Large deviations of Rouse polymer chain: first passage problem

The purpose of this paper is to investigate several analytical methods of solving first passage (FP) problem for the Rouse model, a simplest model of a polymer chain. We show that this problem has to be treated as a multi-dimensional Kramers' problem, which presents rich and unexpected behavior. We first perform direct and forward-flux sampling (FFS) simulations, and measure the mean first-passage time $\tau(z)$ for the free end to reach a certain distance $z$ away from the origin. The results show that the mean FP time is getting faster if the Rouse chain is represented by more beads. Two scaling regimes of $\tau(z)$ are observed, with transition between them varying as a function of chain length. We use these simulations results to test two theoretical approaches. One is a well known asymptotic theory valid in the limit of zero temperature. We show that this limit corresponds to fully extended chain when each chain segment is stretched, which is not particularly realistic. A new theory based on the well known Freidlin-Wentzell theory is proposed, where dynamics is projected onto the minimal action path. The new theory predicts both scaling regimes correctly, but fails to get the correct numerical prefactor in the first regime. Combining our theory with the FFS simulations lead us to a simple analytical expression valid for all extensions and chain lengths. One of the applications of polymer FP problem occurs in the context of branched polymer rheology. In this paper, we consider the arm-retraction mechanism in the tube model, which maps exactly on the model we have solved. The results are compared to the Milner-McLeish theory without constraint release, which is found to overestimate FP time by a factor of 10 or more.

Synthesis and physical properties of lipid-based poly(ester-urethane)s, I: Effect of varying polyester segment length

Four aliphatic thermoplastic poly(ester-urethane)s (PEUs) with similar molecular weights but varying polyesters molecular weight (534-1488 g/mol) were prepared from polyester diols, obtained by melt condensation of Azelaic acid and 1,9-Nonanediol, and 1,7-heptamethylene di-isocyanate (HPMDI) all sourced from vegetable oil feedstock. The thermal, and mechanical properties, and crystal structure of PEUs were investigated using DSC, TGA, DMA, tensile analysis and WAXD. For sufficiently long polyester chain, WAXD data indicated no hydrogen bonds polyethylene (PE)-like crystalline packing and for short polyester chains, small crystal domains with significant H-bonded polyamide (PA)-like packing. Crystallinity decreased with decreasing polyester molecular weights. The polymorphism of PEUs and consequently their melting characteristics were found to be largely controlled by polyester segment length. TGA of the PEUs indicated improved thermal stability with decreasing polyester chain length, suggesting a stabilization effect by urethane groups. Mechanical properties investigated by DMA and tensile analysis were found to scale predictably with the overall crystallinity of PEUs. (C) 2012 Elsevier Ltd. All rights reserved.

Medium Chain Fatty Acids Are Selective Peroxisome Proliferator Activated Receptor (PPAR) gamma Activators and Pan-PPAR Partial Agonists

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Population structure, distribution and abundance patterns of the patagonian smoothhound Musmlus schmitti springer, 1939 (Chondrichthyes,Elasmobranchii, Triakidae) in the rio de la plata and inner continental shelf, SW Atlantic ocean (34 degrees-30'-39 degrees-30's)

A total number of 4824 Mustelus schmitti was sampled. Females ranged from 25 to 93 em in spring and from 28 to 90 cm in summer. Males ranged from 34 to 82 and from 28 to 77 cm, respectively. Length composition of the population showed significant differences between spring and summer being females larger than males. Total length distribution did not show significant differences between cruises. Males density varied significantly between cruises while for the females no significant variation was observed. In the spring cruise, both sexes occurred at depths lower than 50 in. Females occurred in the whole area with adult occurrence only above 35 degrees 30'S. Mature males occurred throughout the area, immature males occurring in two trawls in Samborombon Bay. The summer cruise showed a discontinuous distribution of the species along the study area resulting in spatial segregation in two groups with immature females predominating in both of them.

Persistence Length, Mass Fractal, and Branching in the Aggregating of Vinyltriethoxysilane-Derived Organic/Silica Hybrids

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Population structure, distribution and abundance patterns of the patagonian smoothhound Mustelus schmitti Springer, 1939 (Chondrichthyes, Elasmobranchii, Triakidae) in the rio de La Plata and inner continental shelf , sw Atlantic ocean (34º30'-39º30'S)

Um total de 4824 Mustelus schmitti foi amostrado. As fêmeas apresentaram comprimento total de 25-93 cm na primavera e 28-90 cm no verão enquanto os machos apresentaram 34-82 e de 28-77 cm, respectivamente. A composição de comprimentos da população mostrou diferenças significativas entre primavera e verão sendo as fêmeas maiores do que os machos. A distribuição de comprimento total não variou significativamente entre cruzeiros. A densidade variou significativamente entre cruzeiros nos machos sendo que a variação não foi expressiva nas fêmeas. No cruzeiro da primavera, ambos os sexos ocorreram em profundidades menores do que 50 m, as fêmeas ocorrendo em toda a área de estudo, as adultas somente acima da latitude 35°30'S. Os machos adultos foram observados em toda a área sendo que os imaturos somente em dois arrastos na Bahia de Samborombón. O cruzeiro de verão mostrou uma distribuição descontínua da espécie ao longo da área de estudo, resultando na segregação espacial em dois grupos, com predominância de fêmeas imaturas em ambos.

Length structure of fishes from a protected area in the State of São Paulo, Southeastern Brazil

The aim of this work was to study the length distribution of some fish species from the Protected Area of São Pedro and Analândia, State of São Paulo, Southeastern Brazil. Length distributions were correlated to environmental conditions at each sample site. For the most abundant species, length structure was compared among the streams of each basin and between basins. Differences in length structure were related to differences in growth, habitats, and even population.

Efeito da hidrólise enzimática seguida da moagem em moinho de bolas sobre as características estruturais e físico-químicas do amido de madioquinha-salsa

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Mechanical and Thermal Properties of Thermoplastic Random Copolyesters Made from Lipid- Derived Medium and Long Chain Poly (x-hydroxyfatty acid) s

The physical properties of novel thermoplastic random copolyesters [-(CH2)(n)-COO-/-(CH2)(n)-COO-](x) made of long (n=12) and medium (n=8) chain length -hydroxyfatty esters [HO-(CH2)(n)-COOCH3] derived from bio-based vegetable oil feedstock are described. Poly(-hydroxy tridecanoate/-hydroxy nonanoate) P(-Me13-/-Me9-) random copolyesters (M-n=11,000-18,500 g/mol) with varying molar ratios were examined by TGA, DSC, DMA and tensile analysis, and WAXD. For the whole range of P(-Me13-/-Me9-) compositions, the WAXD data indicated an orthorhombic polyethylene-like crystal packing. Their melting characteristics, determined by DSC, varied with composition suggesting an isomorphic cocrystallization behavior. TGA of the P(-Me13-/-Me9-)s indicated improved thermal stability determined by their molar compositions. The glass transition temperature, investigated by DMA, was also found to vary with composition. The crystallinities of P(-Me13-/-Me9-)s however, were unaffected by the composition. The stiffness (Young's modulus) of these materials was found to be related to their degrees of crystallinity. (c) 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 40492.

Medium Chain Fatty Acids Are Selective Peroxisome Proliferator Activated Receptor (PPAR) gamma Activators and Pan-PPAR Partial Agonists

Thiazolidinediones (TZDs) act through peroxisome proliferator activated receptor (PPAR) gamma to increase insulin sensitivity in type 2 diabetes (T2DM), but deleterious effects of these ligands mean that selective modulators with improved clinical profiles are needed. We obtained a crystal structure of PPAR gamma ligand binding domain (LBD) and found that the ligand binding pocket (LBP) is occupied by bacterial medium chain fatty acids (MCFAs). We verified that MCFAs (C8-C10) bind the PPAR gamma LBD in vitro and showed that they are low-potency partial agonists that display assay-specific actions relative to TZDs; they act as very weak partial agonists in transfections with PPAR gamma LBD, stronger partial agonists with full length PPAR gamma and exhibit full blockade of PPAR gamma phosphorylation by cyclin-dependent kinase 5 (cdk5), linked to reversal of adipose tissue insulin resistance. MCFAs that bind PPAR gamma also antagonize TZD-dependent adipogenesis in vitro. X-ray structure B-factor analysis and molecular dynamics (MD) simulations suggest that MCFAs weakly stabilize C-terminal activation helix (H) 12 relative to TZDs and this effect is highly dependent on chain length. By contrast, MCFAs preferentially stabilize the H2-H3/beta-sheet region and the helix (H) 11-H12 loop relative to TZDs and we propose that MCFA assay-specific actions are linked to their unique binding mode and suggest that it may be possible to identify selective PPAR gamma modulators with useful clinical profiles among natural products.

Age-adjusted recipient pretransplantation telomere length and treatment-related mortality after hematopoietic stem cell transplantation

Telomere attrition induces cell senescence and apoptosis. We hypothesized that age-adjusted pretransplantation telomere length might predict treatment-related mortality (TRM) after hematopoietic stem cell transplantation (HSCT). Between 2000 and 2005, 178 consecutive patients underwent HSCT from HLA-identical sibling donors after myeloablative conditioning regimens, mainly for hematologic malignancies (n = 153). Blood lymphocytes' telomere length was measured by real-time quantitative PCR before HSCT. Age-adjusted pretransplantation telomere lengths were analyzed for correlation with clinical outcomes. After age adjustment, patients' telomere-length distribution was similar among all 4 quartiles except for disease stage. There was no correlation between telomere length and engraftment, GVHD, or relapse. The overall survival was 62% at 5 years (95% confidence interval [CI], 54-70). After a median follow-up of 51 months (range, 1-121 months), 43 patients died because of TRM. The TRM rate inversely correlated with telomere length. TRM in patients in the first (lowest telomere length) quartile was significantly higher than in patients with longer telomeres (P = .017). In multivariate analysis, recipients' age (hazard ratio, 1.1; 95% CI, .0-1.1; P = .0001) and age-adjusted telomere length (hazard ratio, 0.4; 95% CI; 0.2-0.8; P = .01) were independently associated with TRM. In conclusion, age-adjusted recipients' telomere length is an independent biologic marker of TRM after HSCT. (Blood. 2012;120(16):3353-3359)

Diet-Sensitive Sources of Reactive Oxygen Species in Liver Mitochondria: Role of Very Long Chain Acyl-CoA Dehydrogenases

High fat diets and accompanying hepatic steatosis are highly prevalent conditions. Previous work has shown that steatosis is accompanied by enhanced generation of reactive oxygen species (ROS), which may mediate further liver damage. Here we investigated mechanisms leading to enhanced ROS generation following high fat diets (HFD). We found that mitochondria from HFD livers present no differences in maximal respiratory rates and coupling, but generate more ROS specifically when fatty acids are used as substrates. Indeed, many acyl-CoA dehydrogenase isoforms were found to be more highly expressed in HFD livers, although only the very long chain acyl-CoA dehydrogenase (VLCAD) was more functionally active. Studies conducted with permeabilized mitochondria and different chain length acyl-CoA derivatives suggest that VLCAD is also a source of ROS production in mitochondria of HFD animals. This production is stimulated by the lack of NAD+. Overall, our studies uncover VLCAD as a novel, diet-sensitive, source of mitochondrial ROS.

Relaxationsuntersuchungen in unterkühlten und glasig erstarrten Polyalkoholen mittels dielektrischer und NMR Spektroskopie

Es wurde eine homologe Reihe von Polyalkoholen mit der allgemeinen Summenformel CNHN+2(OH)N (N=3-6) hinsichtlich ihrer Glaseigenschaften ober- und unterhalb der Glasübergangstemperatur TG untersucht. Dabei kamen die dielektrische und magnetische Resonanzspektroskopie (NMR) zum Einsatz. Es ergab sich oberhalb TG eine systematische Zunahme aller untersuchten dynamischen Parameter wie Fragilität, Breite der angenommenen Korrelationszeitenverteilungen und der Sprungwinkel der primären Glasrelaxation mit zunehmendem N. Dies kann insgesamt als eine Abnahme des Netzwerkcharakters, der durch Wasserstoffbrückenbindungen bedingt ist, bei zunehmender Kettenlänge interpretiert werden. Unterhalb TG entwickelt sich mit zunehmendem N die Sekundärrelaxation von einem 'Wing Szenario' zu einem ausgeprägten Johari - Goldstein (JG) - Prozess. Ein Sprungmodell, welches eine eingeschränkte Reorientierung auf einem Konusrand beschreibt, erzeugt mit Hilfe der parametrisierten dielektrischen Verlustspektren Sprungwinkel, die mit denen aus aktuellen ²H - NMR spektroskopischen Untersuchungen vergleichbar sind. Durch den Vergleich unterschiedlich deuterierter Derivate von Glyzerin (N=3) und Sorbitol (N=6) wurde gefolgert, dass auch unterhalb TG der Netzwerkcharakter mit zunehmender Kettenlänge abnimmt.Aufgrund der hier durchgeführten Untersuchungen konnte eine Zeitskala für einen Johari - Goldstein - Prozess im Modellglasbildner Glyzerin extrapoliert werden. Eine Deutung des Wings als Hochfrequenzausläufer des JG - Prozesses ist dadurch möglich.Der JG - Prozess kann somit als universeller Glasprozess interpretiert werden, der in verschiedenen Glasbildnern in unterschiedlicher Ausprägung auftritt.

Simulation studies of correlation functions and relaxation in polymeric systems

We investigate the statics and dynamics of a glassy,non-entangled, short bead-spring polymer melt with moleculardynamics simulations. Temperature ranges from slightlyabove the mode-coupling critical temperature to the liquidregime where features of a glassy liquid are absent. Ouraim is to work out the polymer specific effects on therelaxation and particle correlation. We find the intra-chain static structure unaffected bytemperature, it depends only on the distance of monomersalong the backbone. In contrast, the distinct inter-chainstructure shows pronounced site-dependence effects at thelength-scales of the chain and the nearest neighbordistance. There, we also find the strongest temperaturedependence which drives the glass transition. Both the siteaveraged coupling of the monomer and center of mass (CM) andthe CM-CM coupling are weak and presumably not responsiblefor a peak in the coherent relaxation time at the chain'slength scale. Chains rather emerge as soft, easilyinterpenetrating objects. Three particle correlations arewell reproduced by the convolution approximation with theexception of model dependent deviations. In the spatially heterogeneous dynamics of our system weidentify highly mobile monomers which tend to follow eachother in one-dimensional paths forming ``strings''. Thesestrings have an exponential length distribution and aregenerally short compared to the chain length. Thus, arelaxation mechanism in which neighboring mobile monomersmove along the backbone of the chain seems unlikely.However, the correlation of bonded neighbors is enhanced. When liquids are confined between two surfaces in relativesliding motion kinetic friction is observed. We study ageneric model setup by molecular dynamics simulations for awide range of sliding speeds, temperatures, loads, andlubricant coverings for simple and molecular fluids. Instabilities in the particle trajectories are identified asthe origin of kinetic friction. They lead to high particlevelocities of fluid atoms which are gradually dissipatedresulting in a friction force. In commensurate systemsfluid atoms follow continuous trajectories for sub-monolayercoverings and consequently, friction vanishes at low slidingspeeds. For incommensurate systems the velocity probabilitydistribution exhibits approximately exponential tails. Weconnect this velocity distribution to the kinetic frictionforce which reaches a constant value at low sliding speeds. This approach agrees well with the friction obtaineddirectly from simulations and explains Amontons' law on themicroscopic level. Molecular bonds in commensurate systemslead to incommensurate behavior, but do not change thequalitative behavior of incommensurate systems. However,crossed chains form stable load bearing asperities whichstrongly increase friction.

A molecular approach towards tethered bilayer lipid membranes: synthesis and characterization of novel anchor lipids

Tethered bilayer lipid membranes (tBLMs) are a promising model system for the natural cell membrane. They consist of a lipid bilayer that is covalently coupled to a solid support via a spacer group. In this study, we developed a suitable approach to increase the submembrane space in tBLMs. The challenge is to create a membrane with a lower lipid density in order to increase the membrane fluidity, but to avoid defects that might appear due to an increase in the lateral space within the tethered monolayers. Therefore, various synthetic strategies and different monolayer preparation techniques were examined. Synthetical attempts to achieve a large ion reservoir were made in two directions: increasing the spacer length of the tether lipids and increasing the lateral distribution of the lipids in the monolayer. The first resulted in the synthesis of a small library of tether lipids (DPTT, DPHT and DPOT) characterized by 1H and 13C NMR, FD-MS, ATR, DSC and TGA. The synthetic strategy for their preparation includes synthesis of precursor with a double bond anchor that can be easily modified for different substrates (e.g. metal and metaloxide). Here, the double bond was modified into a thiol group suitable for gold surface. Another approach towards the preparation of homogeneous monolayers with decreased two-dimensional packing density was the synthesis of two novel anchor lipids: DPHDL and DDPTT. DPHDL is “self-diluted” tether lipid containing two lipoic anchor moieties. DDPTT has an extended lipophylic part that should lead to the preparation of diluted, leakage free proximal layers that will facilitate the completion of the bilayer. Our tool-box of tether lipids was completed with two fluorescent labeled lipid precursors with respectively one and two phytanyl chains in the hydrophobic region and a dansyl group as a fluorophore. The use of such fluorescently marked lipids is supposed to give additional information for the lipid distribution on the air-water interface. The Langmuir film balance was used to investigate the monolayer properties of four of the synthesized thiolated anchor lipids. The packing density and mixing behaviour were examined. The results have shown that mixing anchor with free lipids can homogeneously dilute the anchor lipid monolayers. Moreover, an increase in the hydrophylicity (PEG chain length) of the anchor lipids leads to a higher packing density. A decrease in the temperature results in a similar trend. However, increasing the number of phytanyl chains per lipid molecule is shown to decrease the packing density. LB-monolayers based on pure and mixed lipids in different ratio and transfer pressure were tested to form tBLMs with diluted inner layers. A combination of the LB-monolayer transfer with the solvent exchange method accomplished successfully the formation of tBLMs based on pure DPOT. Some preliminary investigations of the electrical sealing properties and protein incorporation of self-assembled DPOT and DDPTT-based tBLMs were conducted. The bilayer formation performed by solvent exchange resulted in membranes with high resistances and low capacitances. The appearance of space beneath the membrane is clearly visible in the impedance spectra expressed by a second RC element. The latter brings the conclusion that the longer spacer in DPOT and the bigger lateral space between the DDPTT molecules in the investigated systems essentially influence the electrical parameters of the membrane. Finally, we could show the functional incorporation of the small ion carrier valinomycin in both types of membranes.