HK polymers with increased branching and/or histidine/lysine ratio to determine if either variable affects transfection efficiency. In the presence of liposomes, the branched polymer with the highest number of histidines, HHK4b, was the most effective at enhancing gene expression. Furthermore, when serum was added to the medium during transfection, the combination of HHK4b and liposomes as a gene-delivery vehicle increased luciferase expression 400-fold compared to liposomes alone. In contrast to linear HK polymers, the higher branched HHK polymers were effective carriers of plasmids in the absence of liposomes. Without liposomes, the HHK4b carrier enhanced luciferase expression 15-fold in comparison with the lesser branched HHK2b carrier and increased expression by 5-logs in comparison with the HHK or HK carrier. The interplay of several parameters including increased condensation of DNA, buffering of acidic endosomes and differential binding affinities of polymer with DNA have a role in the enhancement of transfection by the HK polymers. In addition to suggesting that branched HK polymers are promising gene-delivery vehicles, this study provides a framework for the development of more efficient peptide-bond-based polymers of histidine and lysine.

Biochemical evolution III: Polymerization on organophilic silica-rich surfaces, crystal–chemical modeling, formation of first cells, and geological clues

Catalysis at organophilic silica-rich surfaces of zeolites and feldspars might generate replicating biopolymers from simple chemicals supplied by meteorites, volcanic gases, and other geological sources. Crystal–chemical modeling yielded packings for amino acids neatly encapsulated in 10-ring channels of the molecular sieve silicalite-ZSM-5-(mutinaite). Calculation of binding and activation energies for catalytic assembly into polymers is progressing for a chemical composition with one catalytic Al–OH site per 25 neutral Si tetrahedral sites. Internal channel intersections and external terminations provide special stereochemical features suitable for complex organic species. Polymer migration along nano/micrometer channels of ancient weathered feldspars, plus exploitation of phosphorus and various transition metals in entrapped apatite and other microminerals, might have generated complexes of replicating catalytic biomolecules, leading to primitive cellular organisms. The first cell wall might have been an internal mineral surface, from which the cell developed a protective biological cap emerging into a nutrient-rich “soup.” Ultimately, the biological cap might have expanded into a complete cell wall, allowing mobility and colonization of energy-rich challenging environments. Electron microscopy of honeycomb channels inside weathered feldspars of the Shap granite (northwest England) has revealed modern bacteria, perhaps indicative of Archean ones. All known early rocks were metamorphosed too highly during geologic time to permit simple survival of large-pore zeolites, honeycombed feldspar, and encapsulated species. Possible microscopic clues to the proposed mineral adsorbents/catalysts are discussed for planning of systematic study of black cherts from weakly metamorphosed Archaean sediments.

Polygalacturonase-Mediated Solubilization and Depolymerization of Pectic Polymers in Tomato Fruit Cell Walls1 : Regulation by pH and Ionic Conditions

The hydrolysis of cell wall pectins by tomato (Lycopersicon esculentum) polygalacturonase (PG) in vitro is more extensive than the degradation affecting these polymers during ripening. We examined the hydrolysis of polygalacturonic acid and cell walls by PG isozyme 2 (PG2) under conditions widely adopted in the literature (pH 4.5 and containing Na+) and under conditions approximating the apoplastic environment of tomato fruit (pH 6.0 and K+ as the predominate cation). The pH optima for PG2 in the presence of K+ were 1.5 and 0.5 units higher for the hydrolysis of polygalacturonic acid and cell walls, respectively, compared with activity in the presence of Na+. Increasing K+ concentration stimulated pectin solubilization at pH 4.5 but had little influence at pH 6.0. Pectin depolymerization by PG2 was extensive at pH values from 4.0 to 5.0 and was further enhanced at high K+ levels. Oligomers were abundant products in in vitro reactions at pH 4.0 to 5.0, decreased sharply at pH 5.5, and were negligible at pH 6.0. EDTA stimulated PG-mediated pectin solubilization at pH 6.0 but did not promote oligomer production. Ca2+ suppressed PG-mediated pectin release at pH 4.5 yet had minimal influence on the proportional recovery of oligomers. Extensive pectin breakdown in processed tomato might be explained in part by cation- and low-pH-induced stimulation of PG and other wall-associated enzymes.

How the first biopolymers could have evolved.

In this work, we discuss a possible origin of the first biopolymers with stable unique structures. We suggest that at the prebiotic stage of evolution, long organic polymers had to be compact to avoid hydrolysis and had to be soluble and thus must not be exceedingly hydrophobic. We present an algorithm that generates such sequences for model proteins. The evolved sequences turn out to have a stable unique structure, into which they quickly fold. This result illustrates the idea that the unique three-dimensional native structures of first biopolymers could have evolved as a side effect of nonspecific physicochemical factors acting at the prebiotic stage of evolution.

Bacterial cell division protein FtsZ assembles into protofilament sheets and minirings, structural homologs of tubulin polymers.

The bacterial cell division protein FtsZ is a homolog of tubulin, but it has not been determined whether FtsZ polymers are structurally related to the microtubule lattice. In the present study, we have obtained high-resolution electron micrographs of two FtsZ polymers that show remarkable similarity to tubulin polymers. The first is a two-dimensional sheet of protofilaments with a lattice very similar to that of the microtubule wall. The second is a miniring, consisting of a single protofilament in a sharply curved, planar conformation. FtsZ minirings are very similar to tubulin rings that are formed upon disassembly of microtubules but are about half the diameter. This suggests that the curved conformation occurs at every FtsZ subunit, but in tubulin rings the conformation occurs at either beta- or alpha-tubulin subunits but not both. We conclude that the functional polymer of FtsZ in bacterial cell division is a long thin sheet of protofilaments. There is sufficient FtsZ in Escherichia coli to form a protofilament that encircles the cell 20 times. The similarity of polymers formed by FtsZ and tubulin implies that the protofilament sheet is an ancient cytoskeletal system, originally functioning in bacterial cell division and later modified to make microtubules.

Renewable Energy Systems in the City of Northglenn: Draft Zoning Ordinance and Resident Pamphlet

Recent federal incentives and increased demand for home photovoltaic and small wind electrical systems highlights the need for consistent zoning ordinances and guidance materials for Northglenn residents. This Capstone Project assesses perceived impacts related to renewable energy systems, like noise, safety, aesthetics, and environmental considerations, and provides a model ordinance intended to mitigate these issues. It was concluded a model ordinance would ease and stimulate additions of alternative energy systems in Northglenn. Additionally, this research concluded development of public information could stimulate homeowners into positive decisions. The project also identifies potential financial and environmental benefits of installing such systems in an effort to promote sustainable and clean energy production within the city.

Some examples of modeling in chemical engineering: thermal treatment of polymers, phase equilibrium calculations and process design

Presentation submitted to PSE Seminar, Chemical Engineering Department, Center for Advanced Process Design-making (CAPD), Carnegie Mellon University, Pittsburgh (USA), October 2012.

Coordination polymers, metal–organic frameworks and the need for terminology guidelines

Coordination polymers (CPs) and metal–organic frameworks (MOFs) are among the most prolific research areas of inorganic chemistry and crystal engineering in the last 15 years, and yet it still seems that consensus is lacking about what they really are, or are not.

Combined Effect of Poly(hydroxybutyrate) and Plasticizers on Polylactic acid Properties for Film Intended for Food Packaging

Poly(lactic acid) PLA, and poly(hydroxybutyrate) PHB, blends were processed as films and characterized for their use in food packaging. PLA was blended with PHB to enhance the crystallinity. Therefore, PHB addition strongly increased oxygen barrier while decreased the wettability. Two different environmentally-friendly plasticizers, poly(ethylene glycol) (PEG) and acetyl(tributyl citrate) (ATBC), were added to these blends to increase their processing performance, while improving their ductile properties. ATBC showed higher plasticizer efficiency than PEG directly related to the similarity solubility parameters between ATBC and both biopolymers. Moreover, ATBC was more efficiently retained to the polymer matrix during processing than PEG. PLA–PHB–ATBC blends were homogeneous and transparent blends that showed promising performance for the preparation of films by a ready industrial process technology for food packaging applications, showing slightly amber color, improved elongation at break, enhanced oxygen barrier and decreased wettability.