DNA motion capture reveals the mechanical properties of DNA at the mesoscale.

PubMed

Price, Allen C; Pilkiewicz, Kevin R; Graham, Thomas G W; Song, Dan; Eaves, Joel D; Loparo, Joseph J

2015-05-19

Single-molecule studies probing the end-to-end extension of long DNAs have established that the mechanical properties of DNA are well described by a wormlike chain force law, a polymer model where persistence length is the only adjustable parameter. We present a DNA motion-capture technique in which DNA molecules are labeled with fluorescent quantum dots at specific sites along the DNA contour and their positions are imaged. Tracking these positions in time allows us to characterize how segments within a long DNA are extended by flow and how fluctuations within the molecule are correlated. Utilizing a linear response theory of small fluctuations, we extract elastic forces for the different, ∼2-μm-long segments along the DNA backbone. We find that the average force-extension behavior of the segments can be well described by a wormlike chain force law with an anomalously small persistence length. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Bile Salt Mediated Growth of Reverse Wormlike Micelles in Nonpolar Liquids

NASA Astrophysics Data System (ADS)

Tung, Shih-Huang; Huang, Yi-En; Raghavan, Srinivasa

2006-03-01

We report the growth of reverse wormlike micelles induced by the addition of a bile salt in trace amounts to solutions of the phospholipid, lecithin in nonpolar organic solvents. Previous recipes for reverse wormlike micelles have usually required the addition of water to induce reverse micellar growth; here, we show that bile salts, due to their unique ``facially amphiphilic'' structure, can play a role analogous to water and promote the longitudinal aggregation of lecithin molecules into reverse micellar chains. The formation of transient entangled networks of these reverse micelles transforms low-viscosity lecithin organosols into strongly viscoelastic fluids. The zero-shear viscosity increases by more than five orders of magnitude, and it is the molar ratio of bile salt to lecithin that controls this viscosity enhancement. The growth of reverse wormlike micelles is also confirmed by small-angle neutron scattering (SANS) experiments on these fluids.

Constitutive Models for the Force-Extension Behavior of Biological Filaments

NASA Astrophysics Data System (ADS)

Palmer, J. S.; Castro, C. E.; Arslan, M.; Boyce, M. C.

Biopolymer filaments form the molecular backbone of biological structures throughout the body. The biomechanical response of single filaments yields insight into their individual behavior at the molecular level as well as their concerted networked behavior at the cellular and tissue scales. This paper focuses on modeling approaches for axial force vs. extension behavior of single biopolymer filaments within three stiffness regimes: flexible, semiflexible, and stiff. The end-to-end force-extension behaviors of flexible and semiflexible filaments arise as a result of a reduction in configurational space as the filament is straightened and are captured with entropic models including the freely jointed chain model and the worm-like chain model. As the filament is straightened and the end-to-end distance approaches the filament contour length, the contour length is directly axially extended and an internal energy contribution governs the force-extension behavior in this limiting extension regime. On the other hand, for stiff filaments in originally crimped or kinked configurations, the end-to-end force vs. extension behavior results from the unbending (straightening) of the crimped configuration as governed by an internal energy based elastica approximation which is also complemented by an axial stretching contribution once the end-to-end distance approaches the contour length of the filament. Simplified, analytical force-extension relationships are developed for the worm-like chain model for semiflexible filaments, and for the Euler elastica model for stiffer, wavy fibers. For the case of flexible molecules containing modular folded domains, the influence of force-induced unfolding on the force-extension behavior of single molecules and assemblies of multiple molecules is also presented.

Dynamics and motion control of a chain of particles on a rough surface

NASA Astrophysics Data System (ADS)

Behn, C.; Schale, F.; Zeidis, I.; Zimmermann, K.; Bolotnik, N.

2017-05-01

In this paper the mechanics and control of the motion of a straight chain of three particles interconnected with kinematical constraints are investigated. The ground contact is described by dry (discontinuous) or viscous (continuous) friction. Here, we understand this model as a methodological basis for the design of worm-like locomotion systems, i.e., non-pedal mobile robots. This kind of robots will prove an efficient form of locomotion in application to inspection of pipes or for rescue missions. In this paper, a number of issues related to the dynamics and control of artificial limbless locomotion systems are discussed. Simplest models of a limbless locomotor are two-body or three-body systems that move along a horizontal straight line. In the first part of the paper, the controls are assumed in the form of periodic functions with zero average, shifted on a phase one concerning each other. Thus, there is a traveling wave along the chain of particles. In the second part, actuator models are discussed. It is supposed that there are unknown actuator data or the worm system parameter are not known or exactly as well. The focus is on adaptive control algorithms for the worm-like locomotion systems in order to track given reference trajectories, like kinematic gaits. Finally, a prototype together with its signal processing and control software is presented. Theoretically (analytically and numerically) calculated results of the dynamical behavior of the mobile system are compared to experimental data.

Flow of viscoelastic fluids around a sharp microfluidic bend: Role of wormlike micellar structure

NASA Astrophysics Data System (ADS)

Hwang, Margaret Y.; Mohammadigoushki, Hadi; Muller, Susan J.

2017-04-01

We examine the flow and instabilities of three viscoelastic fluids—a semidilute aqueous solution of polyethylene oxide (PEO) and two wormlike micellar solutions of cetylpyridinium chloride and sodium salicylate—around a microfluidic 90∘ bend, in which shear deformation and streamline curvature dominate. Similar to results reported by Gulati et al. [S. Gulati et al., Phys. Rev. E 78, 036314 (2008), 10.1103/PhysRevE.78.036314; S. Gulati et al., J. Rheol. 54, 375 (2010), 10.1122/1.3308643] for PEO solutions, we report a critical Weissenberg number (Wi) for the onset of lip vortex formation upstream of the corner. However, the decreased aspect ratio (channel depth to width) results in a slightly higher critical Wi and a vortex that grows more slowly. We consider wormlike micellar solutions of two salt to surfactant concentration ratios R =0.55 and R =0.79 . At R =0.55 , the wormlike micelles are linear and exhibit strong viscoelastic behavior, but at R =0.79 , the wormlike micelles become branched and exhibit shear-banding behavior. Microfluidic experiments on the R =0.55 solution reveal two flow transitions. The first transition, at Wi =6 , is characterized by the formation of a stationary lip vortex upstream of the bend; at the second transition, at Wi =20 , the vortex fluctuates in time and changes size. The R =0.79 solution also exhibits two transitions. The first transition at Wi =4 is characterized by the appearance of two intermittent vortices, one at the lip and one at the far outside corner. Increasing the flow rate to Wi >160 results in a transition to a second unstable regime, where there is only a lip vortex that fluctuates in size. The difference in flow transitions in PEO and wormlike micellar solutions presumably arises from the additional contribution of wormlike micellar breakage and reformation under shear. The flow transitions in wormlike micellar solutions are also significantly affected by chain branching.

Course 1: Physics of Protein-DNA Interaction

NASA Astrophysics Data System (ADS)

Bruinsma, R. F.

1 Introduction 1.1 The central dogma and bacterial gene expression 1.2 Molecular structure 2 Thermodynamics and kinetics of repressor-DNA interaction 2.1 Thermodynamics and the lac repressor 2.2 Kinetics of repressor-DNA interaction 3 DNA deformability and protein-DNA interaction 3.1 Introduction 3.2 The worm-like chain 3.3 The RST model 4 Electrostatics in water and protein-DNA interaction 4.1 Macro-ions and aqueous electrostatics 4.2 The primitive model 4.3 Manning condensation 4.4 Counter-ion release and non-specific protein-DNA interaction

Long charged macromolecule in an entropic trap with rough surfaces.

PubMed

Mamasakhlisov, Yevgeni Sh; Hayryan, Shura; Hu, Chin-Kun

2012-11-01

The kinetics of the flux of a charged macromolecular solution through an environment of changing geometry with wide and constricted regions is investigated analytically. A model device consisting of alternating deep and shallow slits known as an "entropic trap" is used to represent the environment. The flux is supported by the external electrostatic field. The "wormlike chain" model is used for the macromolecule (dsDNA in the present study). The chain entropy in both the deep and the shallow slits, the work by the electric field, and the energy of the elastic bending of the chain are taken into account accurately. Based on the calculated free energy, the kinetics and the scaling behavior of the chain escaping from the entropic trap are studied. We find that the escape process occurs in two kinetic stages with different time scales and discuss the possible influence of the surface roughness. The scope of the accuracy of the proposed model is discussed.

Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6-7 microm.

PubMed

Seol, Yeonee; Li, Jinyu; Nelson, Philip C; Perkins, Thomas T; Betterton, M D

2007-12-15

The wormlike chain (WLC) model currently provides the best description of double-stranded DNA elasticity for micron-sized molecules. This theory requires two intrinsic material parameters-the contour length L and the persistence length p. We measured and then analyzed the elasticity of double-stranded DNA as a function of L (632 nm-7.03 microm) using the classic solution to the WLC model. When the elasticity data were analyzed using this solution, the resulting fitted value for the persistence length p(wlc) depended on L; even for moderately long DNA molecules (L = 1300 nm), this apparent persistence length was 10% smaller than its limiting value for long DNA. Because p is a material parameter, and cannot depend on length, we sought a new solution to the WLC model, which we call the "finite wormlike chain (FWLC)," to account for effects not considered in the classic solution. Specifically we accounted for the finite chain length, the chain-end boundary conditions, and the bead rotational fluctuations inherent in optical trapping assays where beads are used to apply the force. After incorporating these corrections, we used our FWLC solution to generate force-extension curves, and then fit those curves with the classic WLC solution, as done in the standard experimental analysis. These results qualitatively reproduced the apparent dependence of p(wlc) on L seen in experimental data when analyzed with the classic WLC solution. Directly fitting experimental data to the FWLC solution reduces the apparent dependence of p(fwlc) on L by a factor of 3. Thus, the FWLC solution provides a significantly improved theoretical framework in which to analyze single-molecule experiments over a broad range of experimentally accessible DNA lengths, including both short (a few hundred nanometers in contour length) and very long (microns in contour length) molecules.

Molecular interactions between lecithin and bile salts/acids in oils and their effects on reverse micellization.

PubMed

Njauw, Ching-Wei; Cheng, Chih-Yang; Ivanov, Viktor A; Khokhlov, Alexei R; Tung, Shih-Huang

2013-03-26

It has been known that the addition of bile salts to lecithin organosols induces the formation of reverse wormlike micelles and that the worms are similar to long polymer chains that entangle each other to form viscoelastic solutions. In this study, we further investigated the effects of different bile salts and bile acids on the growth of lecithin reverse worms in cyclohexane and n-decane. We utilized rheological and small-angle scattering techniques to analyze the properties and structures of the reverse micelles. All of the bile salts can transform the originally spherical lecithin reverse micelles into wormlike micelles and their rheological behaviors can be described by the single-relaxation-time Maxwell model. However, their efficiencies to induce the worms are different. In contrast, before phase separation, bile acids can induce only short cylindrical micelles that are not long enough to impart viscoelasticity. We used Fourier transform infrared spectroscopy to investigate the interactions between lecithin and bile salts/acids and found that different bile salts/acids employ different functional groups to form hydrogen bonds with lecithin. Such effects determine the relative positions of the bile salts/acids in the headgroups of lecithin, thus resulting in varying efficiencies to alter the effective critical packing parameter for the formation of wormlike micelles. This work highlights the importance of intermolecular interactions in molecular self-assembly.

Confined wormlike chains in external fields

NASA Astrophysics Data System (ADS)

Morrison, Greg

The confinement of biomolecules is ubiquitous in nature, such as the spatial constraints of viral encapsulation, histone binding, and chromosomal packing. Advances in microfluidics and nanopore fabrication have permitted powerful new tools in single molecule manipulation and gene sequencing through molecular confinement as well. In order to fully understand and exploit these systems, the ability to predict the structure of spatially confined molecules is essential. In this talk, I describe a mean field approach to determine the properties of stiff polymers confined to cylinders and slits, which is relevant for a variety of biological and experimental conditions. I show that this approach is able to not only reproduce known scaling laws for confined wormlike chains, but also provides an improvement over existing weakly bending rod approximations in determining the detailed chain properties (such as correlation functions). Using this approach, we also show that it is possible to study the effect of an externally applied tension or static electric field in a natural and analytically tractable way. These external perturbations can alter the scaling laws and introduce important new length scales into the system, relevant for histone unbinding and single-molecule analysis of DNA.

Synthesis and characterization of a new family of alkylammonium–chromium phosphates with worm-like morphology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Amghouz, Zakariae, E-mail: amghouz.uo@uniovi.es; Departamento de Química Orgánica e Inorgánica, Universidad de Oviedo-CINN, 33006 Oviedo; Espina, Aránzazu

A series of layered alkylammonium–chromium phosphates, formulated as [C{sub n}H{sub 2n+1}NH{sub 3}]Cr(OH)PO{sub 4} (n=2–6), has been synthesized under hydrothermal conditions. The interlayer spacing, increasing linearly with the increase of alkyl-chain length from 13.61 Å (n=2) to 21.20 Å (n=6), is occupied by a double sheet of packed amine molecules with a tilt angle of ca. 51° respect to the inorganic sheet. The powders are constituted by circular plates (diameter=0.5–3 µm, thickness=∼50 nm) with central holes when n=4–6, stacked in axial direction showing worm-like morphologies. The presence of holes, and some corrugated and zig-zag fashions observed on the edge of thinmore » circular plates are the most probable ways for the reduction of the steric tensions between organic and inorganic portions in these hybrid materials. The thermal and thermo-oxidative stability of selected compounds have been studied, including the determination of activation energy data for the decomposition processes. - Graphical abstract: A novel series of layered alkylammonium–chromium phosphates, [C{sub n}H{sub 2n+1}NH{sub 3}]Cr(OH)PO{sub 4} (n=2–6), was obtained and characterized. The interlayer spacing, increasing linearly with the increase of alkyl-chain length, is occupied by a double sheet of packed amine molecules. The powders are constituted by circular plates (diameter=0.5–3 µm, thickness=∼50 nm) with central holes when n=4–6, stacked in axial direction showing worm-like morphologies. - Highlights: • A series of alkylammonium–chromium phosphates has been obtained by the hydrothermal method. • The interlayer spacing increases linearly with the increase of alkyl-chain length. • The interlayer spacing is occupied by a double sheet of packed amine molecules. • The powders are constituted by stacked circular plates showing wormlike morphology. • Thermal behaviour depends on the atmosphere used and the intercalated amine.« less

Dissipative particle dynamics simulations of polymer chains: scaling laws and shearing response compared to DNA experiments.

PubMed

Symeonidis, Vasileios; Em Karniadakis, George; Caswell, Bruce

2005-08-12

Dissipative particle dynamics simulations of several bead-spring representations of polymer chains in dilute solution are used to demonstrate the correct static scaling laws for the radius of gyration. Shear flow results for the wormlike chain simulating single DNA molecules compare well with average extensions from experiments, irrespective of the number of beads. However, coarse graining with more than a few beads degrades the agreement of the autocorrelation of the extension.

Strip waves in vibrated shear-thickening wormlike micellar solutions

NASA Astrophysics Data System (ADS)

Epstein, T.; Deegan, R. D.

2010-06-01

We present an instability in vertically vibrated dilute wormlike micellar solutions. Above a critical driving acceleration the fluid forms elongated solitary domains of high amplitude waves. We model this instability using a Mathieu equation modified to account for the non-Newtonian character of the fluid. We find that our model successfully reproduces the observed transitions.

Relaxation dynamics of internal segments of DNA chains in nanochannels

NASA Astrophysics Data System (ADS)

Jain, Aashish; Muralidhar, Abhiram; Dorfman, Kevin; Dorfman Group Team

We will present relaxation dynamics of internal segments of a DNA chain confined in nanochannel. The results have direct application in genome mapping technology, where long DNA molecules containing sequence-specific fluorescent probes are passed through an array of nanochannels to linearize them, and then the distances between these probes (the so-called ``DNA barcode'') are measured. The relaxation dynamics of internal segments set the experimental error due to dynamic fluctuations. We developed a multi-scale simulation algorithm, combining a Pruned-Enriched Rosenbluth Method (PERM) simulation of a discrete wormlike chain model with hard spheres with Brownian dynamics (BD) simulations of a bead-spring chain. Realistic parameters such as the bead friction coefficient and spring force law parameters are obtained from PERM simulations and then mapped onto the bead-spring model. The BD simulations are carried out to obtain the extension autocorrelation functions of various segments, which furnish their relaxation times. Interestingly, we find that (i) corner segments relax faster than the center segments and (ii) relaxation times of corner segments do not depend on the contour length of DNA chain, whereas the relaxation times of center segments increase linearly with DNA chain size.

Chain conformational and physicochemical properties of fucoidans from sea cucumber.

PubMed

Xu, Xiaoqi; Xue, Changhu; Chang, Yaoguang; Wang, Jun; Jiang, Kunhao

2016-11-05

Although fucoidans from sea cucumber (SC-FUCs) have been proven as potential bioactive polysaccharides and functional food ingridents, their chain conformation and physicochemical properties were still poorly understood. This study investigated the chain conformation of fucoidans from sea cucumber Acaudina molpadioides (Am-FUC), Isostichopus badionotus (Ib-FUC) and Apostichopus japonicus (Aj-FUC), of which primary structure has been recently clarified. Chain conformation parameters demonstrated that studied SC-FUCs adopted random coil conformation in 150mM NaCl solution (pH 7.4). Based on the worm-like cylinder model and atomic force microscopy, the chain stiffness of SC-FUCs was further evaluated as Am-FUC≈Ib-FUC>Aj-FUC. It was suggested that the existence of branch structure increased the chain flexibility, while sulfated pattern exerted limited influence. SC-FUCs demonstrated shear-thinning rheological behavior and negative charge. Am-FUC possessed a higher thermostability than Ib-FUC and Aj-FUC. These results have important implications for understanding the molecular characteristics of SC-FUCs, which could facilitate their further application. Copyright © 2016 Elsevier Ltd. All rights reserved.

Softening of the stiffness of bottle-brush polymers by mutual interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bolisetty, S.; Airaud, C.; Rosenfeldt, S.

2007-04-15

We study bottle-brush macromolecules in a good solvent by small-angle neutron scattering (SANS), static light scattering (SLS), and dynamic light scattering (DLS). These polymers consist of a linear backbone to which long side chains are chemically grafted. The backbone contains about 1600 monomer units (weight average) and every second monomer unit carries side chains with approximately 60 monomer units. The SLS and SANS data extrapolated to infinite dilution lead to the form factor of the polymer that can be described in terms of a wormlike chain with a contour length of 380 nm and a persistence length of 17.5 nm.more » An analysis of the DLS data confirms these model parameters. The scattering intensities taken at finite concentration can be modeled using the polymer reference interaction site model. It reveals a softening of the bottle-brush polymers caused by their mutual interaction. We demonstrate that the persistence decreases from 17.5 nm down to 5 nm upon increasing the concentration from dilute solution to the highest concentration (40.59 g/l) under consideration. The observed softening of the chains is comparable to the theoretically predicted decrease of the electrostatic persistence length of linear polyelectrolyte chains at finite concentrations.« less

Light-responsive expansion-contraction of spherical nanoparticle grafted with azopolymers

NASA Astrophysics Data System (ADS)

Fu, Jie; Zhang, Xinghua; Miao, Bing; Yan, Dadong

2017-04-01

Due to the very importance for both fundamental research and technological applications, smart materials with stimuli-responsive properties have been studied intensively. Theoretical investigation contributes to this endeavor through constructing and analyzing a model system which captures main features of the corresponding complex material, wherefrom useful insight can be provided to the trial-and-error experiments. We here report a theoretical study on the smart spherical nanoparticle grafted with light-responsive azobenzene-containing polymers. Utilizing the photoisomerization ability of the azobenzene group, nanoparticles can undergo a light-induced expansion-contraction transition. The wormlike chain based single chain in mean field theory, which has been developed by us recently, is used to investigate this transition in detail. Exploring a large parameter space, our results definitely determine the parameters, including the chain length and effective Kuhn length of grafted chain, nanoparticle radius, grafting density, and position of the azobenzene group along the chain contour, to admit optimum light-responsive behavior of the smart nanoparticle, which provides a guide for experimentalists to design this type of material in a rational manner.

A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes.

PubMed Central

Klenin, K; Merlitz, H; Langowski, J

1998-01-01

For the interpretation of solution structural and dynamic data of linear and circular DNA molecules in the kb range, and for the prediction of the effect of local structural changes on the global conformation of such DNAs, we have developed an efficient and easy way to set up a program based on a second-order explicit Brownian dynamics algorithm. The DNA is modeled by a chain of rigid segments interacting through harmonic spring potentials for bending, torsion, and stretching. The electrostatics are handled using precalculated energy tables for the interactions between DNA segments as a function of relative orientation and distance. Hydrodynamic interactions are treated using the Rotne-Prager tensor. While maintaining acceptable precision, the simulation can be accelerated by recalculating this tensor only once in a certain number of steps. PMID:9533691

Ultrashort Nucleic Acid Duplexes Exhibit Long Wormlike Chain Behavior with Force-Dependent Edge Effects

NASA Astrophysics Data System (ADS)

Whitley, Kevin D.; Comstock, Matthew J.; Chemla, Yann R.

2018-02-01

Despite their importance in biology and use in nanotechnology, the elastic behavior of nucleic acids on "ultrashort" (<15 nt ) length scales remains poorly understood. Here, we use optical tweezers combined with fluorescence imaging to observe directly the hybridization of oligonucleotides (7-12 nt) to a complementary strand under tension and to measure the difference in end-to-end extension between the single-stranded and duplex states. Data are consistent with long-polymer models at low forces (<8 pN ) but smaller than predicted at higher forces (>8 pN ), the result of the sequence-dependent duplex edge effects.

Probing Protein-Protein Interactions by Dynamic Force Correlation Spectroscopy

NASA Astrophysics Data System (ADS)

Barsegov, V.; Thirumalai, D.

2005-10-01

We develop a formalism for single molecule dynamic force spectroscopy to map the energy landscape of protein-protein complex (P1P2). The joint distribution P(τ1,τ2) of unbinding lifetimes τ1 and τ2, measurable in a compression-tension cycle, which accounts for the internal relaxation dynamics of the proteins under tension, shows that the histogram of τ1 is not Poissonian. The theory is applied to the forced unbinding of protein P1, modeled as a wormlike chain, from P1P2. We propose a new class of experiments which can resolve the effect of internal protein dynamics on the unbinding lifetimes.

Electrostatic effects on hyaluronic acid configuration

NASA Astrophysics Data System (ADS)

Berezney, John; Saleh, Omar

2015-03-01

In systems of polyelectrolytes, such as solutions of charged biopolymers, the electrostatic repulsion between charged monomers plays a dominant role in determining the molecular conformation. Altering the ionic strength of the solvent thus affects the structure of such a polymer. Capturing this electrostatically-driven structural dependence is important for understanding many biological systems. Here, we use single molecule manipulation experiments to collect force-extension behavior on hyaluronic acid (HA), a polyanion which is a major component of the extracellular matrix in all vertebrates. By measuring HA elasticity in a variety of salt conditions, we are able to directly assess the contribution of electrostatics to the chain's self-avoidance and local stiffness. Similar to recent results from our group on single-stranded nucleic acids, our data indicate that HA behaves as a swollen chain of electrostatic blobs, with blob size proportional to the solution Debye length. Our data indicate that the chain structure within the blob is not worm-like, likely due to long-range electrostatic interactions. We discuss potential models of this effect.

Generalized theory of semiflexible polymers.

PubMed

Wiggins, Paul A; Nelson, Philip C

2006-03-01

DNA bending on length scales shorter than a persistence length plays an integral role in the translation of genetic information from DNA to cellular function. Quantitative experimental studies of these biological systems have led to a renewed interest in the polymer mechanics relevant for describing the conformational free energy of DNA bending induced by protein-DNA complexes. Recent experimental results from DNA cyclization studies have cast doubt on the applicability of the canonical semiflexible polymer theory, the wormlike chain (WLC) model, to DNA bending on biologically relevant length scales. This paper develops a theory of the chain statistics of a class of generalized semiflexible polymer models. Our focus is on the theoretical development of these models and the calculation of experimental observables. To illustrate our methods, we focus on a specific, illustrative model of DNA bending. We show that the WLC model generically describes the long-length-scale chain statistics of semiflexible polymers, as predicted by renormalization group arguments. In particular, we show that either the WLC or our present model adequately describes force-extension, solution scattering, and long-contour-length cyclization experiments, regardless of the details of DNA bend elasticity. In contrast, experiments sensitive to short-length-scale chain behavior can in principle reveal dramatic departures from the linear elastic behavior assumed in the WLC model. We demonstrate this explicitly by showing that our toy model can reproduce the anomalously large short-contour-length cyclization factors recently measured by Cloutier and Widom. Finally, we discuss the applicability of these models to DNA chain statistics in the context of future experiments.

The elasticity of soap bubbles containing wormlike micelles.

PubMed

Sabadini, Edvaldo; Ungarato, Rafael F S; Miranda, Paulo B

2014-01-28

Slow-motion imaging of the rupture of soap bubbles generally shows the edges of liquid films retracting at a constant speed (known as the Taylor-Culick velocity). Here we investigate soap bubbles formed from simple solutions of a cationic surfactant (cetyltrimethylammonium bromide - CTAB) and sodium salicylate. The interaction of salicylate ions with CTAB leads to the formation of wormlike micelles (WLM), which yield a viscoelastic behavior to the liquid film of the bubble. We demonstrate that these elastic bubbles collapse at a velocity up to 30 times higher than the Taylor-Culick limit, which has never been surpassed. This is because during the bubble inflation, the entangled WLM chains stretch, storing elastic energy. This extra energy is then released during the rupture of the bubble, yielding an additional driving force for film retraction (besides surface tension). This new mechanism for the bursting of elastic bubbles may have important implications to the breakup of viscoelastic sprays in industrial applications.

Theory of high-force DNA stretching and overstretching.

PubMed

Storm, C; Nelson, P C

2003-05-01

Single-molecule experiments on single- and double-stranded DNA have sparked a renewed interest in the force versus extension of polymers. The extensible freely jointed chain (FJC) model is frequently invoked to explain the observed behavior of single-stranded DNA, but this model does not satisfactorily describe recent high-force stretching data. We instead propose a model (the discrete persistent chain) that borrows features from both the FJC and the wormlike chain, and show that it resembles the data more closely. We find that most of the high-force behavior previously attributed to stretch elasticity is really a feature of the corrected entropic elasticity; the true stretch compliance of single-stranded DNA is several times smaller than that found by previous authors. Next we elaborate our model to allow coexistence of two conformational states of DNA, each with its own stretch and bend elastic constants. Our model is computationally simple and gives an excellent fit through the entire overstretching transition of nicked, double-stranded DNA. The fit gives the first value for the bend stiffness of the overstretched state. In particular, we find the effective bend stiffness for DNA in this state to be about 12 nm k(B)T, a value quite different from either the B-form or single-stranded DNA.

Internal friction of single polypeptide chains at high stretch.

PubMed

Khatri, Bhavin S; Byrne, Katherine; Kawakami, Masaru; Brockwell, David J; Smith, D Alastair; Radford, Sheena E; McLeish, Tom C B

2008-01-01

Experiments that measure the viscoelasticity of single molecules from the Brownian fluctuations of an atomic force microscope (AFM) have provided a new window onto their internal dynamics in an underlying conformational landscape. Here we develop and apply these methods to examine the internal friction of unfolded polypeptide chains at high stretch. The results reveal a power law dependence of internal friction with tension (exponent 1.3 +/- 0.5) and a relaxation time approximately independent of force. To explain these results we develop a frictional worm-like chain (FWLC) model based on the Rayleigh dissipation function of a stiff chain with dynamical resistance to local bending. We analyse the dissipation rate integrated over the chain length by its Fourier components to calculate an effective tension-dependent friction constant for the end-to-end vector of the chain. The result is an internal friction that increases as a power law with tension with an exponent 3/2, consistent with experiment. Extracting the intrinsic bending friction constant of the chain it is found to be approximately 7 orders of magnitude greater than expected from solvent friction alone; a possible explanation we offer is that the underlying energy landscape for bending amino acids and/or peptide bond is rough, consistent with recent results on both proteins and polysaccharides.

Structure of flexible and semiflexible polyelectrolyte chains in confined spaces of slit micro/nanochannels.

PubMed

Jeon, Jonggu; Chun, Myung-Suk

2007-04-21

Understanding the behavior of a polyelectrolyte in confined spaces has direct relevance in design and manipulation of microfluidic devices, as well as transport in living organisms. In this paper, a coarse-grained model of anionic semiflexible polyelectrolyte is applied, and its structure and dynamics are fully examined with Brownian dynamics (BD) simulations both in bulk solution and under confinement between two negatively charged parallel plates. The modeling is based on the nonlinear bead-spring discretization of a continuous chain with additional long-range electrostatic, Lennard-Jones, and hydrodynamic interactions between pairs of beads. The authors also consider the steric and electrostatic interactions between the bead and the confining wall. Relevant model parameters are determined from experimental rheology data on the anionic polysaccharide xanthan reported previously. For comparison, both flexible and semiflexible models are developed accompanying zero and finite intrinsic persistence lengths, respectively. The conformational changes of the polyelectrolyte chain induced by confinements and their dependence on the screening effect of the electrolyte solution are faithfully characterized with BD simulations. Depending on the intrinsic rigidity and the medium ionic strength, the polyelectrolyte can be classified as flexible, semiflexible, or rigid. Confined flexible and semiflexible chains exhibit a nonmonotonic variation in size, as measured by the radius of gyration and end-to-end distance, with changing slit width. For the semiflexible chain, this is coupled to the variations in long-range bond vector correlation. The rigid chain, realized at low ionic strength, does not have minima in size but exhibits a sigmoidal transition. The size of confined semiflexible and rigid polyelectrolytes can be well described by the wormlike chain model once the electrostatic effects are taken into account by the persistence length measured at long length scale.

Formation of Worm-Like Micelles in Mixed N-Hexadecyl-N-Methylpyrrolidinium Bromide-Based Cationic Surfactant and Anionic Surfactant Systems

PubMed Central

Dai, Caili; Yan, Zhihu; You, Qing; Du, Mingyong; Zhao, Mingwei

2014-01-01

Through the descriptive and rheological characterization of worm-like micelles formed by N-hexadecyl-N-methylpyrrolidinium bromide and sodium laurate, the formation and properties of the worm-like micelles were affected by the concentrations of sodium laurate and temperature. Additionally, cryogenic transmission electron microscopy images further validated the formation of worm-like micelles. PMID:25019152

Sequence-Dependent Persistence Length of Long DNA

NASA Astrophysics Data System (ADS)

Chuang, Hui-Min; Reifenberger, Jeffrey G.; Cao, Han; Dorfman, Kevin D.

2017-12-01

Using a high-throughput genome-mapping approach, we obtained circa 50 million measurements of the extension of internal human DNA segments in a 41 nm ×41 nm nanochannel. The underlying DNA sequences, obtained by mapping to the reference human genome, are 2.5-393 kilobase pairs long and contain percent GC contents between 32.5% and 60%. Using Odijk's theory for a channel-confined wormlike chain, these data reveal that the DNA persistence length increases by almost 20% as the percent GC content increases. The increased persistence length is rationalized by a model, containing no adjustable parameters, that treats the DNA as a statistical terpolymer with a sequence-dependent intrinsic persistence length and a sequence-independent electrostatic persistence length.

Statistical model of a flexible inextensible polymer chain: The effect of kinetic energy.

PubMed

Pergamenshchik, V M; Vozniak, A B

2017-01-01

Because of the holonomic constraints, the kinetic energy contribution in the partition function of an inextensible polymer chain is difficult to find, and it has been systematically ignored. We present the first thermodynamic calculation incorporating the kinetic energy of an inextensible polymer chain with the bending energy. To explore the effect of the translation-rotation degrees of freedom, we propose and solve a statistical model of a fully flexible chain of N+1 linked beads which, in the limit of smooth bending, is equivalent to the well-known wormlike chain model. The partition function with the kinetic and bending energies and correlations between orientations of any pair of links and velocities of any pair of beads are found. This solution is precise in the limits of small and large rigidity-to-temperature ratio b/T. The last exact solution is essential as even very "harmless" approximation results in loss of the important effects when the chain is very rigid. For very high b/T, the orientations of different links become fully correlated. Nevertheless, the chain does not go over into a hard rod even in the limit b/T→∞: While the velocity correlation length diverges, the correlations themselves remain weak and tend to the value ∝T/(N+1). The N dependence of the partition function is essentially determined by the kinetic energy contribution. We demonstrate that to obtain the correct energy and entropy in a constrained system, the T derivative of the partition function has to be applied before integration over the constraint-setting variable.

Statistical model of a flexible inextensible polymer chain: The effect of kinetic energy

NASA Astrophysics Data System (ADS)

Pergamenshchik, V. M.; Vozniak, A. B.

2017-01-01

Because of the holonomic constraints, the kinetic energy contribution in the partition function of an inextensible polymer chain is difficult to find, and it has been systematically ignored. We present the first thermodynamic calculation incorporating the kinetic energy of an inextensible polymer chain with the bending energy. To explore the effect of the translation-rotation degrees of freedom, we propose and solve a statistical model of a fully flexible chain of N +1 linked beads which, in the limit of smooth bending, is equivalent to the well-known wormlike chain model. The partition function with the kinetic and bending energies and correlations between orientations of any pair of links and velocities of any pair of beads are found. This solution is precise in the limits of small and large rigidity-to-temperature ratio b /T . The last exact solution is essential as even very "harmless" approximation results in loss of the important effects when the chain is very rigid. For very high b /T , the orientations of different links become fully correlated. Nevertheless, the chain does not go over into a hard rod even in the limit b /T →∞ : While the velocity correlation length diverges, the correlations themselves remain weak and tend to the value ∝T /(N +1 ). The N dependence of the partition function is essentially determined by the kinetic energy contribution. We demonstrate that to obtain the correct energy and entropy in a constrained system, the T derivative of the partition function has to be applied before integration over the constraint-setting variable.

Polymerization of anionic wormlike micelles.

PubMed

Zhu, Zhiyuan; González, Yamaira I; Xu, Hangxun; Kaler, Eric W; Liu, Shiyong

2006-01-31

Polymerizable anionic wormlike micelles are obtained upon mixing the hydrotropic salt p-toluidine hydrochloride (PTHC) with the reactive anionic surfactant sodium 4-(8-methacryloyloxyoctyl)oxybenzene sulfonate (MOBS). Polymerization captures the cross-sectional radius of the micelles (approximately 2 nm), induces micellar growth, and leads to the formation of a stable single-phase dispersion of wormlike micellar polymers. The unpolymerized and polymerized micelles were characterized using static and dynamic laser light scattering, small-angle neutron scattering, 1H NMR, and stopped-flow light scattering. Stopped-flow light scattering was also used to measure the average lifetime of the unpolymerized wormlike micelles. A comparison of the average lifetime of unpolymerized wormlike micelles with the surfactant monomer propagation rate was used to elucidate the mechanism of polymerization. There is a significant correlation between the ratio of the average lifetime to the monomer propagation rate and the average aggregation number of the polymerized wormlike micelles.

Polyelectrolyte properties of single stranded DNA measured using SAXS and single molecule FRET: beyond the wormlike chain model

PubMed Central

Meisburger, Steve P.; Sutton, Julie L.; Chen, Huimin; Pabit, Suzette A.; Kirmizialtin, Serdal; Elber, Ron; Pollack, Lois

2013-01-01

Nucleic acids are highly charged polyelectrolytes that interact strongly with salt ions. Rigid, base-paired regions are successfully described with worm like chain models, but non base-paired single stranded regions have fundamentally different polymer properties because of their greater flexibility. Recently, attention has turned to single stranded nucleic acids due to the growing recognition of their biological importance, as well as the availability of sophisticated experimental techniques sensitive to the conformation of individual molecules. We investigate polyelectrolyte properties of poly(dT), an important and widely studied model system for flexible single stranded nucleic acids, in physiologically important mixed mono- and di-valent salt. We report measurements of the form factor and interparticle interactions using SAXS, end to end distances using smFRET, and number of excess ions using ASAXS. We present a coarse-grained model that accounts for flexibility, excluded volume, and electrostatic interactions in these systems. Predictions of the model are validated against experiment. We also discuss the state of all-atom, explicit solvent Molecular Dynamics simulations of poly(dT), the next step in understanding the complexities of ion interactions with these highly charged and flexible polymers. PMID:23606337

Can More Nanoparticles Induce Larger Viscosities of Nanoparticle-Enhanced Wormlike Micellar System (NEWMS)?

PubMed

Zhao, Mingwei; Zhang, Yue; Zou, Chenwei; Dai, Caili; Gao, Mingwei; Li, Yuyang; Lv, Wenjiao; Jiang, Jianfeng; Wu, Yining

2017-09-18

There have been many reports about the thickening ability of nanoparticles on the wormlike micelles in the recent years. Through the addition of nanoparticles, the viscosity of wormlike micelles can be increased. There still exists a doubt: can viscosity be increased further by adding more nanoparticles? To answer this issue, in this work, the effects of silica nanoparticles and temperature on the nanoparticles-enhanced wormlike micellar system (NEWMS) were studied. The typical wormlike micelles (wormlike micelles) are prepared by 50 mM cetyltrimethyl ammonium bromide (CTAB) and 60 mM sodium salicylate (NaSal). The rheological results show the increase of viscoelasticity in NEWMS by adding nanoparticles, with the increase of zero-shear viscosity and relaxation time. However, with the further increase of nanoparticles, an interesting phenomenon appears. The zero-shear viscosity and relaxation time reach the maximum and begin to decrease. The results show a slight increasing trend for the contour length of wormlike micelles by adding nanoparticles, while no obvious effect on the entanglement and mesh size. In addition, with the increase of temperature, remarkable reduction of contour length and relaxation time can be observed from the calculation. NEWMS constantly retain better viscoelasticity compared with conventional wormlike micelles without silica nanoparticles. According to the Arrhenius equation, the activation energy E a shows the same increase trend of NEWMS. Finally, a mechanism is proposed to explain this interesting phenomenon.

Microfluidic flows of wormlike micellar solutions.

PubMed

Zhao, Ya; Cheung, Perry; Shen, Amy Q

2014-09-01

The widespread use of wormlike micellar solutions is commonly found in household items such as cosmetic products, industrial fluids used in enhanced oil recovery and as drag reducing agents, and in biological applications such as drug delivery and biosensors. Despite their extensive use, there are still many details about the microscopic micellar structure and the mechanisms by which wormlike micelles form under flow that are not clearly understood. Microfluidic devices provide a versatile platform to study wormlike micellar solutions under various flow conditions and confined geometries. A review of recent investigations using microfluidics to study the flow of wormlike micelles is presented here with an emphasis on three different flow types: shear, elongation, and complex flow fields. In particular, we focus on the use of shear flows to study shear banding, elastic instabilities of wormlike micellar solutions in extensional flow (including stagnation and contraction flow field), and the use of contraction geometries to measure the elongational viscosity of wormlike micellar solutions. Finally, we showcase the use of complex flow fields in microfluidics to generate a stable and nanoporous flow-induced structured phase (FISP) from wormlike micellar solutions. This review shows that the influence of spatial confinement and moderate hydrodynamic forces present in the microfluidic device can give rise to a host of possibilities of microstructural rearrangements and interesting flow phenomena. Copyright © 2014 Elsevier B.V. All rights reserved.

Self assembled linear polymeric chains with tuneable semiflexibility using isotropic interactions.

PubMed

Abraham, Alex; Chatterji, Apratim

2018-04-21

We propose a two-body spherically symmetric (isotropic) potential such that particles interacting by the potential self-assemble into linear semiflexible polymeric chains without branching. By suitable control of the potential parameters, we can control the persistence length of the polymer and can even introduce a controlled number of branches. Thus we show how to achieve effective directional interactions starting from spherically symmetric potentials. The self-assembled polymers have an exponential distribution of chain lengths akin to what is observed for worm-like micellar systems. On increasing particle density, the polymeric chains self-organize to an ordered line-hexagonal phase where every chain is surrounded by six parallel chains, the transition is first order. On further increase in monomer density, the order is destroyed and we get a branched gel-like phase. This potential can be used to model semi-flexible equilibrium polymers with tunable semiflexibility and excluded volume. The use of the potential is computationally cheap and hence can be used to simulate and probe equilibrium polymer dynamics with long chains. The potential also gives a plausible method of tuning colloidal interactions in experiments such that one can obtain self-assembling polymeric chains made up of colloids and probe polymer dynamics using an optical microscope. Furthermore, we show how a modified potential leads to the observation of an intermediate nematic phase of self-assembled chains in between the low density disordered phase and the line-ordered hexagonal phase.

Self assembled linear polymeric chains with tuneable semiflexibility using isotropic interactions

NASA Astrophysics Data System (ADS)

Abraham, Alex; Chatterji, Apratim

2018-04-01

We propose a two-body spherically symmetric (isotropic) potential such that particles interacting by the potential self-assemble into linear semiflexible polymeric chains without branching. By suitable control of the potential parameters, we can control the persistence length of the polymer and can even introduce a controlled number of branches. Thus we show how to achieve effective directional interactions starting from spherically symmetric potentials. The self-assembled polymers have an exponential distribution of chain lengths akin to what is observed for worm-like micellar systems. On increasing particle density, the polymeric chains self-organize to an ordered line-hexagonal phase where every chain is surrounded by six parallel chains, the transition is first order. On further increase in monomer density, the order is destroyed and we get a branched gel-like phase. This potential can be used to model semi-flexible equilibrium polymers with tunable semiflexibility and excluded volume. The use of the potential is computationally cheap and hence can be used to simulate and probe equilibrium polymer dynamics with long chains. The potential also gives a plausible method of tuning colloidal interactions in experiments such that one can obtain self-assembling polymeric chains made up of colloids and probe polymer dynamics using an optical microscope. Furthermore, we show how a modified potential leads to the observation of an intermediate nematic phase of self-assembled chains in between the low density disordered phase and the line-ordered hexagonal phase.

Worm-like mesoporous TiO2 thin films templated using comb copolymer for dye-sensitized solar cells with polymer electrolyte

NASA Astrophysics Data System (ADS)

Lee, Jae Hun; Park, Cheol Hun; Jung, Jung Pyo; Kim, Jong Hak

2015-12-01

A comb copolymer consisting of hydrophobic poly(2-[3-(2H-benzotriazol-2-yl)-4-hydroxyphenyl] ethyl methacrylate) (PBEM) and hydrophilic poly(oxyethylene methacrylate) (POEM) is synthesized via one-pot free radical polymerization. The PBEM-POEM comb copolymer is used as an agent to direct the structure toward one consisting of worm-like mesoporous TiO2 (WM-TiO2) films. The selective, preferential interaction between the titania precursor and the hydrophilic POEM chains is responsible for the formation of a well-organized worm-like mesostructure. The morphology of the WM-TiO2 films is characterized by scanning electron microscopy (SEM) and atomic force microscopy (AFM). In particular, the effects of film thickness on the optical and electrochemical properties are systematically investigated. The introduction of the WM-TiO2 layer between the nanocrystalline TiO2 (NC-TiO2) layer and fluorine-doped tin oxide (FTO) glass results in increased transmittance of visible light due to an antireflective property, decreased interfacial resistance and suppressed charge recombination at the interfaces of NC-TiO2/FTO glass. As a result, the photovoltaic conversion efficiency of the dye-sensitized solar cell (DSSC) with a polymer electrolyte is improved from 5.3% to 6.6% at an optimum film thickness (310 nm). The obtained efficiency represents a higher efficiency for the N719-based DSSC with a solvent-free, polymer electrolyte.

Study of the Formation and Solution Properties of Worm-Like Micelles Formed Using Both N-Hexadecyl-N-Methylpiperidinium Bromide-Based Cationic Surfactant and Anionic Surfactant

PubMed Central

Yan, Zhihu; Dai, Caili; Feng, Haishun; Liu, Yifei; Wang, Shilu

2014-01-01

The viscoelastic properties of worm-like micelles formed by mixing the cationic surfactant N-hexadecyl-N-methylpiperidinium bromide (C16MDB) with the anionic surfactant sodium laurate (SL) in aqueous solutions were investigated using rheological measurements. The effects of sodium laurate and temperature on the worm-like micelles and the mechanism of the observed shear thinning phenomenon and pseudoplastic behavior were systematically investigated. Additionally, cryogenic transmission electron microscopy images further ascertained existence of entangled worm-like micelles. PMID:25296131

Modeling the Inhomogeneous Response of Steady and Transient Flows of Entangled Micellar Solutions

NASA Astrophysics Data System (ADS)

McKinley, Gareth

2008-03-01

Surfactant molecules can self-assemble in solution into long flexible structures known as wormlike micelles. These structures entangle, forming a viscoelastic network similar to those in entangled polymer melts and solutions. However, in contrast to `inert' polymeric networks, wormlike micelles continuously break and reform leading to an additional relaxation mechanism and the name `living polymers'. Observations in both classes of entangled fluids have shown that steady and transient shearing flows of these solutions exhibit spatial inhomogeneities such as `shear-bands' at sufficiently large applied strains. In the present work, we investigate the dynamical response of a class of two-species elastic network models which can capture, in a self-consistent manner, the creation and destruction of elastically-active network segments, as well as diffusive coupling between the microstructural conformations and the local state of stress in regions with large spatial gradients of local deformation. These models incorporate a discrete version of the micellar breakage and reforming dynamics originally proposed by Cates and capture, at least qualitatively, non-affine tube deformation and chain disentanglement. The `flow curves' of stress and apparent shear rate resulting from an assumption of homogeneous deformation is non-monotonic and linear stability analysis shows that the region of non-monotonic response is unstable. Calculation of the full inhomogeneous flow field results in localized shear bands that grow linearly in extent across the gap as the apparent shear rate increases. Time-dependent calculations in step strain, large amplitude oscillatory shear (LAOS) and in start up of steady shear flow show that the velocity profile in the gap and the total stress measured at the bounding surfaces are coupled and evolve in a complex non-monotonic manner as the shear bands develop and propagate.

Damage, Self-Healing, and Hysteresis in Spider Silks

PubMed Central

De Tommasi, D.; Puglisi, G.; Saccomandi, G.

2010-01-01

Abstract In this article, we propose a microstructure-based continuum model to describe the material behavior of spider silks. We suppose that the material is composed of a soft fraction with entropic elasticity and a hard, damageable fraction. The hard fraction models the presence of stiffer, crystal-rich, oriented regions and accounts for the effect of softening induced by the breaking of hydrogen bonds. To describe the observed presence of crystals with different size, composition, and orientation, this hard fraction is modeled as a distribution of materials with variable properties. The soft fraction describes the remaining regions of amorphous material and is here modeled as a wormlike chain. During stretching, we consider the effect of bond-breaking as a transition from the hard- to the soft-material phase. As we demonstrate, a crucial effect of bond-breaking that accompanies the softening of the material is an increase in contour length associated with chains unraveling. The model describes also the self-healing properties of the material by assuming partial bond reconnection upon unloading. Despite its simplicity, the proposed mechanical system reproduces the main experimental effects observed in cyclic loading of spider silks. Moreover, our approach is amenable to two- or three-dimensional extensions and may prove to be a useful tool in the field of microstructure optimization for bioinspired materials. PMID:20441758

High flexibility of DNA on short length scales probed by atomic force microscopy.

PubMed

Wiggins, Paul A; van der Heijden, Thijn; Moreno-Herrero, Fernando; Spakowitz, Andrew; Phillips, Rob; Widom, Jonathan; Dekker, Cees; Nelson, Philip C

2006-11-01

The mechanics of DNA bending on intermediate length scales (5-100 nm) plays a key role in many cellular processes, and is also important in the fabrication of artificial DNA structures, but previous experimental studies of DNA mechanics have focused on longer length scales than these. We use high-resolution atomic force microscopy on individual DNA molecules to obtain a direct measurement of the bending energy function appropriate for scales down to 5 nm. Our measurements imply that the elastic energy of highly bent DNA conformations is lower than predicted by classical elasticity models such as the worm-like chain (WLC) model. For example, we found that on short length scales, spontaneous large-angle bends are many times more prevalent than predicted by the WLC model. We test our data and model with an interlocking set of consistency checks. Our analysis also shows how our model is compatible with previous experiments, which have sometimes been viewed as confirming the WLC.

An effective model of DNA like helicoidal structure: with length fluctuation nonlinearity

NASA Astrophysics Data System (ADS)

Tseytlin, Y. M.

2011-03-01

One of the natural helicoidal nanostructure, which thermomechanical features are studied carefully with the help of different mechanical models, is a DNA cell / molecule. Our study proves that the experimentally determined nonlinear fluctuations of the molecular length of DNA can be better understood by modeling the molecule as a helicoidal pretwisted nanostrip sensor with nonlinear function. The calculations presented here are in good agreement with the experimental data within 10%. Other used by many researchers mechanical models such as an elastic rod, wormlike chain (WLC), accordion bellows, or an elastic core wrapped with rigid wires do not show the possible variance nonlinearity of thermomechanical DNA molecular length fluctuations. We have found that the nonlinear variance of the length fluctuations is an intrinsic property of the micro-nano-sensors with helicoidal shape. This model allows us to estimate the persistence length and twist-stretch coupling of a DNA molecule as well. It also shows the molecule's overwinding possibility at initial stretching with correct numerical representation.

Methods for modeling cytoskeletal and DNA filaments

NASA Astrophysics Data System (ADS)

Andrews, Steven S.

2014-02-01

This review summarizes the models that researchers use to represent the conformations and dynamics of cytoskeletal and DNA filaments. It focuses on models that address individual filaments in continuous space. Conformation models include the freely jointed, Gaussian, angle-biased chain (ABC), and wormlike chain (WLC) models, of which the first three bend at discrete joints and the last bends continuously. Predictions from the WLC model generally agree well with experiment. Dynamics models include the Rouse, Zimm, stiff rod, dynamic WLC, and reptation models, of which the first four apply to isolated filaments and the last to entangled filaments. Experiments show that the dynamic WLC and reptation models are most accurate. They also show that biological filaments typically experience strong hydrodynamic coupling and/or constrained motion. Computer simulation methods that address filament dynamics typically compute filament segment velocities from local forces using the Langevin equation and then integrate these velocities with explicit or implicit methods; the former are more versatile and the latter are more efficient. Much remains to be discovered in biological filament modeling. In particular, filament dynamics in living cells are not well understood, and current computational methods are too slow and not sufficiently versatile. Although primarily a review, this paper also presents new statistical calculations for the ABC and WLC models. Additionally, it corrects several discrepancies in the literature about bending and torsional persistence length definitions, and their relations to flexural and torsional rigidities.

Conformation and structural changes of diblock copolymers with octopus-like micelle formation in the presence of external stimuli

NASA Astrophysics Data System (ADS)

Dammertz, K.; Saier, A. M.; Marti, O.; Amirkhani, M.

2014-04-01

External stimuli such as vapours and electric fields can be used to manipulate the formation of AB-diblock copolymers on surfaces. We study the conformational variation of PS-b-PMMA (polystyrene-block-poly(methyl methacrylate)), PS and PMMA adsorbed on mica and their response to saturated water or chloroform atmospheres. Using specimens with only partial polymer coverage, new unanticipated effects were observed. Water vapour, a non-solvent for all three polymers, was found to cause high surface mobility. In contrast, chloroform vapour (a solvent for all three polymers) proved to be less efficient. Furthermore, the influence of an additional applied electric field was investigated. A dc field oriented parallel to the sample surface induces the formation of polymer islands which assemble into wormlike chains. Moreover, PS-b-PMMA forms octopus-like micelles (OLMs) on mica. Under the external stimuli mentioned above, the wormlike formations of OLMs are able to align in the direction of the external electric field. In the absence of an electric field, the OLMs disaggregate and exhibit phase separated structures under chloroform vapour.

Synthesis and characterization of a new family of alkylammonium-chromium phosphates with worm-like morphology

NASA Astrophysics Data System (ADS)

Amghouz, Zakariae; Espina, Aránzazu; García, José R.

2015-01-01

A series of layered alkylammonium-chromium phosphates, formulated as [CnH2n+1NH3]Cr(OH)PO4 (n=2-6), has been synthesized under hydrothermal conditions. The interlayer spacing, increasing linearly with the increase of alkyl-chain length from 13.61 Å (n=2) to 21.20 Å (n=6), is occupied by a double sheet of packed amine molecules with a tilt angle of ca. 51° respect to the inorganic sheet. The powders are constituted by circular plates (diameter=0.5-3 μm, thickness= 50 nm) with central holes when n=4-6, stacked in axial direction showing worm-like morphologies. The presence of holes, and some corrugated and zig-zag fashions observed on the edge of thin circular plates are the most probable ways for the reduction of the steric tensions between organic and inorganic portions in these hybrid materials. The thermal and thermo-oxidative stability of selected compounds have been studied, including the determination of activation energy data for the decomposition processes.

Modeling the relaxation of internal DNA segments during genome mapping in nanochannels.

PubMed

Jain, Aashish; Sheats, Julian; Reifenberger, Jeffrey G; Cao, Han; Dorfman, Kevin D

2016-09-01

We have developed a multi-scale model describing the dynamics of internal segments of DNA in nanochannels used for genome mapping. In addition to the channel geometry, the model takes as its inputs the DNA properties in free solution (persistence length, effective width, molecular weight, and segmental hydrodynamic radius) and buffer properties (temperature and viscosity). Using pruned-enriched Rosenbluth simulations of a discrete wormlike chain model with circa 10 base pair resolution and a numerical solution for the hydrodynamic interactions in confinement, we convert these experimentally available inputs into the necessary parameters for a one-dimensional, Rouse-like model of the confined chain. The resulting coarse-grained model resolves the DNA at a length scale of approximately 6 kilobase pairs in the absence of any global hairpin folds, and is readily studied using a normal-mode analysis or Brownian dynamics simulations. The Rouse-like model successfully reproduces both the trends and order of magnitude of the relaxation time of the distance between labeled segments of DNA obtained in experiments. The model also provides insights that are not readily accessible from experiments, such as the role of the molecular weight of the DNA and location of the labeled segments that impact the statistical models used to construct genome maps from data acquired in nanochannels. The multi-scale approach used here, while focused towards a technologically relevant scenario, is readily adapted to other channel sizes and polymers.

Numerical methods for multi-scale modeling of non-Newtonian flows

NASA Astrophysics Data System (ADS)

Symeonidis, Vasileios

This work presents numerical methods for the simulation of Non-Newtonian fluids in the continuum as well as the mesoscopic level. The former is achieved with Direct Numerical Simulation (DNS) spectral h/p methods, while the latter employs the Dissipative Particle Dynamics (DPD) technique. Physical results are also presented as a motivation for a clear understanding of the underlying numerical approaches. The macroscopic simulations employ two non-Newtonian models, namely the Reiner-Ravlin (RR) and the viscoelastic FENE-P model. (1) A spectral viscosity method defined by two parameters ε, M is used to stabilize the FENE-P conformation tensor c. Convergence studies are presented for different combinations of these parameters. Two boundary conditions for the tensor c are also investigated. (2) Agreement is achieved with other works for Stokes flow of a two-dimensional cylinder in a channel. Comparison of the axial normal stress and drag coefficient on the cylinder is presented. Further, similar results from unsteady two- and three-dimensional turbulent flows past a flat plate in a channel are shown. (3) The RR problem is formulated for nearly incompressible flows, with the introduction of a mathematically equivalent tensor formulation. A spectral viscosity method and polynomial over-integration are studied. Convergence studies, including a three-dimensional channel flow with a parallel slot, investigate numerical problems arising from elemental boundaries and sharp corners. (4) The round hole pressure problem is presented for Newtonian and RR fluids in geometries with different hole sizes. Comparison with experimental data is made for the Newtonian case. The flaw in the experimental assumptions of undisturbed pressure opposite the hole is revealed, while good agreement with the data is shown. The Higashitani-Pritchard kinematical theory for RR, fluids is recovered for round holes and an approximate formula for the RR Stokes hole pressure is presented. The mesoscopic simulations assume bead-spring representations of polymer chains and investigate different integrating schemes of the DPD equations and different intra-polymer force combinations. (1) A novel family of time-staggered integrators is presented, taking advantage of the time-scale disparity between polymer-solvent and solvent-solvent interactions. Convergence tests for relaxation parameters for the velocity-Verlet and Lowe's schemes are presented. (2) Wormlike chains simulating lambda- DNA molecules subject to constant shear are studied, and direct comparison with Brownian Dynamics and experimental results is made. The effect of the number of beads per chain is examined through the extension autocorrelation function. (3) The Schmidt number (Sc) for each numerical scheme is investigated and the dependence on the scheme's parameters is shown. Re-visiting the wormlike chain problem under shear, we recover a better agreement with the experimental data through proper adjustment of Sc.

Hierarchical self-assembly: Self-organized nanostructures in a nematically ordered matrix of self-assembled polymeric chains

NASA Astrophysics Data System (ADS)

Mubeena, Shaikh; Chatterji, Apratim

2015-03-01

We report many different nanostructures which are formed when model nanoparticles of different sizes (diameter σn) are allowed to aggregate in a background matrix of semiflexible self-assembled polymeric wormlike micellar chains. The different nanostructures are formed by the dynamical arrest of phase-separating mixtures of micellar monomers and nanoparticles. The different morphologies obtained are the result of an interplay of the available free volume, the elastic energy of deformation of polymers, the density (chemical potential) of the nanoparticles in the polymer matrix, and, of course, the ratio of the size of self-assembling nanoparticles and self-avoidance diameter of polymeric chains. We have used a hybrid semi-grand-canonical Monte Carlo simulation scheme to obtain the (nonequilibrium) phase diagram of the self-assembled nanostructures. We observe rodlike structures of nanoparticles which get self-assembled in the gaps between the nematically ordered chains, as well as percolating gel-like network of conjoined nanotubes. We also find a totally unexpected interlocked crystalline phase of nanoparticles and monomers, in which each crystal plane of nanoparticles is separated by planes of perfectly organized polymer chains. We identified the condition which leads to such interlocked crystal structure. We suggest experimental possibilities of how the results presented in this paper could be used to obtain different nanostructures in the laboratory.

Examining the Self-Assembly of Rod-Coil Block Copolymers via Physics Based Polymer Models and Polarized X-Ray Scattering

NASA Astrophysics Data System (ADS)

Hannon, Adam; Sunday, Daniel; Windover, Donald; Liman, Christopher; Bowen, Alec; Khaira, Gurdaman; de Pablo, Juan; Delongchamp, Dean; Kline, R. Joseph

Photovoltaics, flexible electronics, and stimuli-responsive materials all require enhanced methodology to examine their nanoscale molecular orientation. The mechanical, electronic, optical, and transport properties of devices made from these materials are all a function of this orientation. The polymer chains in these materials are best modeled as semi-flexible to rigid rods. Characterizing the rigidity and molecular orientation of these polymers non-invasively is currently being pursued by using polarized resonant soft X-ray scattering (P-RSoXS). In this presentation, we show recent work on implementing such a characterization process using a rod-coil block copolymer system in the rigid-rod limit. We first demonstrate how we have used physics based models such as self-consistent field theory (SCFT) in non-polarized RSoXS work to fit scattering profiles for thin film coil-coil PS- b-PMMA block copolymer systems. We then show by using a wormlike chain partition function in the SCFT formulism to model the rigid-rod block, the methodology can be used there as well to extract the molecular orientation of the rod block from a simulated P-RSoXS experiment. The results from the work show the potential of the technique to extract thermodynamic and morphological sample information.

Worm-like micelles of CTAB and sodium salicylate under turbulent flow.

PubMed

Rodrigues, Roberta K; da Silva, Marcelo A; Sabadini, Edvaldo

2008-12-16

Polymers with high molecular weight and worm-like micelles are drag-reducing agents under turbulent flow. However, in contrast to the polymeric systems, the worm-like micelles do not undergo mechanical degradation due to the turbulence, because their macromolecular structure can be spontaneously restored. This very favorable property, together with their drag-reduction capability, offer the possibility to use such worm-like micelles in heating and cooling systems to recirculate water while expending less energy. The formation, growth, and stability of worm-like micelles formed by cetyltrimethylammonium bromide (CTAB) and sodium salicylate (NaSal) were investigated using the self-fluorescence of salicylate ions and the ability of the giant micelles to promote hydrodynamic drag reduction under turbulent flow. The turbulence in solutions of CTAB-Sal was produced within the double-gap cell of a rotational rheometer. Detailed diagrams were obtained for different ratios of Sal and CTAB, which revealed transitions associated with the thermal stability of giant micelles under turbulent flow.

Kinetics of interior loop formation in semiflexible chains.

PubMed

Hyeon, Changbong; Thirumalai, D

2006-03-14

Loop formation between monomers in the interior of semiflexible chains describes elementary events in biomolecular folding and DNA bending. We calculate analytically the interior distance distribution function for semiflexible chains using a mean field approach. Using the potential of mean force derived from the distance distribution function we present a simple expression for the kinetics of interior looping by adopting Kramers theory. For the parameters, that are appropriate for DNA, the theoretical predictions in comparison with the case are in excellent agreement with explicit Brownian dynamics simulations of wormlike chain (WLC) model. The interior looping times (tauIC) can be greatly altered in the cases when the stiffness of the loop differs from that of the dangling ends. If the dangling end is stiffer than the loop then tauIC increases for the case of the WLC with uniform persistence length. In contrast, attachment of flexible dangling ends enhances rate of interior loop formation. The theory also shows that if the monomers are charged and interact via screened Coulomb potential then both the cyclization (tauc) and interior looping (tauIC) times greatly increase at low ionic concentration. Because both tauc and tauIC are determined essentially by the effective persistence length [lp(R)] we computed lp(R) by varying the range of the repulsive interaction between the monomers. For short range interactions lp(R) nearly coincides with the bare persistence length which is determined largely by the backbone chain connectivity. This finding rationalizes the efficacy of describing a number of experimental observations (response of biopolymers to force and cyclization kinetics) in biomolecules using WLC model with an effective persistence length.

Competition between B-Z and B-L transitions in a single DNA molecule: Computational studies

NASA Astrophysics Data System (ADS)

Kwon, Ah-Young; Nam, Gi-Moon; Johner, Albert; Kim, Seyong; Hong, Seok-Cheol; Lee, Nam-Kyung

2016-02-01

Under negative torsion, DNA adopts left-handed helical forms, such as Z-DNA and L-DNA. Using the random copolymer model developed for a wormlike chain, we represent a single DNA molecule with structural heterogeneity as a helical chain consisting of monomers which can be characterized by different helical senses and pitches. By Monte Carlo simulation, where we take into account bending and twist fluctuations explicitly, we study sequence dependence of B-Z transitions under torsional stress and tension focusing on the interaction with B-L transitions. We consider core sequences, (GC) n repeats or (TG) n repeats, which can interconvert between the right-handed B form and the left-handed Z form, imbedded in a random sequence, which can convert to left-handed L form with different (tension dependent) helical pitch. We show that Z-DNA formation from the (GC) n sequence is always supported by unwinding torsional stress but Z-DNA formation from the (TG) n sequence, which are more costly to convert but numerous, can be strongly influenced by the quenched disorder in the surrounding random sequence.

Tension-induced binding of semiflexible biopolymers

NASA Astrophysics Data System (ADS)

Benetatos, Panayotis; von der Heydt, Alice; Zippelius, Annette

2015-03-01

We investigate theoretically the effect of polymer tension on the collective behaviour of reversible cross-links. We use a model of two parallel-aligned, weakly-bending wormlike chains with a regularly spaced sequence of binding sites subjected to a tensile force. Reversible cross-links attach and detach at the binding sites with an affinity controlled by a chemical potential. In a mean-field approach, we calculate the free energy of the system and we show the emergence of a free energy barrier which controls the reversible (un)binding. The tension affects the conformational entropy of the chains which competes with the binding energy of the cross-links. This competition gives rise to a sudden increase in the fraction of bound sites as the polymer tension increases. The force-induced first-order transition in the number of cross-links implies a sudden force-induced stiffening of the effective stretching modulus of the polymers. This mechanism may be relevant to the formation and stress-induced strengthening of stress fibers in the cytoskeleton. We acknowledge support by the Deutsche Forschungsgemeinschaft (DFG) via grant SFB-937/A1.

Movement of liquid droplets containing polymers on substrate

NASA Astrophysics Data System (ADS)

Hu, Guohui; Wang, Heng

2016-11-01

It is of both fundamental and practical interests to study the flow physics in the manipulation of droplets. As a microreactor, the macromolecules or particles inside the droplets might have significant influences on their movement. In the present study, the many-body dissipative particle dynamics (MDPD) is utilized to investigate the translocation of droplets containing polymer on a substrate driven by the wettability gradient, where the polymer is modelled as worm-like chain (WLC). The internal flows of the droplets are analyzed, as well as the comparison to the polymer-free moving droplets. The effects of physical parameters, such as the interaction potential between liquid particle and polymer beads, the mass of the beads, on the translocation speed are also addressed in the present study. These results might be helpful to the optimization in design of the microfluidic systems.

DNA curvature and flexibility in vitro and in vivo

PubMed Central

Peters, Justin P.; Maher, L. James

2014-01-01

It has been more than 50 years since the elucidation of the structure of double-helical DNA. Despite active research and progress in DNA biology and biochemistry, much remains to be learned in the field of DNA biophysics. Predicting the sequence-dependent curvature and flexibility of DNA is difficult. Applicability of the conventional worm-like chain polymer model of DNA has been challenged. The fundamental forces responsible for the remarkable resistance of DNA to bending and twisting remain controversial. The apparent “softening” of DNA measured in vivo in the presence of kinking proteins and superhelical strain is incompletely understood. New methods and insights are being applied to these problems. This review places current work on DNA biophysics in historical context and illustrates the ongoing interplay between theory and experiment in this exciting field. PMID:20478077

Colloidal chirality in wormlike micellar systems exclusively originated from achiral species: Role of secondary assembly and stimulus responsivity.

PubMed

Zhao, Wenrong; Hao, Jingcheng

2016-09-15

Colloidal chirality in wormlike micellar systems exclusively originated from achiral species and discussion of the role of secondary assembly of fiber-like aggregates in chirality generation were presented in this paper. Herein, formation of colloidal wormlike micelles for the first time incorporated chirality and redox-responsiveness into one design via noncovalent interaction. A dual-stimuli-responsive gel of wormlike micelles which were designed by employing a dual-responsive cationic surfactant (FTMA) and a strong gelator (AzoNa4) and regulated by redox reaction and host-guest inclusion is presented. Both the redox and host-guest interaction play an important role in regulating the viscosity and supramolecular chirality of gels of the wormlike micelles. The supramolecular chirality and viscosity of the wormlike micelle gels were switched reversibly by exerting chemical redox onto the ferrocenyl groups. For the amphiphile FTMA containing redox-active ferrocenyl group, reversible control of the oxidation state of ferrocenyl groups leads to the charge and hydrophobicity changes of FTMA, therefore change its self-assembly behavior. Of equal interest, β-CD successfully detached the wormlike micelles via the recognition-inclusion behavior with FTMA and invalidate the H-bond and hydrophobic interaction between FTMA and AzoH4. This designed system provides a new strategy to tune the supramolecular chirality of colloidal aggregates and explore the specific packing mode detail within the micelles or the secondary assembly of the inter-micelles. We anticipate this dual-responsive H-bond-directed chiral gel switch could propose a new strategy when researchers designing new, multi-responsive functional gel materials. Copyright © 2016 Elsevier Inc. All rights reserved.

Statistics of wormlike chains. II. Phase transition of polymer liquid crystals and its mixture with low molecular weight liquid crystals

NASA Astrophysics Data System (ADS)

Zhang, W. X.; Zhao, S. R.; Sun, C. P.

1997-02-01

A general self-consistent field (SCF) for the mixture of polymer and low molecular weight (LMW) molecules has been derived by variation principle. Considering a Maier-Saupe type of interaction, the analytical expressions of the SCF for polymer liquid crystals (PLCs) and the mixture of PLCs and LMW liquid crystals are obtained, from which the phase behaviors of PLCs as well as the mixture are studied. The theoretical results are in agreement with experimental results by adjusting a parameter.

Small angle neutron scattering (SANS) study of gastric mucin solutions

NASA Astrophysics Data System (ADS)

Hong, Z.; Bansil, R.; Waigh, T.; Turner, B.; Bhaskar, K. R.; Afdhal, N.; Lal, J.

2002-03-01

We report the first results from a SANS study of purified porcine gastric mucin solutions in D2O. The ability of this glycoprotein to protect the stomach epithelium from acid damage, may be due to a pH dependent conformational transition which leads to gelation at low pH Cao et. al. (Biophysical. J. 76, 1250, 1999). SANS measurements were made over the concentration range of 1 -15 mg/ml at pH 7, 4 and 2. The data indicate that at pH 7 the excluded volume exponent is 1.7, characteristic of swollen chains whereas at pH 2 this exponent increases to 2, indicating theta or poor solvent conditions, consistent with the hydrophobic interactions increasing at lower pH. From a Guinier analysis of the 1mg/ml data at low q's (0.003- 0.007 Å-1) we estimate the cross section radius of the effective cylinder to be 23nm and its length as 96nm in an unbuffered sample, i.e. close to pH 7. In the intermediate q-range (0.01 -0.1Å-1) at pH 7 a fit to the Debye chain gives radius of gyration Rg of 16nm. Mucin is best modelled as an elongated micelle with a cylindrical or worm-like chain to represent the protein core and the sugar chains forming the corona. Results of such calculations will be presented.

The snakelike chain character of unstructured RNA.

PubMed

Jacobson, David R; McIntosh, Dustin B; Saleh, Omar A

2013-12-03

In the absence of base-pairing and tertiary structure, ribonucleic acid (RNA) assumes a random-walk conformation, modulated by the electrostatic self-repulsion of the charged, flexible backbone. This behavior is often modeled as a Kratky-Porod "wormlike chain" (WLC) with a Barrat-Joanny scale-dependent persistence length. In this study we report measurements of the end-to-end extension of poly(U) RNA under 0.1 to 10 pN applied force and observe two distinct elastic-response regimes: a low-force, power-law regime characteristic of a chain of swollen blobs on long length scales and a high-force, salt-valence-dependent regime consistent with ion-stabilized crumpling on short length scales. This short-scale structure is additionally supported by force- and salt-dependent quantification of the RNA ion atmosphere composition, which shows that ions are liberated under stretching; the number of ions liberated increases with increasing bulk salt concentration. Both this result and the observation of two elastic-response regimes directly contradict the WLC model, which predicts a single elastic regime across all forces and, when accounting for scale-dependent persistence length, the opposite trend in ion release with salt concentration. We conclude that RNA is better described as a "snakelike chain," characterized by smooth bending on long length scales and ion-stabilized crumpling on short length scales. In monovalent salt, these two regimes are separated by a characteristic length that scales with the Debye screening length, highlighting the determining importance of electrostatics in RNA conformation. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Correlation functions of main-chain polymer nematics constrained by tensorial and vectorial conservation laws

NASA Astrophysics Data System (ADS)

Svenšek, Daniel; Podgornik, Rudolf

2015-09-01

We present and analyze correlation functions of a main-chain polymer nematic in a continuum worm-like chain description for two types of constraints formalized by the tensorial and vectorial conservation laws, both originating in the microscopic chain integrity, i.e., the connectivity of the polymer chains. In particular, our aim is to identify the features of the correlation functions that are most susceptible to the differences between the two constraints. Besides the density and director autocorrelations in both the tensorial and vectorial cases, we calculate also the density-director correlation functions, the latter being a direct signature of the presence of a specific constraint. Its amplitude is connected to the strength of the constraint and is zero if none of the constraints are present, i.e., for a standard non-polymeric nematic. Generally, the correlation functions with the constraints differ substantially from the correlation functions in the non-polymeric case, if the constraints are strong which in practice requires long chains. Moreover, for the tensorial conservation law to be well distinguishable from the vectorial one, the chain persistence length should be much smaller than the total length of the chain, so that hairpins (chain backfolding) are numerous and the polar order is small.

Mechanical transduction via a single soft polymer

NASA Astrophysics Data System (ADS)

Hou, Ruizheng; Wang, Nan; Bao, Weizhu; Wang, Zhisong

2018-04-01

Molecular machines from biology and nanotechnology often depend on soft structures to perform mechanical functions, but the underlying mechanisms and advantages or disadvantages over rigid structures are not fully understood. We report here a rigorous study of mechanical transduction along a single soft polymer based on exact solutions to the realistic three-dimensional wormlike-chain model and augmented with analytical relations derived from simpler polymer models. The results reveal surprisingly that a soft polymer with vanishingly small persistence length below a single chemical bond still transduces biased displacement and mechanical work up to practically significant amounts. This "soft" approach possesses unique advantages over the conventional wisdom of rigidity-based transduction, and potentially leads to a unified mechanism for effective allosterylike transduction and relay of mechanical actions, information, control, and molecules from one position to another in molecular devices and motors. This study also identifies an entropy limit unique to the soft transduction, and thereby suggests a possibility of detecting higher efficiency for kinesin motor and mutants in future experiments.

Winding single-molecule double-stranded DNA on a nanometer-sized reel

PubMed Central

You, Huijuan; Iino, Ryota; Watanabe, Rikiya; Noji, Hiroyuki

2012-01-01

A molecular system of a nanometer-sized reel was developed from F1–ATPase, a rotary motor protein. By combination with magnetic tweezers and optical tweezers, single-molecule double-stranded DNA (dsDNA) was wound around the molecular reel. The bending stiffness of dsDNA was determined from the winding tension (0.9–6.0 pN) and the diameter of the wound loop (21.4–8.5 nm). Our results were in good agreement with the conventional worm-like chain model and a persistence length of 54 ± 9 nm was estimated. This molecular reel system offers a new platform for single-molecule study of micromechanics of sharply bent DNA molecules and is expected to be applicable to the elucidation of the molecular mechanism of DNA-associating proteins on sharply bent DNA strands. PMID:22772992

Self-Assemblies of novel molecules, VECAR

NASA Astrophysics Data System (ADS)

Shrestha, Bijay; Kim, Hye-Young; Lee, Soojin; Novak, Brian; Moldovan, Dorel

2015-03-01

VECAR is a newly synthesized molecule, which is an amphiphilic antioxidant molecule that consists of two molecular groups, vitamin-E and Carnosine, linked by a hydrocarbon chain. The hydrocarbon chain is hydrophobic and both vitamin-E and Carnosine ends are hydrophilic. In the synthesis process, the length of the hydrophobic chain of VECAR molecules can vary from the shortest (n =0) to the longest (n =18), where n indicates the number of carbon atoms in the chain. We conducted MD simulation studies of self-assembly of VECAR molecules in water using GROMACS on LONI HPC resources. Our study shows that there is a strong correlation between the shape and atomistic structure of the self-assembled nano-structures (SANs) and the chain-length (n) of VECAR molecules. We will report the results of data analyses including the atomistic structure of each SANs and the dynamic and energetic mechanisms of their formation as function of time. In summary, both VECAR molecules of chain-length n =18 and 9 form worm-like micelles, which may be used as a drug delivery system. This research is supported by the Louisiana Board of Regents-RCS Grant (LEQSF(2012-15)-RD-A-19).

Multivariate Analysis of Mixed Lipid Aggregate Phase Transitions Monitored Using Raman Spectroscopy.

PubMed

Neal, Sharon L

2018-01-01

The phase behavior of aqueous 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC)/1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) mixtures between 8.0 ℃ and 41.0 ℃ were monitored using Raman spectroscopy. Temperature-dependent Raman matrices were assembled from series of spectra and subjected to multivariate analysis. The consensus of pseudo-rank estimation results is that seven to eight components account for the temperature-dependent changes observed in the spectra. The spectra and temperature response profiles of the mixture components were resolved by applying a variant of the non-negative matrix factorization (NMF) algorithm described by Lee and Seung (1999). The rotational ambiguity of the data matrix was reduced by augmenting the original temperature-dependent spectral matrix with its cumulative counterpart, i.e., the matrix formed by successive integration of the spectra across the temperature index (columns). Successive rounds of constrained NMF were used to isolate component spectra from a significant fluorescence background. Five major components exhibiting varying degrees of gel and liquid crystalline lipid character were resolved. Hydrogen-bonded water networks exhibiting varying degrees of organization are associated with the lipid components. Spectral parameters were computed to compare the chain conformation, packing, and hydration indicated by the resolved spectra. Based on spectral features and relative amounts of the components observed, four components reflect long chain lipid response. The fifth component could reflect the response of the short chain lipid, DHPC, but there were no definitive spectral features confirming this assignment. A minor component of uncertain assignment that exhibits a striking response to the DMPC pre-transition and chain melting transition also was recovered. While none of the spectra resolved exhibit features unequivocally attributable to a specific aggregate morphology or step in the gelation process, the results are consistent with the evolution of mixed phase bicelles (nanodisks) and small amounts of worm-like DMPC/DHPC aggregates, and perhaps DHPC micelles, at low temperature to suspensions of branched and entangled worm-like aggregates above the DMPC gel phase transition and perforated multi-lamellar aggregates at high temperature.

The Snakelike Chain Character of Unstructured RNA

PubMed Central

Jacobson, David R.; McIntosh, Dustin B.; Saleh, Omar A.

2013-01-01

In the absence of base-pairing and tertiary structure, ribonucleic acid (RNA) assumes a random-walk conformation, modulated by the electrostatic self-repulsion of the charged, flexible backbone. This behavior is often modeled as a Kratky-Porod “wormlike chain” (WLC) with a Barrat-Joanny scale-dependent persistence length. In this study we report measurements of the end-to-end extension of poly(U) RNA under 0.1 to 10 pN applied force and observe two distinct elastic-response regimes: a low-force, power-law regime characteristic of a chain of swollen blobs on long length scales and a high-force, salt-valence-dependent regime consistent with ion-stabilized crumpling on short length scales. This short-scale structure is additionally supported by force- and salt-dependent quantification of the RNA ion atmosphere composition, which shows that ions are liberated under stretching; the number of ions liberated increases with increasing bulk salt concentration. Both this result and the observation of two elastic-response regimes directly contradict the WLC model, which predicts a single elastic regime across all forces and, when accounting for scale-dependent persistence length, the opposite trend in ion release with salt concentration. We conclude that RNA is better described as a “snakelike chain,” characterized by smooth bending on long length scales and ion-stabilized crumpling on short length scales. In monovalent salt, these two regimes are separated by a characteristic length that scales with the Debye screening length, highlighting the determining importance of electrostatics in RNA conformation. PMID:24314087

Formation of wormlike aggregates of fluorocarbon-hydrocarbon hybrid surfactant by Langmuir-Blodgett transfer and alignment of gold nanoparticles.

PubMed

Kondo, Yukishige; Fukuoka, Hiroshi; Nakano, Shuichi; Hayashi, Kohei; Tsukagoshi, Tatsuya; Matsumoto, Mutsuyoshi; Yoshino, Norio

2007-05-22

A novel anionic fluorocarbon-hydrocarbon hybrid surfactant (SS-Hyb-Na+) with a disulfide group has been synthesized from 11-bromo-1-undecanal and perfluorohexylethyl iodide via three steps. The Langmuir-Blodgett (LB) transfer of the 1:100 (mol/mol) mixed monolayer of SS-Hyb-Na+ and stearyl alcohol (C18OH) formed on an aqueous solution containing a cationic polymer, poly(diallyldimethylammonium chloride) (PDDA+Cl-) onto a hydrophobic silicon wafer yields the formation of wormlike aggregates consisting of SS-Hyb-/PDDA+ polyion complexes. It is found that the aggregates align along the withdrawal direction of the wafer substrate. When the wafer on which the wormlike aggregates exist is immersed into the dispersion of gold nanoparticles (Au NPs) prepared by the citrate reduction method, Au NPs align along the wormlike structures. Even though the surface of the wafer is placed either vertical or parallel to the monolayer compression direction during the LB transfer, the one-dimensional (1D) array of Au NPs is observed along the withdrawal direction of the wafer. This indicates that the wormlike aggregates of SS-Hyb-/PDDA+ complexes are aligned during the LB transfer, and the aligned aggregates behave as a scaffold in the 1D array of Au NPs.

Synergistic Growth of Giant Wormlike Micelles in Ternary Mixed Surfactant Solutions: Effect of Octanoic Acid.

PubMed

Georgieva, Gergana S; Anachkov, Svetoslav E; Lieberwirth, Ingo; Koynov, Kaloian; Kralchevsky, Peter A

2016-12-06

The synergistic growth of giant wormlike micelles in ternary mixed solutions composed of an anionic surfactant (sodium laurylethersulfate, SLES), a zwitterionic surfactant (cocamidopropyl betaine, CAPB), and octanoic acid (HC8) is studied. Rheological data and their analysis in terms of Cole-Cole plots and micellar characteristic times are presented, and the micellar structures behind the observed rheological behavior are revealed by cryo-TEM micrographs. The surfactant composition is fixed near the maximal micelle size of the binary SLES + CAPB system, whereas the concentration of HC8 is varied. At a given HC8 concentration, the viscosity of the ternary micellar solutions exhibits a very high and sharp peak. Polarized-light optical microscopy indicates that all investigated solutions are isotropic rather than liquid-crystalline. The cryo-TEM imaging shows complex phase behavior: wormlike micelles to the left of the peak, giant entangled wormlike micelles at the peak, and long wormlike micelles coexisting with multiconnected micellar aggregates to the right of the peak. The formation of multiconnected micelles leads to a drop in viscosity at the higher concentrations. The results contribute to a better understanding of the structure-rheology relations in micellar surfactant solutions and could be useful for controlling the properties of formulations in personal-care and house-hold detergency.

How a short double-stranded DNA bends

NASA Astrophysics Data System (ADS)

Shin, Jaeoh; Lee, O.-Chul; Sung, Wokyung

2015-04-01

A recent experiment using fluorescence microscopy showed that double-stranded DNA fragments shorter than 100 base pairs loop with the probabilities higher by the factor of 102-106 than predicted by the worm-like chain (WLC) model [R. Vafabakhsh and T. Ha, Science 337, 1101(2012)]. Furthermore, the looping probabilities were found to be nearly independent of the loop size. The results signify a breakdown of the WLC model for DNA mechanics which works well on long length scales and calls for fundamental understanding for stressed DNA on shorter length scales. We develop an analytical, statistical mechanical model to investigate what emerges to the short DNA under a tight bending. A bending above a critical level initiates nucleation of a thermally induced bubble, which could be trapped for a long time, in contrast to the bubbles in both free and uniformly bent DNAs, which are either transient or unstable. The trapped bubble is none other than the previously hypothesized kink, which releases the bending energy more easily as the contour length decreases. It leads to tremendous enhancement of the cyclization probabilities, in a reasonable agreement with experiment.

Is DNA a worm-like chain in Couette flow? In search of persistence length, a critical review.

PubMed

Rittman, Martyn; Gilroy, Emma; Koohya, Hashem; Rodger, Alison; Richards, Adair

2009-01-01

Persistence length is the foremost measure of DNA flexibility. Its origins lie in polymer theory which was adapted for DNA following the determination of BDNA structure in 1953. There is no single definition of persistence length used, and the links between published definitions are based on assumptions which may, or may not be, clearly stated. DNA flexibility is affected by local ionic strength, solvent environment, bound ligands and intrinsic sequence-dependent flexibility. This article is a review of persistence length providing a mathematical treatment of the relationships between four definitions of persistence length, including: correlation, Kuhn length, bending, and curvature. Persistence length has been measured using various microscopy, force extension and solution methods such as linear dichroism and transient electric birefringence. For each experimental method a model of DNA is required to interpret the data. The importance of understanding the underlying models, along with the assumptions required by each definition to determine a value of persistence length, is highlighted for linear dichroism data, where it transpires that no model is currently available for long DNA or medium to high shear rate experiments.

Chain conformation, rheological and charge properties of fucoidan extracted from sea cucumber Thelenota ananas: A semi-flexible coil negative polyelectrolyte.

PubMed

Xu, Xiaoqi; Xue, Changhu; Chang, Yaoguang; Liu, Guanchen

2017-12-15

As a bioactive and functional polysaccharide, sea cucumber fucoidan has received increasing attention. Chain conformation and physicochemical properties of fucoidan extracted from Thelenota ananas (Ta-FUC) was investigated by utilizing HPSEC-MALLS-Visc-RI, microelectrophoresis and steady shear measurements. The conformation parameter α s (0.61±0.02), the Mark-Houwink-Kuhn-Sakurada exponent α η (0.92±0.01), α h (0.64±0.01) and the Smidsrød-Haug stiffness parameter B (0.036±0.010) consistently manifested that Ta-FUC adopted a semi-flexible coil conformation in NaCl solution. Based on a wormlike cylinder model, stiffness parameters, including persistence length q (13.27±0.80nm) and cylinder diameter d (0.79nm), were calculated. This polysaccharide demonstrated shear-thinning rheological behaviour, and critical concentration from dilute to semidilute concentration regime was determined as 3.6mg/ml. Ta-FUC exhibited as a negative polyelectrolyte in wide pH and ionic strength ranges. These molecular characteristics and physicochemical properties would facilitate further application of Ta-FUC as a functional ingredient in food. Copyright © 2017 Elsevier Ltd. All rights reserved.

From carbon nanotubes to carbon atomic chains

NASA Astrophysics Data System (ADS)

Casillas García, Gilberto; Zhang, Weijia; José-Yacamán, Miguel

2010-10-01

Carbyne is a linear allotrope of carbon. It is formed by a linear arrangement of carbon atoms with sp-hybridization. We present a reliable and reproducible experiment to obtain these carbon atomic chains using few-layer-graphene (FLG) sheets and a HRTEM. First the FLG sheets were synthesized from worm-like exfoliated graphite and then drop-casted on a lacey-carbon copper grid. Once in the TEM, two holes are opened near each other in a FLG sheet by focusing the electron beam into a small spot. Due to the radiation, the carbon atoms rearrange themselves between the two holes and form carbon fibers. The beam is concentrated on the carbon fibers in order excite the atoms and induce a tension until multi wall carbon nanotube (MWCNT) is formed. As the radiation continues the MWCNT breaks down until there is only a single wall carbon nanotube (SWCNT). Then, when the SWCNT breaks, an atomic carbon chain is formed, lasts for several seconds under the radiation and finally breaks. This demonstrates the stability of this carbon structure.

Stagnation point flow of wormlike micellar solutions in a microfluidic cross-slot device: effects of surfactant concentration and ionic environment.

PubMed

Haward, Simon J; McKinley, Gareth H

2012-03-01

We employ the techniques of microparticle image velocimetry and full-field birefringence microscopy combined with mechanical measurements of the pressure drop to perform a detailed characterization of the extensional rheology and elastic flow instabilities observed for a range of wormlike micellar solutions flowing through a microfluidic cross-slot device. As the flow rate through the device is increased, the flow first bifurcates from a steady symmetric to a steady asymmetric configuration characterized by a birefringent strand of highly aligned micellar chains oriented along the shear-free centerline of the flow field. At higher flow rates the flow becomes three dimensional and time dependent and is characterized by aperiodic spatiotemporal fluctuations of the birefringent strand. The extensional properties and critical conditions for the onset of flow instabilities in the fluids are highly dependent on the fluid formulation (surfactant concentration and ionic strength) and the resulting changes in the linear viscoelasticity and nonlinear shear rheology of the fluids. By combining the measurements of critical conditions for the flow transitions with the viscometric material properties and the degree of shear-thinning characterizing each test fluid, it is possible to construct a stability diagram for viscoelastic flow of complex fluids in the cross-slot geometry.

Structure and oil responsiveness of viscoelastic fluids based on mixed anionic/cationic wormlike surfactant micelles

NASA Astrophysics Data System (ADS)

Shibaev, A. V.; Makarov, A. V.; Aleshina, A. L.; Rogachev, A. V.; Kuklin, A. I.; Philippova, O. E.

2017-05-01

In this work, a combination of small-angle neutron scattering, dynamic light scattering and rheometry was applied in order to investigate the structure and oil responsiveness of anionic/cationic wormlike surfactant micelles formed in a mixture of potassium oleate and n-octyltrimethylammonium bromide (C8TAB). A new facile method of calculating the structure factor of charged interacting wormlike micelles was proposed. It was shown that the mean distance between the micelles decreases upon the increase of the amount of cationic co-surfactant and lowering of the net micellar charge. It was demonstrated that highly viscous fluids containing mixed anionic/cationic wormlike micelles are highly responsive to oil due to its solubilization inside the micellar cores, which leads to the disruption of micelles and formation of microemulsion droplets. Experimental data suggest that solubilization of oil proceeds differently in the case of mixed anionic/cationic micelles in the absence of salt, and anionic micelles of the same surfactant in the presence of KCl.

Microstructure and Rheology of a Flow-Induced Structured Phase in Wormlike Micellar Solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cardiel Rivera, Joshua J.; Dohnalkova, Alice; Dubash, Neville

2013-04-30

Surfactant molecules found in soaps and detergents can self-assemble into a great variety of morphologies (e.g., spherical micelles, cylindrical micelles, and lamellar phases). The resulting morphology is highly affected by ionic strength, temperature, and flow conditions. In particular, cylindrical micelles in the presence of inorganic or organic salts can self-assemble into large flexible and elongated wormlike micelles. In equilibrium, the wormlike micelles transition from slightly entangled to branched and, finally, to multi-connected structures with increasing salt concentration. In our work, by introducing external flow conditions via microfluidics, these micellar structures can follow very different trajectories on the phase map andmore » new nanoporous structures can be created. This flow induced approach offers great potential to create novel materials and nanoporous scaffolds from wormlike micelles under ambient temperature and pressure, without any chemical and thermal means (1). As a result, this work provides attractive solutions for synthesizing new biocompatible materials under ambient conditions with biosensing, encapsulation, catalysis, photonics, and self-healing applications.« less

The elastic free energy of a tandem modular protein under force.

PubMed

Valle-Orero, Jessica; Eckels, Edward C; Stirnemann, Guillaume; Popa, Ionel; Berkovich, Ronen; Fernandez, Julio M

2015-05-01

Recent studies have provided a theoretical framework for including entropic elasticity in the free energy landscape of proteins under mechanical force. Accounting for entropic elasticity using polymer physics models has helped explain the hopping behavior seen in single molecule experiments in the low force regime. Here, we expand on the construction of the free energy of a single protein domain under force proposed by Berkovich et al. to provide a free energy landscape for N tandem domains along a continuous polypeptide. Calculation of the free energy of individual domains followed by their concatenation provides a continuous free energy landscape whose curvature is dominated by the worm-like chain at forces below 20 pN. We have validated our free energy model using Brownian dynamics and reproduce key features of protein folding. This free energy model can predict the effects of changes in the elastic properties of a multidomain protein as a consequence of biological modifications such as phosphorylation or the formation of disulfide bonds. This work lays the foundations for the modeling of tissue elasticity, which is largely determined by the properties of tandem polyproteins. Copyright © 2015. Published by Elsevier Inc.

Wormlike micelle formation by acylglutamic acid with alkylamines.

PubMed

Sakai, Kenichi; Nomura, Kazuyuki; Shrestha, Rekha Goswami; Endo, Takeshi; Sakamoto, Kazutami; Sakai, Hideki; Abe, Masahiko

2012-12-21

Rheological properties of alkyl dicarboxylic acid-alkylamine complex systems have been characterized. The complex materials employed in this study consist of an amino acid-based surfactant (dodecanoylglutamic acid, C12Glu) and a tertiary alkylamine (dodecyldimethylamine, C12DMA) or a secondary alkylamine (dodecylmethylamine, C12MA). (1)H NMR and mass spectroscopic data have suggested that C12Glu forms a stoichiometric 1:1 complex with C12DMA and C12MA. Rheological measurements have suggested that the complex systems yield viscoelastic wormlike micellar solutions and the rheological behavior is strongly dependent on the aqueous solution pH. This pH-dependent behavior results from the structural transformation of the wormlike micelles to occur in the narrow pH range 5.5-6.2 (in the case of C12Glu-C12DMA system); i.e., positive curved aggregates such as spherical or rodlike micelles tend to be formed at high pH values. Our current study offers a unique way to obtain viscoelastic wormlike micellar solutions by means of alkyl dicarboxylic acid-alkylamine complex as gemini-like amphiphiles.

Persistence length of wormlike micelles composed of ionic surfactants: self-consistent-field predictions.

PubMed

Lauw, Y; Leermakers, F A M; Stuart, M A Cohen

2007-07-19

The persistence length of a wormlike micelle composed of ionic surfactants C(n)E(m)X(k) in an aqueous solvent is predicted by means of the self-consistent-field theory where C(n)E(m) is the conventional nonionic surfactant and X(k) is an additional sequence of k weakly charged (pH-dependent) segments. By considering a toroidal micelle at infinitesimal curvature, we evaluate the bending modulus of the wormlike micelle that corresponds to the total persistence length, consisting of an elastic/intrinsic and an electrostatic contribution. The total persistence length increases with pH and decreases with increasing background salt concentration. We estimate that the electrostatic persistence length l(p,e)(0) scales with respect to the Debye length kappa(-1) as l(p,e)(0) approximately kappa(-p) where p approximately 1.98 for wormlike micelles consisting of C(20)E(10)X(1) surfactants and p approximately 1.54 for wormlike micelles consisting of C(20)E(10)X(2) surfactants. The total persistence length l(p,t)(0) is a weak function of the head group length m but scales with the tail length n as l(p,t)(0) approximately n(x) where x approximately 2-2.6, depending on the corresponding head group length. Interestingly, l(p,t)(0) varies nonmonotonically with the number of charged groups k due to the opposing trends in the electrostatic and elastic bending rigidities upon variation of k.

Probing the elastic limit of DNA bending

PubMed Central

Le, Tung T.; Kim, Harold D.

2014-01-01

Sharp bending of double-stranded DNA (dsDNA) plays an essential role in genome structure and function. However, the elastic limit of dsDNA bending remains controversial. Here, we measured the opening rates of small dsDNA loops with contour lengths ranging between 40 and 200 bp using single-molecule Fluorescence Resonance Energy Transfer. The relationship of loop lifetime to loop size revealed a critical transition in bending stress. Above the critical loop size, the loop lifetime changed with loop size in a manner consistent with elastic bending stress, but below it, became less sensitive to loop size, indicative of softened dsDNA. The critical loop size increased from ∼60 bp to ∼100 bp with the addition of 5 mM magnesium. We show that our result is in quantitative agreement with the kinkable worm-like chain model, and furthermore, can reproduce previously reported looping probabilities of dsDNA over the range between 50 and 200 bp. Our findings shed new light on the energetics of sharply bent dsDNA. PMID:25122748

Tension-dependent structural deformation alters single-molecule transition kinetics.

PubMed

Sudhanshu, B; Mihardja, S; Koslover, E F; Mehraeen, S; Bustamante, C; Spakowitz, A J

2011-02-01

We analyze the response of a single nucleosome to tension, which serves as a prototypical biophysical measurement where tension-dependent deformation alters transition kinetics. We develop a statistical-mechanics model of a nucleosome as a wormlike chain bound to a spool, incorporating fluctuations in the number of bases bound, the spool orientation, and the conformations of the unbound polymer segments. With the resulting free-energy surface, we perform dynamic simulations that permit a direct comparison with experiments. This simple approach demonstrates that the experimentally observed structural states at nonzero tension are a consequence of the tension and that these tension-induced states cease to exist at zero tension. The transitions between states exhibit substantial deformation of the unbound polymer segments. The associated deformation energy increases with tension; thus, the application of tension alters the kinetics due to tension-induced deformation of the transition states. This mechanism would arise in any system where the tether molecule is deformed in the transition state under the influence of tension.

Tension-dependent structural deformation alters single-molecule transition kinetics

PubMed Central

Sudhanshu, B.; Mihardja, S.; Koslover, E. F.; Mehraeen, S.; Bustamante, C.; Spakowitz, A. J.

2011-01-01

We analyze the response of a single nucleosome to tension, which serves as a prototypical biophysical measurement where tension-dependent deformation alters transition kinetics. We develop a statistical-mechanics model of a nucleosome as a wormlike chain bound to a spool, incorporating fluctuations in the number of bases bound, the spool orientation, and the conformations of the unbound polymer segments. With the resulting free-energy surface, we perform dynamic simulations that permit a direct comparison with experiments. This simple approach demonstrates that the experimentally observed structural states at nonzero tension are a consequence of the tension and that these tension-induced states cease to exist at zero tension. The transitions between states exhibit substantial deformation of the unbound polymer segments. The associated deformation energy increases with tension; thus, the application of tension alters the kinetics due to tension-induced deformation of the transition states. This mechanism would arise in any system where the tether molecule is deformed in the transition state under the influence of tension. PMID:21245354

Distance distributions of short polypeptides recovered by fluorescence resonance energy transfer in the 10 A domain.

PubMed

Sahoo, Harekrushna; Roccatano, Danilo; Zacharias, Martin; Nau, Werner M

2006-06-28

Fluorescence resonance energy transfer (FRET) between tryptophan (Trp) as donor and 2,3-diazabicyclo[2.2.2]oct-2-ene (Dbo) as acceptor was studied by steady-state and time-resolved fluorescence spectroscopy. The unique feature of this FRET pair is its exceptionally short Förster radius (10 A), which allows one to recover distance distributions in very short structureless peptides. The technique was applied to Trp-(GlySer)n-Dbo-NH2 peptides with n = 0-10, for which the average probe/quencher distance ranged between 8.7 and 13.7 A experimentally (in propylene glycol, analysis according to wormlike chain model) and 8.6-10.2 A theoretically (for n = 0-6, GROMOS96 molecular dynamics simulations). The larger FRET efficiency in steady-state compared to time-resolved fluorescence experiments was attributed to a static quenching component, suggesting that a small but significant part (ca. 10%) of the conformations are already in van der Waals contact when excitation occurs.

Switching wormlike micelles of selenium-containing surfactant using redox reaction.

PubMed

Zhang, Yongmin; Kong, Weiwei; Wang, Cheng; An, Pengyun; Fang, Yun; Feng, Yujun; Qin, Zhirong; Liu, Xuefeng

2015-10-14

A novel redox-switchable wormlike micellar system was developed based on a mixture of selenium-containing zwitterionic surfactant and commercially available anionic surfactant sodium dodecyl sulfate, which reversibly and quickly responds to H2O2 and vitamin C, and shows circulatory gel/sol transition, reflecting changes in aggregate morphology from entangled worms to vesicles.

A symplectic integration method for elastic filaments

NASA Astrophysics Data System (ADS)

Ladd, Tony; Misra, Gaurav

2009-03-01

Elastic rods are a ubiquitous coarse-grained model of semi-flexible biopolymers such as DNA, actin, and microtubules. The Worm-Like Chain (WLC) is the standard numerical model for semi-flexible polymers, but it is only a linearized approximation to the dynamics of an elastic rod, valid for small deflections; typically the torsional motion is neglected as well. In the standard finite-difference and finite-element formulations of an elastic rod, the continuum equations of motion are discretized in space and time, but it is then difficult to ensure that the Hamiltonian structure of the exact equations is preserved. Here we discretize the Hamiltonian itself, expressed as a line integral over the contour of the filament. This discrete representation of the continuum filament can then be integrated by one of the explicit symplectic integrators frequently used in molecular dynamics. The model systematically approximates the continuum partial differential equations, but has the same level of computational complexity as molecular dynamics and is constraint free. Numerical tests show that the algorithm is much more stable than a finite-difference formulation and can be used for high aspect ratio filaments, such as actin. We present numerical results for the deterministic and stochastic motion of single filaments.

Structure formation in binary mixtures of lipids and detergents: self-assembly and vesicle division.

PubMed

Noguchi, Hiroshi

2013-01-14

Self-assembly dynamics in binary surfactant mixtures and structure changes of lipid vesicles induced by detergent solution are studied using coarse-grained molecular simulations. Disk-shaped micelles, the bicelles, are stabilized by detergents surrounding the rim of a bilayer disk of lipids. The self-assembled bicelles are considerably smaller than bicelles formed from vesicle rupture, and their size is determined by the concentrations of lipids and detergents and the interactions between the two species. The detergent-adsorption induces spontaneous curvature of the vesicle bilayer and results in vesicle division into two vesicles or vesicle rupture into worm-like micelles. The division occurs mainly via the inverse pathway of the modified stalk model. For large spontaneous curvature of the monolayers of the detergents, a pore is often opened, thereby leading to vesicle division or worm-like micelle formation.

A pH-responsive wormlike micellar system of a noncovalent interaction-based surfactant with a tunable molecular structure.

PubMed

Kang, Wanli; Wang, Pengxiang; Fan, Haiming; Yang, Hongbin; Dai, Caili; Yin, Xia; Zhao, Yilu; Guo, Shujun

2017-02-08

Responsive wormlike micelles are very useful in a number of applications, whereas it is still challenging to create dramatic viscosity changes in wormlike micellar systems. Here we developed a pH-responsive wormlike micellar system based on a noncovalent constructed surfactant, which is formed by the complexation of N-erucamidopropyl-N,N-dimethylamine (UC 22 AMPM) and citric acid at the molar ratio of 3 : 1 (EACA). The phase behavior, aggregate microstructure and viscoelasticity of EACA solutions were investigated by macroscopic appearance observation, rheological and cryo-TEM measurements. It was found that the phase behavior of EACA solutions undergoes transition from transparent viscoelastic fluids to opalescent solutions and then phase separation with white floaters upon increasing the pH. Upon increasing the pH from 2.03 to 6.17, the viscosity of wormlike micelles in the transparent solutions continuously increased and reached ∼683 000 mPa s at pH 6.17. As the pH was adjusted to 7.31, the opalescent solution shows a water-like flowing behaviour and the η 0 rapidly declines to ∼1 mPa s. Thus, dramatic viscosity changes of about 6 magnitudes can be triggered by varying the pH values without any deterioration of the EACA system. This drastic variation in rheological behavior is attributed to the pH dependent interaction between UC 22 AMPM and citric acid. Furthermore, the dependence on concentration and temperature of the rheological behavior of EACA solutions was also studied to assist in obtaining the desired pH-responsive viscosity changes.

Disassembly and reassembly of amyloid fibrils in water-ethanol mixtures.

PubMed

Jordens, Sophia; Adamcik, Jozef; Amar-Yuli, Idit; Mezzenga, Raffaele

2011-01-10

This work presents the structural analysis of amyloid-like β-lactoglobulin fibrils incubated in ethanol-water mixtures after their formation in water. We observe for the first time the disassembly of semiflexible heat-denatured β-lactoglobulin fibrils and reassembly into highly flexible wormlike fibrils in ethanol-water solutions. Tapping mode atomic force microscopy is performed to follow structural changes. Our results show that in addition to their growth in length, there is a continuous nucleation process of new wormlike objects with time at the expense of the original β-lactoglobulin fibrils. The persistence length of wormlike fibrils (29.43 nm in the presence of 50% ethanol), indicative of their degree of flexibility, differs by 2 orders of magnitude from that of untreated β-lactoglobulin fibrils (2368.75 nm in pure water). Interestingly, wormlike fibrils do not exhibit a multiple strands nature like the pristine fibrils, as revealed by the lower maximum height and the lack of clear height periodicity along their contour length profile. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) demonstrates that the set of polypeptides obtained by ethanol degradation differs in some fractions from that present in pristine β-lactoglobulin fibrils. ATR-FTIR (attenuated total reflectance-Fourier transform infrared) spectroscopy also supports a different composition of the secondary structure of wormlike fibrils with a decreased amount of α-helix and increased random coils and turns content. These findings can contribute to deciphering the molecular mechanisms of protein aggregation into amyloid fibrils and their disassembly as well as enabling tailor-made production of protein fibrils.

Preparation of wormlike polymeric nanoparticles coated with silica for delivery of methotrexate and evaluation of anticancer activity against MCF7 cells.

PubMed

Gharebaghi, Farhad; Dalali, Naser; Ahmadi, Ebrahim; Danafar, Hossein

2017-04-01

Methotrexate is one of the most effective drugs that is commonly used in the treatment of cancer. However, its application is limited due to low solubility, high toxicity and rapid metabolism. Therefore, in the present study, worm-like polymeric nanoparticles as carrier of methotrexate were prepared using biodegradable copolymers (mPEG-PCL). The impact of nanoparticles' geometry on the loading, delivery and drug's anti-cancer activity was investigated. The di-block copolymer mPEG-PCL was being synthesized by a ring opening polymerization of ɛ-caprolactone in the presence of mPEG as the initiator and Sn(oct) 2 as the catalyst. It was used for the preparation of worm-like micelles and coated with silica, so that their structures are stable after drying. The synthesized copolymers and nanoparticles were characterized by FTIR, HNMR, GPC, XRD, TGA, DLS, and FE-SEM analyses. The efficiencies of drug loading and release of nanoparticles as in vitro, was studied by high performance liquid chromatography. The MTT method was used to estimate the toxicity on MCF-7 cell category. The obtained results showed that the nanoparticles were worm-like particles with less than 150 nm diameter and about 1 µm length. The loading and encapsulation efficiencies of drug by the worm-like nanoparticles were 3.5 ± 0.14% and 65.6 ± 0.12%, respectively, while they were obtained as 2.1 ± 0.08% and 26 ± 0.10%, respectively, for spherical nanoparticles. The methotrexate diffusional behavior of worm-like nanoparticles was compared with that of the spherical ones. On the other hand, the anti-cancer activity of MTX-loaded nanoparticles was more than the free drug. The results of the MTT assay showed strong and dose-dependent inhibition of cell (MCF-7 category) growth by the nanoparticles compared with MTX. The inhibitory concentrations (IC 50 i.e. reduction viability of cell to 50%) obtained for worm-like, spherical nanoparticles and free drug (incubation times 72 h) were 8.25 ± 0.20, 9.15 ± 0.17, 12.28 ± 0.15 µg/mL, respectively. It can be concluded that application of non-spherical nanoparticles is a better and more effective strategy for controlled and slow release of methotrexate in the treatment of cancer.

Smart worm-like micelles responsive to CO2/N2 and light dual stimuli.

PubMed

Jiang, Jianzhong; Wang, Guozheng; Ma, Yuxuan; Cui, Zhenggang; Binks, Bernard P

2017-04-12

CO 2 /N 2 and light dual stimuli-responsive worm-like micelles (WLMs) were obtained by addition of a relatively small amount of a switchable surfactant, 4-butyl-4'-(4-N,N-dimethylhexyloxy-amine) azobenzene bicarbonate (AZO-B6-CO 2 ), sensitive to the same triggers to a binary aqueous solution of cetyltrimethylammonium bromide (CTAB) and sodium salicylate (NaSal).

Advances in the mechanical modeling of filamentous actin and its cross-linked networks on multiple scales.

PubMed

Unterberger, Michael J; Holzapfel, Gerhard A

2014-11-01

The protein actin is a part of the cytoskeleton and, therefore, responsible for the mechanical properties of the cells. Starting with the single molecule up to the final structure, actin creates a hierarchical structure of several levels exhibiting a remarkable behavior. The hierarchy spans several length scales and limitations in computational power; therefore, there is a call for different mechanical modeling approaches for the different scales. On the molecular level, we may consider each atom in molecular dynamics simulations. Actin forms filaments by combining the molecules into a double helix. In a model, we replace molecular subdomains using coarse-graining methods, allowing the investigation of larger systems of several atoms. These models on the nanoscale inform continuum mechanical models of large filaments, which are based on worm-like chain models for polymers. Assemblies of actin filaments are connected with cross-linker proteins. Models with discrete filaments, so-called Mikado models, allow us to investigate the dependence of the properties of networks on the parameters of the constituents. Microstructurally motivated continuum models of the networks provide insights into larger systems containing cross-linked actin networks. Modeling of such systems helps to gain insight into the processes on such small scales. On the other hand, they call for verification and hence trigger the improvement of established experiments and the development of new methods.

Rouse-Bueche Theory and The Calculation of The Monomeric Friction Coefficient in a Filled System

NASA Astrophysics Data System (ADS)

Martinetti, Luca; Macosko, Christopher; Bates, Frank

According to flexible chain theories of viscoelasticity, all relaxation and retardation times of a polymer melt (hence, any dynamic property such as the diffusion coefficient) depend on the monomeric friction coefficient, ζ0, i.e. the average drag force per monomer per unit velocity encountered by a Gaussian submolecule moving through its free-draining surroundings. Direct experimental access to ζ0 relies on the availability of a suitable polymer dynamics model. Thus far, no method has been suggested that is applicable to filled systems, such as filled rubbers or microphase-segregated A-B-A thermoplastic elastomers at temperatures where one of the blocks is glassy. Building upon the procedure proposed by Ferry for entangled and unfilled polymer melts, the Rouse-Bueche theory is applied to an undiluted triblock copolymer to extract ζ0 from the linear viscoelastic behavior in the rubber-glass transition region, and to estimate the size of Gaussian submolecules. At iso-free volume conditions, the so-obtained matrix monomeric friction factor is consistent with the corresponding value for the homopolymer melt. In addition, the characteristic Rouse dimensions are in good agreement with independent estimates based on the Kratky-Porod worm-like chain model. These results seem to validate the proposed approach for estimating ζ0 in a filled system. Although preliminary tested on a thermoplastic elastomer of the A-B-A type, the method may be extended and applied to filled homopolymers as well.

Smart wormlike micelles.

PubMed

Chu, Zonglin; Dreiss, Cécile A; Feng, Yujun

2013-09-07

A major scientific challenge of the past decade pertaining to the field of soft matter has been to craft 'adaptable' materials, inspired by nature, which can dynamically alter their structure and functionality on demand, in response to triggers produced by environmental changes. Amongst these, 'smart' surfactant wormlike micelles, responsive to external stimuli, are a particularly recent area of development, yet highly promising, given the versatility of the materials but simplicity of the design-relying on small amphiphilic molecules and their spontaneous self-assembly. The switching 'on' and 'off' of the micellar assembly structures has been reported using electrical, optical, thermal or pH triggers and is now envisaged for multiple stimuli. The structural changes, in turn, can induce major variations in the macroscopic characteristics, affecting properties such as viscosity and elasticity and sometimes even leading to a spontaneous and effective 'sol-gel' transition. These original smart materials based on wormlike micelles have been successfully used in the oil industry, and offer a significant potential in a wide range of other technological applications, including biomedicine, cleaning processes, drag reduction, template synthesis, to name but a few. This review will report results in this field published over the last few years, describe the potential and practical applications of stimuli-responsive wormlike micelles and point out future challenges.

Electrostatic persistence length.

PubMed

Fixman, Marshall

2010-03-11

The persistence length is calculated for polyelectrolyte chains with fixed bond lengths and bond angles (pi-theta), and a potential energy consisting of the screened Coulomb interaction between beads, potential wells alpha phi(i)2 for the dihedral angles phi(i), and coupling terms beta phi(i) phi(i+/-1). This model defines a librating chain that reduces in appropriate limits to the freely rotating or wormlike chains, it can accommodate local crumpling or extreme stiffness, and it is easy to simulate. A planar-quadratic (pq), analytic approximation is based on an expansion of the electrostatic energy in eigenfunctions of the quadratic form that describes the backbone energy, and on the assumption that the quadratic form not only is positive but also adequately confines the chain in an infinite phase space of dihedral angles to the physically unique part with all |phi(i)| < pi. The pq approximation is available under these weak constraints, but the simulations confirm its quantitative accuracy only under the expected condition that alpha is large, that is, for very stiff chains. Stiff chains can also be simulated with small alpha and small theta and compared to an OSF approximation suitably generalized to chains with finite rather than vanishing theta, and increasing agreement with OSF is found the smaller is theta. The two approximations, one becoming exact as alpha --> infinity with fixed theta, the other as theta --> 0 with fixed alpha, are quantitatively similar in behavior, both giving a persistence length P = P0 + aD2 for stiff chains, where D is the Debye length. However, the coefficient apq is about twice the value of aOSF. Under other conditions the simulations show that P may or not be linear in D2 at small or moderate D, depending on the magnitudes of alpha, beta, theta, and the charge density but always becomes linear at large D. Even at a moderately low charge density, corresponding to fewer than 20% of the beads being charged, and with strong crumpling induced by large beta, increasing D dissolves blobs and recovers a linear dependence of P on D2, although a lower power of D gives an adequate fit at moderate D. For the class of models considered, it is concluded that the only universal feature is the asymptotic linearity of P in D2, regardless of flexibility or stiffness.

Persistence length changes dramatically as RNA folds.

PubMed

Caliskan, G; Hyeon, C; Perez-Salas, U; Briber, R M; Woodson, S A; Thirumalai, D

2005-12-31

We determine the persistence length l(p) for a bacterial group I ribozyme as a function of concentration of monovalent and divalent cations by fitting the distance distribution functions P(r) obtained from small angle x-ray scattering intensity data to the asymptotic form of the calculated P(WLC)(r) for a wormlike chain. The l(p) values change dramatically over a narrow range of Mg(2+) concentration from approximately 21 Angstroms in the unfolded state (U) to approximately 10 Angstroms in the compact (I(C)) and native states. Variations in l(p) with increasing Na(+) concentration are more gradual. In accord with the predictions of polyelectrolyte theory we find l(p) alpha 1/kappa(2) where kappa is the inverse Debye-screening length.

A hypothetical hierarchical mechanism of the self-assembly of the Escherichia coli RNA polymerase σ(70) subunit.

PubMed

Koroleva, O N; Dubrovin, E V; Tolstova, A P; Kuzmina, N V; Laptinskaya, T V; Yaminsky, I V; Drutsa, V L

2016-02-21

Diverse morphology of aggregates of amyloidogenic proteins has been attracting much attention in the last few years, and there is still no complete understanding of the relationships between various types of aggregates. In this work, we propose the model, which universally explains the formation of morphologically different (wormlike and rodlike) aggregates on the example of a σ(70) subunit of RNA polymerase, which has been recently shown to form amyloid fibrils. Aggregates were studied using AFM in solution and depolarized dynamic light scattering. The obtained results demonstrate comparably low Young's moduli of the wormlike structures (7.8-12.3 MPa) indicating less structured aggregation of monomeric proteins than that typical for β-sheet formation. To shed light on the molecular interaction of the protein during the aggregation, early stages of fibrillization of the σ(70) subunit were modeled using all-atom molecular dynamics. Simulations have shown that the σ(70) subunit is able to form quasi-symmetric extended dimers, which may further interact with each other and grow linearly. The proposed general model explains different pathways of σ(70) subunit aggregation and may be valid for other amyloid proteins.

Instabilities in wormlike micelle systems. From shear-banding to elastic turbulence.

PubMed

Fardin, M-A; Lerouge, S

2012-09-01

Shear-banding is ubiquitous in complex fluids. It is related to the organization of the flow into macroscopic bands bearing different viscosities and local shear rates and stacked along the velocity gradient direction. This flow-induced transition towards a heterogeneous flow state has been reported in a variety of systems, including wormlike micellar solutions, telechelic polymers, emulsions, clay suspensions, colloidal gels, star polymers, granular materials, or foams. In the past twenty years, shear-banding flows have been probed by various techniques, such as rheometry, velocimetry and flow birefringence. In wormlike micelle solutions, many of the data collected exhibit unexplained spatio-temporal fluctuations. Different candidates have been identified, the main ones being wall slip, interfacial instability between bands or bulk instability of one of the bands. In this review, we present experimental evidence for a purely elastic instability of the high shear rate band as the main origin for fluctuating shear-banding flows.

Viscoelastic wormlike micelles formed by ionic liquid-type surfactant [C16imC8]Br towards template-assisted synthesis of CdS quantum dots.

PubMed

Hu, Yimin; Han, Jie; Ge, Lingling; Guo, Rong

2018-01-31

In this paper, viscoelastic wormlike micelles consisting of cationic liquid-type surfactant, 1-hexadecyl-3-octyl imidazolium bromide ([C 16 imC 8 ]Br), water and different additives were utilized for the synthesis of CdS quantum dots. First, the influence of different additives, such as [Cd(NH 3 ) 6 ]Cl 2 and ethanethioamid (precursors for the synthesis of CdS quantum dots), and temperature on the viscoelasticity of the [C 16 imC 8 ]Br aqueous solution was studied by dynamic and steady rheology. Furthermore, the synthesized CdS quantum dots and their photoluminescence properties were characterized by transmission electron microscopy (TEM), UV-Vis absorption spectroscopy, X-ray diffraction (XRD) and energy-dispersive X-ray spectroscopy (EDX). In the end, the mechanism for the synthesis of CdS quantum dots in [C 16 imC 8 ]Br wormlike micelles is proposed.

Influence of surface interactions on folding and forced unbinding of semiflexible chains.

PubMed

Barsegov, V; Thirumalai, D

2005-11-24

We have investigated the folding and forced unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe, at an elementary level, a number of biologically relevant phenomena that include adhesive interactions between proteins and tethering of receptors to cell walls. The binding interface is modeled as a solid surface, and the wormlike chain (WLC) is used for the semiflexible chain (SC). Using Langevin simulations, in the overdamped limit we examine the ordering kinetics of racquet-like and toroidal structures in the presence of an attractive interaction between the surface and the polymer chain. For a range of interactions, temperature, and the persistence length, l(p), we obtained the monomer density distribution, n(x), (x is the perpendicular distance of a tagged chain end from the surface) for all of the relevant morphologies. There is a single peak in n(x) inside the range of attractive forces, b, for chains in the extended conformations, whereas in racquet and toroidal structures there is an additional peak at x approximately b. The simulated results for n(x) are in good agreement with theory. The formation of toroids on the surface appears to be a first-order transition as evidenced by the bimodal distribution in n(x). The theoretical result underestimates the simulated n(x) for x < b and follows n(x) closely for x >/= b; the calculated density agrees exactly with n(x) in the range x < b. The chain-surface interaction is probed by subjecting the surface structures to a pulling force, f. The average extension, x( f), as a function of f exhibits a sigmoidal profile with sharp all-or-none transition at the unfolding force threshold f = f(c) which increases for more structured states. Simulated x(f) compare well with the theoretical predictions. The critical force, f(c), is a function of l(s)/l(c) for a fixed temperature, where l(c) and l(s) are the length scales that express the strength of the intramolecular and SC-surface attraction, respectively. For a fixed l(s), f(c) increases as l(p) decreases.

Nanorod Mobility within Entangled Wormlike Micelle Solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Jonghun; Grein-Iankovski, Aline; Narayanan, Suresh

In the semi-dilute regime, wormlike micelles form an isotropic entangled microstructure that is similar to that of an entangled polymer solution with a characteristic, nanometer-scale entanglement mesh size. We report a combined x-ray photon correlation spectroscopy (XPCS) and rheology study to investigate the translational dynamics of gold nanorods in semi-dilute solutions of entangled wormlike micelles formed by the surfactant cetylpyridinium chloride (CPyCl) and the counter-ion sodium salicylate (NaSal). The CPyCl concentration is varied to tune the entanglement mesh size over a range that spans from approximately equal to the nanorod diameter to larger than the nanorod length. The NaSal concentrationmore » is varied along with the CPyCl concentration so that the solutions have the maximum viscosity for given CPyCl concentration. On short time scales the nanorods are localized on a length scale matching that expected from the high-frequency elastic modulus of the solutions as long as the mesh size is smaller than the rod length. On longer time scales, the nanorods undergo free diffusion. At the highest CPyCl concentrations, the nanorod diffusivity approaches the value expected based on the macroscopic viscosity of the solutions, but it increases with decreasing CPyCl concentration more rapidly than expected from the macroscopic viscosity. A recent model by Cai et al. [Cai, L.-H.; Panyukov, S.; Rubinstein, M. Macromolecules 2015, 48, 847-862.] for nanoparticle “hopping” diffusion in entangled polymer solutions accounts quantitatively for this enhanced diffusivity.« less

Nanorod Mobility within Entangled Wormlike Micelle Solutions

DOE PAGES

Lee, Jonghun; Grein-Iankovski, Aline; Narayanan, Suresh; ...

2016-12-20

In the semi-dilute regime, wormlike micelles form an isotropic entangled microstructure that is similar to that of an entangled polymer solution with a characteristic, nanometer-scale entanglement mesh size. We report a combined x-ray photon correlation spectroscopy (XPCS) and rheology study to investigate the translational dynamics of gold nanorods in semi-dilute solutions of entangled wormlike micelles formed by the surfactant cetylpyridinium chloride (CPyCl) and the counter-ion sodium salicylate (NaSal). The CPyCl concentration is varied to tune the entanglement mesh size over a range that spans from approximately equal to the nanorod diameter to larger than the nanorod length. The NaSal concentrationmore » is varied along with the CPyCl concentration so that the solutions have the maximum viscosity for given CPyCl concentration. On short time scales the nanorods are localized on a length scale matching that expected from the high-frequency elastic modulus of the solutions as long as the mesh size is smaller than the rod length. On longer time scales, the nanorods undergo free diffusion. At the highest CPyCl concentrations, the nanorod diffusivity approaches the value expected based on the macroscopic viscosity of the solutions, but it increases with decreasing CPyCl concentration more rapidly than expected from the macroscopic viscosity. A recent model by Cai et al. [Cai, L.-H.; Panyukov, S.; Rubinstein, M. Macromolecules 2015, 48, 847-862.] for nanoparticle “hopping” diffusion in entangled polymer solutions accounts quantitatively for this enhanced diffusivity.« less

Macroscopic modeling and simulations of supercoiled DNA with bound proteins

NASA Astrophysics Data System (ADS)

Huang, Jing; Schlick, Tamar

2002-11-01

General methods are presented for modeling and simulating DNA molecules with bound proteins on the macromolecular level. These new approaches are motivated by the need for accurate and affordable methods to simulate slow processes (on the millisecond time scale) in DNA/protein systems, such as the large-scale motions involved in the Hin-mediated inversion process. Our approaches, based on the wormlike chain model of long DNA molecules, introduce inhomogeneous potentials for DNA/protein complexes based on available atomic-level structures. Electrostatically, treat those DNA/protein complexes as sets of effective charges, optimized by our discrete surface charge optimization package, in which the charges are distributed on an excluded-volume surface that represents the macromolecular complex. We also introduce directional bending potentials as well as non-identical bead hydrodynamics algorithm to further mimic the inhomogeneous effects caused by protein binding. These models thus account for basic elements of protein binding effects on DNA local structure but remain computational tractable. To validate these models and methods, we reproduce various properties measured by both Monte Carlo methods and experiments. We then apply the developed models to study the Hin-mediated inversion system in long DNA. By simulating supercoiled, circular DNA with or without bound proteins, we observe significant effects of protein binding on global conformations and long-time dynamics of the DNA on the kilo basepair length.

Vertical structures in vibrated wormlike micellar solutions

NASA Astrophysics Data System (ADS)

Epstein, Tamir; Deegan, Robert

2008-11-01

Vertically vibrated shear thickening particulate suspensions can support a free-standing interfaces oriented parallel to gravity. We find that shear thickening worm-like micellar solutions also support such vertical interfaces. Above a threshold in acceleration, the solution spontaneously accumulates into a labyrinthine pattern characterized by a well-defined vertical edge. The formation of vertical structures is of interest because they are unique to shear-thickening fluids, and they indicate the existence of an unknown stress bearing mechanism.

Bilayers and wormlike micelles at high pH in fatty acid soap systems.

PubMed

Xu, Wenlong; Liu, Huizhong; Song, Aixin; Hao, Jingcheng

2016-03-01

Bilayers at high pH in the fatty acid systems of palmitic acid/KOH/H2O, palmitic acid/CsOH/H2O, stearic acid/KOH/H2O and stearic acid/CsOH/H2O can form spontaneously (Xu et al., 2014, 2015). In this work, the bilayers can still be observed at 25°C with an increase of the concentration of fatty acids. We found that wormlike micelles can also be prepared in the fatty acid soap systems at high pH, even though the temperature was increased to be 50°C. The viscoelasticity, apparent viscosity, yield stress of the bilayers were determined by the rheological measurements. Wormlike micelles were identified by cryogenic transmission electron microscopy (cryo-TEM) and emphasized by the rheological characterizations, which are in accordance with the Maxwell fluids with good fit of Cole-Cole plots. The phase transition temperature was determined by differential scanning calorimetry (DSC) and the transition process was recorded. The regulating role of counterions of fatty acids were discussed by (CH3)4N(+), (C2H5)4N(+), (C3H7)4N(+), and (C4H9)4N(+) as comparison, concluding that counterions with appropriate hydrated radius were the vital factor in the formation wormlike micelles. Copyright © 2015 Elsevier Inc. All rights reserved.

Soft-templating synthesis of mesoporous graphitic carbon nitride with enhanced photocatalytic H2 evolution under visible light.

PubMed

Yan, Hongjian

2012-04-07

g-C(3)N(4) with worm-like pore and narrow pore size distribution was synthesized by using Pluronic P123 as soft-template. The worm-like porous g-C(3)N(4) not only possesses high BET surface area but also redshifts its absorbance edge up to 800 nm, and shows photocatalytic activity even when the irradiation light λ > 700 nm. This journal is © The Royal Society of Chemistry 2012

Influence of system size and solvent flow on the distribution of wormlike micelles in a contraction-expansion geometry

NASA Astrophysics Data System (ADS)

Stukan, M. R.; Boek, E. S.; Padding, J. T.; Crawshaw, J. P.

2008-05-01

Viscoelastic wormlike micelles are formed by surfactants assembling into elongated cylindrical structures. These structures respond to flow by aligning, breaking and reforming. Their response to the complex flow fields encountered in porous media is particularly rich. Here we use a realistic mesoscopic Brownian Dynamics model to investigate the flow of a viscoelastic surfactant (VES) fluid through individual pores idealized as a step expansion-contraction of size around one micron. In a previous study, we assumed the flow field to be Newtonian. Here we extend the work to include the non-Newtonian flow field previously obtained by experiment. The size of the simulations is also increased so that the pore is much larger than the radius of gyration of the micelles. For the non-Newtonian flow field at the higher flow rates in relatively large pores, the density of the micelles becomes markedly non-uniform. In this case, we find that the density in the large, slowly moving entry corner regions is substantially increased.

Semiflexible polymer dynamics with a bead-spring model

NASA Astrophysics Data System (ADS)

Barkema, Gerard T.; Panja, Debabrata; van Leeuwen, J. M. J.

2014-11-01

We study the dynamical properties of semiflexible polymers with a recently introduced bead-spring model. We focus on double-stranded DNA (dsDNA). The two parameters of the model, T* and ν, are chosen to match its experimental force-extension curve. In comparison to its groundstate value, the bead-spring Hamiltonian is approximated in the first order by the Hessian that is quadratic in the bead positions. The eigenmodes of the Hessian provide the longitudinal (stretching) and transverse (bending) eigenmodes of the polymer, and the corresponding eigenvalues match well with the established phenomenology of semiflexible polymers. At the Hessian approximation of the Hamiltonian, the polymer dynamics is linear. Using the longitudinal and transverse eigenmodes, for the linearized problem, we obtain analytical expressions of (i) the autocorrelation function of the end-to-end vector, (ii) the autocorrelation function of a bond (i.e. a spring, or a tangent) vector at the middle of the chain, and (iii) the mean-square displacement of a tagged bead in the middle of the chain, as the sum over the contributions from the modes—the so-called ‘mode sums’. We also perform simulations with the full dynamics of the model. The simulations yield numerical values of the correlations functions (i-iii) that agree very well with the analytical expressions for the linearized dynamics. This does not however mean that the nonlinearities are not present. In fact, we also study the mean-square displacement of the longitudinal component of the end-to-end vector that showcases strong nonlinear effects in the polymer dynamics, and we identify at least an effective t7/8 power-law regime in its time-dependence. Nevertheless, in comparison to the full mean-square displacement of the end-to-end vector the nonlinear effects remain small at all times—it is in this sense we state that our results demonstrate that the linearized dynamics suffices for dsDNA fragments that are shorter than or comparable to the persistence length. Our results are consistent with those of the wormlike chain (WLC) model, the commonly used descriptive tool of semiflexible polymers.

Worming Their Way into Shape: Toroidal Formations in Micellar Solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cardiel Rivera, Joshua J.; Tonggu, Lige; Dohnalkova, Alice

2013-11-01

We report the formation of nanostructured toroidal micellar bundles (nTMB) from a semidilute wormlike micellar solution, evidenced by both cryogenicelectron microscopy and transmission electron microscopy images. Our strategy for creating nTMB involves a two-step protocol consisting of a simple prestraining process followed by flow through a microfluidic device containing an array of microposts, producing strain rates in the wormlike micelles on the order of 105 s^1. In combination with microfluidic confinement, these unusually large strain rates allow for the formation of stable nTMB. Electron microscopy images reveal a variety of nTMB morphologies and provide the size distribution of the nTMB.more » Small-angle neutron scattering indicates the underlying microstructural transition from wormlike micelles to nTMB. We also show that other flow-induced approaches such as sonication can induce and control the emergence of onion-like and nTMB structures, which may provide a useful tool for nanotemplating.« less

Unsteady sedimentation of a sphere in wormlike micellar fluids

NASA Astrophysics Data System (ADS)

Zhang, Yiran; Muller, Susan J.

2018-04-01

The unsteady sedimentation of a sphere in wormlike micellar fluids is studied experimentally through shear and extensional rheometry, sphere trajectory tracking, and particle image velocimetry. Unsteady sphere sedimentation characterized by fluctuations in the sphere settling velocity was observed for a range of sphere size and density in two non-shear-banding wormlike micellar solutions, a cetylpyridinium chloride (CpCl)-sodium salicylate (NaSal) solution and a cetyltrimethylammonium p-toluenesulfonate (CTAT)-NaCl solution. The onset of the transition from steady to unsteady sphere motion is characterized by an extensional Deborah number, D eext , defined locally in the negative wake of the falling sphere. This instability criterion is in agreement with previous findings by Mohammadigoushki and Muller [J. Rheol. 60, 587 (2016), 10.1122/1.4948800] in the wormlike micelle system of cetyltrimethylammonium bromide (CTAB) and NaSal, and appears to be universally valid independent of micelle chemistry or solution rheology (e.g., shear banding or not). Moreover, the frequency at which the sphere velocity fluctuates is found to be linearly correlated with an average shear Deborah number D es , which is a measure of the overall flow strength. This suggests that a constant critical strain is accumulated before the flow instability takes place in each velocity oscillation. The velocity fluctuations are found to become increasingly disordered with increasing elastic Mach number, M ae , indicating that the interactions between the flow instability and elastic wave propagation result in more chaotic velocity fluctuations.

Mechanical model for a collagen fibril pair in extracellular matrix.

PubMed

Chan, Yue; Cox, Grant M; Haverkamp, Richard G; Hill, James M

2009-04-01

In this paper, we model the mechanics of a collagen pair in the connective tissue extracellular matrix that exists in abundance throughout animals, including the human body. This connective tissue comprises repeated units of two main structures, namely collagens as well as axial, parallel and regular anionic glycosaminoglycan between collagens. The collagen fibril can be modeled by Hooke's law whereas anionic glycosaminoglycan behaves more like a rubber-band rod and as such can be better modeled by the worm-like chain model. While both computer simulations and continuum mechanics models have been investigated for the behavior of this connective tissue typically, authors either assume a simple form of the molecular potential energy or entirely ignore the microscopic structure of the connective tissue. Here, we apply basic physical methodologies and simple applied mathematical modeling techniques to describe the collagen pair quantitatively. We found that the growth of fibrils was intimately related to the maximum length of the anionic glycosaminoglycan and the relative displacement of two adjacent fibrils, which in return was closely related to the effectiveness of anionic glycosaminoglycan in transmitting forces between fibrils. These reveal the importance of the anionic glycosaminoglycan in maintaining the structural shape of the connective tissue extracellular matrix and eventually the shape modulus of human tissues. We also found that some macroscopic properties, like the maximum molecular energy and the breaking fraction of the collagen, were also related to the microscopic characteristics of the anionic glycosaminoglycan.

Entropic effects, shape, and size of mixed micelles formed by copolymers with complex architectures

NASA Astrophysics Data System (ADS)

Kalogirou, Andreas; Gergidis, Leonidas N.; Moultos, Othonas; Vlahos, Costas

2015-11-01

The entropic effects in the comicellization behavior of amphiphilic A B copolymers differing in the chain size of solvophilic A parts were studied by means of molecular dynamics simulations. In particular, mixtures of miktoarm star copolymers differing in the molecular weight of solvophilic arms were investigated. We found that the critical micelle concentration values show a positive deviation from the analytical predictions of the molecular theory of comicellization for chemically identical copolymers. This can be attributed to the effective interactions between copolymers originated from the arm size asymmetry. The effective interactions induce a very small decrease in the aggregation number of preferential micelles triggering the nonrandom mixing between the solvophilic moieties in the corona. Additionally, in order to specify how the chain architecture affects the size distribution and the shape of mixed micelles we studied star-shaped, H-shaped, and homo-linked-rings-linear mixtures. In the first case the individual constituents form micelles with preferential and wide aggregation numbers and in the latter case the individual constituents form wormlike and spherical micelles.

Entropic effects, shape, and size of mixed micelles formed by copolymers with complex architectures.

PubMed

Kalogirou, Andreas; Gergidis, Leonidas N; Moultos, Othonas; Vlahos, Costas

2015-11-01

The entropic effects in the comicellization behavior of amphiphilic AB copolymers differing in the chain size of solvophilic A parts were studied by means of molecular dynamics simulations. In particular, mixtures of miktoarm star copolymers differing in the molecular weight of solvophilic arms were investigated. We found that the critical micelle concentration values show a positive deviation from the analytical predictions of the molecular theory of comicellization for chemically identical copolymers. This can be attributed to the effective interactions between copolymers originated from the arm size asymmetry. The effective interactions induce a very small decrease in the aggregation number of preferential micelles triggering the nonrandom mixing between the solvophilic moieties in the corona. Additionally, in order to specify how the chain architecture affects the size distribution and the shape of mixed micelles we studied star-shaped, H-shaped, and homo-linked-rings-linear mixtures. In the first case the individual constituents form micelles with preferential and wide aggregation numbers and in the latter case the individual constituents form wormlike and spherical micelles.

Micro-rheological behaviour and nonlinear rheology of networks assembled from polysaccharides from the plant cell wall

NASA Astrophysics Data System (ADS)

Vincent, R. R. R.; Mansel, B. W.; Kramer, A.; Kroy, K.; Williams, M. A. K.

2013-03-01

The same fundamental questions that have driven enquiry into cytoskeletal mechanics can be asked of the considerably less-studied, yet arguably just as important, biopolymer matrix in the plant cell wall. In this case, it is well-known that polysaccharides, rather than filamentous and tubular protein assemblies, play a major role in satisfying the mechanical requirements of a successful cell wall, but developing a clear structure-function understanding has been exacerbated by the familiar issue of biological complexity. Herein, in the spirit of the mesoscopic approaches that have proved so illuminating in the study of cytoskeletal networks, the linear microrheological and strain-stiffening responses of biopolymeric networks reconstituted from pectin, a crucial cell wall polysaccharide, are examined. These are found to be well-captured by the glassy worm-like chain (GWLC) model of self-assembled semi-flexible filaments. Strikingly, the nonlinear mechanical response of these pectin networks is found to be much more sensitive to temperature changes than their linear response, a property that is also observed in F-actin networks, and is well reproduced by the GWLC model. Additionally, microrheological measurements suggest that over long timescales (>10 s) internal stresses continue to redistribute facilitating low frequency motions of tracer particles.

The Circularization of Amyloid Fibrils Formed by Apolipoprotein C-II

PubMed Central

Hatters, Danny M.; MacRaild, Christopher A.; Daniels, Rob; Gosal, Walraj S.; Thomson, Neil H.; Jones, Jonathan A.; Davis, Jason J.; MacPhee, Cait E.; Dobson, Christopher M.; Howlett, Geoffrey J.

2003-01-01

Amyloid fibrils have historically been characterized by diagnostic dye-binding assays, their fibrillar morphology, and a “cross-β” x-ray diffraction pattern. Whereas the latter demonstrates that amyloid fibrils have a common β-sheet core structure, they display a substantial degree of morphological variation. One striking example is the remarkable ability of human apolipoprotein C-II amyloid fibrils to circularize and form closed rings. Here we explore in detail the structure of apoC-II amyloid fibrils using electron microscopy, atomic force microscopy, and x-ray diffraction studies. Our results suggest a model for apoC-II fibrils as ribbons ∼2.1-nm thick and 13-nm wide with a helical repeat distance of 53 nm ± 12 nm. We propose that the ribbons are highly flexible with a persistence length of 36 nm. We use these observed biophysical properties to model the apoC-II amyloid fibrils either as wormlike chains or using a random-walk approach, and confirm that the probability of ring formation is critically dependent on the fibril flexibility. More generally, the ability of apoC-II fibrils to form rings also highlights the degree to which the common cross-β superstructure can, as a function of the protein constituent, give rise to great variation in the physical properties of amyloid fibrils. PMID:14645087

NMR and SAXS characterization of the denatured state of the chemotactic protein Che Y: Implications for protein folding initiation

PubMed Central

Garcia, Pascal; Serrano, Luis; Durand, Dominique; Rico, Manuel; Bruix, Marta

2001-01-01

The denatured state of a double mutant of the chemotactic protein CheY (F14N/V83T) has been analyzed in the presence of 5 M urea, using small angle X-ray scattering (SAXS) and heteronuclear magnetic resonance. SAXS studies show that the denatured protein follows a wormlike chain model. Its backbone can be described as a chain composed of rigid elements connected by flexible links. A comparison of the contour length obtained for the chain at 5 M urea with the one expected for a fully expanded chain suggests that ∼25% of the residues are involved in residual structures. Conformational shifts of the α-protons, heteronuclear 15N-{1H} NOEs and 15N relaxation properties have been used to identify some regions in the protein that deviate from a random coil behavior. According to these NMR data, the protein can be divided into two subdomains, which largely coincide with the two folding subunits identified in a previous kinetic study of the folding of the protein. The first of these subdomains, spanning residues 1–70, is shown here to exhibit a restricted mobility as compared to the rest of the protein. Two regions, one in each subdomain, were identified as deviating from the random coil chemical shifts. Peptides corresponding to these sequences were characterized by NMR and their backbone 1H chemical shifts were compared to those in the intact protein under identical denaturing conditions. For the region located in the first subdomain, this comparison shows that the observed deviation from random coil parameters is caused by interactions with the rest of the molecule. The restricted flexibility of the first subdomain and the transient collapse detected in that subunit are consistent with the conclusions obtained by applying the protein engineering method to the characterization of the folding reaction transition state. PMID:11369848

Stiffening of Red Blood Cells Induced by Cytoskeleton Disorders: A Joint Theory-Experiment Study.

PubMed

Lai, Lipeng; Xu, Xiaofeng; Lim, Chwee Teck; Cao, Jianshu

2015-12-01

The functions and elasticities of the cell are largely related to the structures of the cytoskeletons underlying the lipid bilayer. Among various cell types, the red blood cell (RBC) possesses a relatively simple cytoskeletal structure. Underneath the membrane, the RBC cytoskeleton takes the form of a two-dimensional triangular network, consisting of nodes of actins (and other proteins) and edges of spectrins. Recent experiments focusing on the malaria-infected RBCs (iRBCs) show that there is a correlation between the elongation of spectrins in the cytoskeletal network and the stiffening of the iRBCs. Here we rationalize the correlation between these two observations by combining the wormlike chain model for single spectrins and the effective medium theory for the network elasticity. We specifically focus on how the disorders in the cytoskeletal network affect its macroscopic elasticity. Analytical and numerical solutions from our model reveal that the stiffness of the membrane increases with increasing end-to-end distances of spectrins, but has a nonmonotonic dependence on the variance of the end-to-end distance distributions. These predictions are verified quantitatively by our atomic force microscopy and micropipette aspiration measurements of iRBCs. The model may, from a molecular level, provide guidelines for future identification of new treatment methods for RBC-related diseases, such as malaria infection. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

The Statistical Segment Length of DNA: Opportunities for Biomechanical Modeling in Polymer Physics and Next-Generation Genomics.

PubMed

Dorfman, Kevin D

2018-02-01

The development of bright bisintercalating dyes for deoxyribonucleic acid (DNA) in the 1990s, most notably YOYO-1, revolutionized the field of polymer physics in the ensuing years. These dyes, in conjunction with modern molecular biology techniques, permit the facile observation of polymer dynamics via fluorescence microscopy and thus direct tests of different theories of polymer dynamics. At the same time, they have played a key role in advancing an emerging next-generation method known as genome mapping in nanochannels. The effect of intercalation on the bending energy of DNA as embodied by a change in its statistical segment length (or, alternatively, its persistence length) has been the subject of significant controversy. The precise value of the statistical segment length is critical for the proper interpretation of polymer physics experiments and controls the phenomena underlying the aforementioned genomics technology. In this perspective, we briefly review the model of DNA as a wormlike chain and a trio of methods (light scattering, optical or magnetic tweezers, and atomic force microscopy (AFM)) that have been used to determine the statistical segment length of DNA. We then outline the disagreement in the literature over the role of bisintercalation on the bending energy of DNA, and how a multiscale biomechanical approach could provide an important model for this scientifically and technologically relevant problem.

Design and control of an IPMC wormlike robot.

PubMed

Arena, Paolo; Bonomo, Claudia; Fortuna, Luigi; Frasca, Mattia; Graziani, Salvatore

2006-10-01

This paper presents an innovative wormlike robot controlled by cellular neural networks (CNNs) and made of an ionic polymer-metal composite (IPMC) self-actuated skeleton. The IPMC actuators, from which it is made of, are new materials that behave similarly to biological muscles. The idea that inspired the work is the possibility of using IPMCs to design autonomous moving structures. CNNs have already demonstrated their powerfulness as new structures for bio-inspired locomotion generation and control. The control scheme for the proposed IPMC moving structure is based on CNNs. The wormlike robot is totally made of IPMCs, and each actuator has to carry its own weight. All the actuators are connected together without using any other additional part, thereby constituting the robot structure itself. Worm locomotion is performed by bending the actuators sequentially from "tail" to "head," imitating the traveling wave observed in real-world undulatory locomotion. The activation signals are generated by a CNN. In the authors' opinion, the proposed strategy represents a promising solution in the field of autonomous and light structures that are capable of reconfiguring and moving in line with spatial-temporal dynamics generated by CNNs.

Buckling of stiff polymers: Influence of thermal fluctuations

NASA Astrophysics Data System (ADS)

Emanuel, Marc; Mohrbach, Hervé; Sayar, Mehmet; Schiessel, Helmut; Kulić, Igor M.

2007-12-01

The buckling of biopolymers is a frequently studied phenomenon The influence of thermal fluctuations on the buckling transition is, however, often ignored and not completely understood. A quantitative theory of the buckling of a wormlike chain based on a semiclassical approximation of the partition function is presented. The contribution of thermal fluctuations to the force-extension relation that allows one to go beyond the classical Euler buckling is derived in the linear and nonlinear regimes as well. It is shown that the thermal fluctuations in the nonlinear buckling regime increase the end-to-end distance of the semiflexible rod if it is confined to two dimensions as opposed to the three-dimensional case. The transition to a buckled state softens at finite temperature. We derive the scaling behavior of the transition shift with increasing ratio of contour length versus persistence length.

Simulation of self-assembly of polyzwitterions into vesicles

DOE PAGES

Mahalik, Jyoti P.; Muthukumar, Murugappan

2016-08-19

Using the Langevin dynamics method and a coarse-grained model, we have researched the formation of vesicles by hydrophobic polymers consisting of periodically placed zwitterion side groups in dilute salt-free aqueous solutions. The zwitterions, being permanent charge dipoles, provide long-range electrostatic correlations which are interfered by the conformational entropy of the polymer. Our simulations are geared towards gaining conceptual understanding in these correlated dipolar systems, where theoretical calculations are at present formidable. A competition between hydrophobic interactions and dipole-dipole interactions leads to a series of self-assembled structures. As the spacing d between the successive zwitterion side groups decreases, single chains undergomore » globule → disk → worm-like structures. We have calculated the Flory-Huggins χ parameter for these systems in terms of d and monitored the radius of gyration, hydrodynamic radius, spatial correlations among hydrophobic and dipole monomers, and dipole-dipole orientational correlation functions. During the subsequent stages of self-assembly, these structures lead to larger globules and vesicles as d is decreased up to a threshold value, below which no large scale morphology forms. Finally the vesicles form via a polynucleation mechanism whereby disk-like structures form first, followed by their subsequent merger.« less

Interfacial instability of wormlike micellar solutions sheared in a Taylor-Couette cell

NASA Astrophysics Data System (ADS)

Mohammadigoushki, Hadi; Muller, Susan J.

2014-11-01

We report experiments on wormlike micellar solutions sheared in a custom-made Taylor-Couette (TC) cell. The computer controlled TC cell allows us to rotate both cylinders independently. Wormlike micellar solutions containing water, CTAB, and NaNo3 with different compositions are highly elastic and exhibit shear banding. We visualized the flow field in the θ-z as well as r-z planes, using multiple cameras. When subject to low shear rates, the flow is stable and azimuthal, but becomes unstable above a certain threshold shear rate. This shear rate coincides with the onset of shear banding. Visualizing the θ-z plane shows that this instability is characterized by stationary bands equally spaced in the z direction. Increasing the shear rate results to larger wave lengths. Above a critical shear rate, experiments reveal a chaotic behavior reminiscent of elastic turbulence. We also studied the effect of ramp speed on the onset of instability and report an acceleration below which the critical Weissenberg number for onset of instability is unaffected. Moreover, visualizations in the r-z direction reveals that the interface between the two bands undulates with shear bands evolving towards the outer cylinder regardless of which cylinder is rotating.

Identification and Analysis of Partial Shading Breakdown Sites in CuIn xGa (1-x)Se 2 Modules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Palmiotti, Elizabeth; Johnston, Steven; Gerber, Andreas

In this paper, CuIn xGa (1-x) (CIGS) mini-modules are stressed under reverse bias, resembling partial shading conditions, to predict and characterize where failures occur. Partial shading can cause permanent damage in the form of 'wormlike' defects on thin-film modules due to thermal runaway. This results in module-scale power losses. We have used dark lock-in thermography (DLIT) to spatially observe localized heating when reverse-bias breakdown occurs on various CIGS mini-modules. For better understanding of how and where these defects originated and propagated, we have developed techniques where the current is limited during reverse-bias stressing. This allows for DLIT-based detection and detailedmore » studying of the region where breakdown is initiated before thermal runaway leads to permanent damage. Statistics of breakdown sites using current-limited conditions has allowed for reasonable identification of the as-grown defects where permanent breakdown will likely originate. Scanning electron microscope results and wormlike defect analysis show that breakdown originates in defects such as small pits, craters, or cracks in the CIGS layer, and the wormlike defects propagate near the top CIGS interface.« less

Identification and Analysis of Partial Shading Breakdown Sites in CuIn xGa (1-x)Se 2 Modules

DOE PAGES

Palmiotti, Elizabeth; Johnston, Steven; Gerber, Andreas; ...

2017-12-20

In this paper, CuIn xGa (1-x) (CIGS) mini-modules are stressed under reverse bias, resembling partial shading conditions, to predict and characterize where failures occur. Partial shading can cause permanent damage in the form of 'wormlike' defects on thin-film modules due to thermal runaway. This results in module-scale power losses. We have used dark lock-in thermography (DLIT) to spatially observe localized heating when reverse-bias breakdown occurs on various CIGS mini-modules. For better understanding of how and where these defects originated and propagated, we have developed techniques where the current is limited during reverse-bias stressing. This allows for DLIT-based detection and detailedmore » studying of the region where breakdown is initiated before thermal runaway leads to permanent damage. Statistics of breakdown sites using current-limited conditions has allowed for reasonable identification of the as-grown defects where permanent breakdown will likely originate. Scanning electron microscope results and wormlike defect analysis show that breakdown originates in defects such as small pits, craters, or cracks in the CIGS layer, and the wormlike defects propagate near the top CIGS interface.« less

The Conformations of Confined Polymers in an External Potential

NASA Astrophysics Data System (ADS)

Morrison, Greg

The confinement of biomolecules is ubiquitous in nature, such as the spatial constraints of viral encapsulation, histone binding, and chromosomal packing. Advances in microfluidics and nanopore fabrication have permitted powerful new tools in single molecule manipulation and gene sequencing through molecular confinement as well. In order to fully understand and exploit these systems, the ability to predict the structure of spatially confined molecules is essential. In this talk, I describe a mean field approach to determine the properties of stiff polymers confined to cylinders and slits, which is relevant for a variety of biological and experimental conditions. I show that this approach is able to not only reproduce known scaling laws for confined wormlike chains, but also provides an improvement over existing weakly bending rod approximations in determining the detailed chain properties (such as correlation functions). Using this approach, we also show that it is possible to study the effect of an externally applied tension or static electric field in a natural and analytically tractable way. These external perturbations can alter the scaling laws and introduce important new length scales into the system, relevant for histone unbinding and single-molecule analysis of DNA.

Distribution of transverse chain fluctuations in harmonically confined semiflexible polymers

NASA Astrophysics Data System (ADS)

Sharma, Rati; Cherayil, Binny J.

2012-05-01

Two different experimental studies of polymer dynamics based on single-molecule fluorescence imaging have recently found evidence of heterogeneities in the widths of the putative tubes that surround filaments of F-actin during their motion in concentrated solution. In one [J. Glaser, D. Chakraborty, K. Kroy, I. Lauter, M. Degawa, N. Kirchesner, B. Hoffmann, R. Merkel, and M. Giesen, Phys. Rev. Lett. 105, 037801 (2010)], 10.1103/PhysRevLett.105.037801, the observations were explained in terms of the statistics of a worm-like chain confined to a potential determined self-consistently by a binary collision approximation, and in the other [B. Wang, J. Guan, S. M. Anthony, S. C. Bae, K. S. Schweizer, and S. Granick, Phys. Rev. Lett. 104, 118301 (2010)], 10.1103/PhysRevLett.104.118301, they were explained in terms of the scaling properties of a random fluid of thin rods. In this paper, we show, using an exact path integral calculation, that the distribution of the length-averaged transverse fluctuations of a harmonically confined weakly bendable rod (one possible realization of a semiflexible chain in a tube), is in good qualitative agreement with the experimental data, although it is qualitatively different in analytic structure from the earlier theoretical predictions. We also show that similar path integral techniques can be used to obtain an exact expression for the time correlation function of fluctuations in the tube cross section.

Shear-banding and superdiffusivity in entangled polymer solutions

NASA Astrophysics Data System (ADS)

Shin, Seunghwan; Dorfman, Kevin D.; Cheng, Xiang

2017-12-01

Using high-resolution confocal rheometry, we study the shear profiles of well-entangled DNA solutions under large-amplitude oscillatory shear in a rectilinear planar shear cell. With increasing Weissenberg number (Wi), we observe successive transitions from normal Newtonian linear shear profiles to wall-slip dominant shear profiles and, finally, to shear-banding profiles at high Wi. To investigate the microscopic origin of the observed shear banding, we study the dynamics of micron-sized tracers embedded in DNA solutions. Surprisingly, tracer particles in the shear frame exhibit transient superdiffusivity and strong dynamic heterogeneity. The probability distribution functions of particle displacements follow a power-law scaling at large displacements, indicating a Lévy-walk-type motion, reminiscent of tracer dynamics in entangled wormlike micelle solutions and sheared colloidal glasses. We further characterize the length and time scales associated with the abnormal dynamics of tracer particles. We hypothesize that the unusual particle dynamics arise from localized shear-induced chain disentanglement.

Self-assembly of micelles in organic solutions of lecithin and bile salt: Mesoscale computer simulation

NASA Astrophysics Data System (ADS)

Markina, A.; Ivanov, V.; Komarov, P.; Khokhlov, A.; Tung, S.-H.

2016-11-01

We propose a coarse-grained model for studying the effects of adding bile salt to lecithin organosols by means of computer simulation. This model allows us to reveal the mechanisms of experimentally observed increasing of viscosity upon increasing the bile salt concentration. We show that increasing the bile salt to lecithin molar ratio induces the growth of elongated micelles of ellipsoidal and cylindrical shape due to incorporation of disklike bile salt molecules. These wormlike micelles can entangle into transient network displaying perceptible viscoelastic properties.

Elastin-like Polypeptide Linkers for Single-Molecule Force Spectroscopy.

PubMed

Ott, Wolfgang; Jobst, Markus A; Bauer, Magnus S; Durner, Ellis; Milles, Lukas F; Nash, Michael A; Gaub, Hermann E

2017-06-27

Single-molecule force spectroscopy (SMFS) is by now well established as a standard technique in biophysics and mechanobiology. In recent years, the technique has benefitted greatly from new approaches to bioconjugation of proteins to surfaces. Indeed, optimized immobilization strategies for biomolecules and refined purification schemes are being steadily adapted and improved, which in turn has enhanced data quality. In many previously reported SMFS studies, poly(ethylene glycol) (PEG) was used to anchor molecules of interest to surfaces and/or cantilever tips. The limitation, however, is that PEG exhibits a well-known trans-trans-gauche to all-trans transition, which results in marked deviation from standard polymer elasticity models such as the worm-like chain, particularly at elevated forces. As a result, the assignment of unfolding events to protein domains based on their corresponding amino acid chain lengths is significantly obscured. Here, we provide a solution to this problem by implementing unstructured elastin-like polypeptides as linkers to replace PEG. We investigate the suitability of tailored elastin-like polypeptides linkers and perform direct comparisons to PEG, focusing on attributes that are critical for single-molecule force experiments such as linker length, monodispersity, and bioorthogonal conjugation tags. Our results demonstrate that by avoiding the ambiguous elastic response of mixed PEG/peptide systems and instead building the molecular mechanical systems with only a single bond type with uniform elastic properties, we improve data quality and facilitate data analysis and interpretation in force spectroscopy experiments. The use of all-peptide linkers allows alternative approaches for precisely defining elastic properties of proteins linked to surfaces.

A multiscale approach to simulating the conformational properties of unbound multi-C₂H₂ zinc finger proteins.

PubMed

Liu, Lei; Wade, Rebecca C; Heermann, Dieter W

2015-09-01

The conformational properties of unbound multi-Cys2 His2 (mC2H2) zinc finger proteins, in which zinc finger domains are connected by flexible linkers, are studied by a multiscale approach. Three methods on different length scales are utilized. First, atomic detail molecular dynamics simulations of one zinc finger and its adjacent flexible linker confirmed that the zinc finger is more rigid than the flexible linker. Second, the end-to-end distance distributions of mC2H2 zinc finger proteins are computed using an efficient atomistic pivoting algorithm, which only takes excluded volume interactions into consideration. The end-to-end distance distribution gradually changes its profile, from left-tailed to right-tailed, as the number of zinc fingers increases. This is explained by using a worm-like chain model. For proteins of a few zinc fingers, an effective bending constraint favors an extended conformation. Only for proteins containing more than nine zinc fingers, is a somewhat compacted conformation preferred. Third, a mesoscale model is modified to study both the local and the global conformational properties of multi-C2H2 zinc finger proteins. Simulations of the CCCTC-binding factor (CTCF), an important mC2H2 zinc finger protein for genome spatial organization, are presented. © 2015 Wiley Periodicals, Inc.

Self-assembly of amphiphilic molecules in organic liquids

NASA Astrophysics Data System (ADS)

Tung, Shih-Huang

2007-12-01

Amphiphilic molecules are well-known for their ability to self-assemble in water to form structures such as micelles and vesicles. In comparison, much less is known about amphiphilic self-assembly in nonpolar organic liquids. Such "reverse" self assembly can produce many of the counterparts to structures found in water. In this dissertation, we focus on the formation and dynamics of such reverse structures. We seek to obtain fundamental insight into the driving forces for reverse self-assembly processes. Three specific types of reverse structures are studied: (a) reverse wormlike micelles, i.e., long, flexible micellar chains; (b) reverse vesicles, i.e., hollow containers enclosed by reverse bilayers; and (c) organogel networks. While our focus is on the fundamentals, we note that reverse structures can be useful in a variety of applications ranging from drug delivery, controlled release, hosts for enzymatic reactions, and templates for nanomaterials synthesis. In the first part of this study, we describe a new route for forming reverse wormlike micelles in nonpolar organic liquids. This route involves the addition of trace amounts of a bile salt to solutions of the phospholipid, lecithin. We show that bile salts, due to their unique "facially amphiphilic" structure, can promote the aggregation of lecithin molecules into these reverse micellar chains. The resulting samples are viscoelastic and show interesting rheological properties. Unusual trends are seen in the temperature dependence of their rheology, which indicates the importance of hydrogen-bonding interactions in the formation of these micelles. Another remarkable feature of their rheology is the presence of strain-stiffening, where the material becomes stiffer at high deformations. Strain-stiffening has been seen before for elastic gels of biopolymers; here, we demonstrate the same properties for viscoelastic micellar solutions. The second reverse aggregate we deal with is the reverse vesicle. We present a new route for forming stable unilamellar reverse vesicles, and this involves mixing short- and long-chain lipids (lecithins) with a trace of sodium chloride. The ratio of the short to long-chain lipid controls the type and size of self-assembled structure formed, and as this ratio is increased, a transition from reverse micelles to vesicles occurs. The structural changes can be explained in terms of molecular geometry, with the sodium chloride acting as a "glue" in binding lipid headgroups together through electrostatic interactions. The final part of this dissertation focuses on organogels. The two-tailed anionic surfactant, AOT, is well-known to form spherical reverse micelles in organic solvents. We have found that trace amounts (e.g., less than 1 mM) of the dihydroxy bile salt, sodium deoxycholate (SDC) can transform these dilute micellar solutions into self-supporting, transparent organogels. The structure and rheology of these organogels is reminiscent of the self-assembled networks formed by proteins such as actin in water. The organogels are based on networks of long, rigid, cylindrical filaments, with SDC molecules stacked together in the filament core.

Structure formation in binary mixtures of surfactants: vesicle opening-up to bicelles and octopus-like micelles

NASA Astrophysics Data System (ADS)

Noguchi, Hiroshi

Micelle formation in binary mixtures of surfactants is studied using a coarse-grained molecular simulation. When a vesicle composed of lipid and detergent types of molecules is ruptured, a disk-shaped micelle, the bicelle, is typically formed. It is found that cup-shaped vesicles and bicelles connected with worm-like micelles are also formed depending on the surfactant ratio and critical micelle concentration. The obtained octopus shape of micelles agree with those observed in the cryo-TEM images reported in [S. Jain and F. S. Bates, Macromol. 37, 1511 (2004).]. Two types of connection structures between the worm-like micelles and the bicelles are revealed.

A shear-induced network of aligned wormlike micelles in a sugar-based molecular gel. From gelation to biocompatibility assays.

PubMed

Fitremann, Juliette; Lonetti, Barbara; Fratini, Emiliano; Fabing, Isabelle; Payré, Bruno; Boulé, Christelle; Loubinoux, Isabelle; Vaysse, Laurence; Oriol, Luis

2017-10-15

A new low molecular weight hydrogelator with a saccharide (lactobionic) polar head linked by azide-alkyne click chemistry was prepared in three steps. It was obtained in high purity without chromatography, by phase separation and ultrafiltration of the aqueous gel. Gelation was not obtained reproducibly by conventional heating-cooling cycles and instead was obtained by shearing the aqueous solutions, from 2 wt% to 0.25 wt%. This method of preparation favored the formation of a quite unusual network of interconnected large but thin 2D-sheets (7nm-thick) formed by the association side-by-side of long and aligned 7nm diameter wormlike micelles. It was responsible for the reproducible gelation at the macroscopic scale. A second network made of helical fibres with a 10-13nm diameter, more or less intertwined was also formed but was scarcely able to sustain a macroscopic gel on its own. The gels were analysed by TEM (Transmission Electronic Microscopy), cryo-TEM and SAXS (Small Angle X-ray Scattering). Molecular modelling was also used to highlight the possible conformations the hydrogelator can take. The gels displayed a weak and reversible transition near 20°C, close to room temperature, ascribed to the wormlike micelles 2D-sheets network. Heating over 30°C led to the loss of the gel macroscopic integrity, but gel fragments were still observed in suspension. A second transition near 50°C, ascribed to the network of helical fibres, finally dissolved completely these fragments. The gels showed thixotropic behaviour, recovering slowly their initial elastic modulus, in few hours, after injection through a needle. Stable gels were tested as scaffold for neural cell line culture, showing a reduced biocompatibility. This new gelator is a clear illustration of how controlling the pathway was critical for gel formation and how a new kind of self-assembly was obtained by shearing. Copyright © 2017 Elsevier Inc. All rights reserved.

Interfacial instability of wormlike micellar solutions sheared in a Taylor-Couette cell

NASA Astrophysics Data System (ADS)

Mohammadigoushki, Hadi; Muller, Susan J.

2014-10-01

We report experiments on wormlike micellar solutions sheared in a custom-made Taylor-Couette (TC) cell. The computer controlled TC cell allows us to rotate both cylinders independently. Wormlike micellar solutions containing water, CTAB, and NaNo3 with different compositions are highly elastic and exhibit shear banding within a range of shear rate. We visualized the flow field in the θ-z as well as r-z planes, using multiple cameras. When subject to low shear rates, the flow is stable and azimuthal, but becomes unstable above a certain threshold shear rate. This shear rate coincides with the onset of shear banding. Visualizing the θ-z plane shows that this instability is characterized by stationary bands equally spaced in the z direction. Increasing the shear rate results to larger wave lengths. Above a critical shear rate, experiments reveal a chaotic behavior reminiscent of elastic turbulence. We also studied the effect of ramp speed on the onset of instability and report an acceleration below which the critical Weissenberg number for onset of instability is unaffected. Moreover, visualizations in the r-z direction reveals that the interface between the two bands undulates. The shear band evolves towards the outer cylinder upon increasing the shear rate, regardless of which cylinder is rotating.

The Nanomechanical Properties of Lactococcus lactis Pili Are Conditioned by the Polymerized Backbone Pilin

PubMed Central

Castelain, Mickaël; Duviau, Marie-Pierre; Canette, Alexis; Schmitz, Philippe; Loubière, Pascal; Cocaign-Bousquet, Muriel; Piard, Jean-Christophe; Mercier-Bonin, Muriel

2016-01-01

Pili produced by Lactococcus lactis subsp. lactis are putative linear structures consisting of repetitive subunits of the major pilin PilB that forms the backbone, pilin PilA situated at the distal end of the pilus, and an anchoring pilin PilC that tethers the pilus to the peptidoglycan. We determined the nanomechanical properties of pili using optical-tweezers force spectroscopy. Single pili were exposed to optical forces that yielded force-versus-extension spectra fitted using the Worm-Like Chain model. Native pili subjected to a force of 0–200 pN exhibit an inextensible, but highly flexible ultrastructure, reflected by their short persistence length. We tested a panel of derived strains to understand the functional role of the different pilins. First, we found that both the major pilin PilB and sortase C organize the backbone into a full-length organelle and dictate the nanomechanical properties of the pili. Second, we found that both PilA tip pilin and PilC anchoring pilin were not essential for the nanomechanical properties of pili. However, PilC maintains the pilus on the bacterial surface and may play a crucial role in the adhesion- and biofilm-forming properties of L. lactis. PMID:27010408

Actin filament curvature biases branching direction

NASA Astrophysics Data System (ADS)

Wang, Evan; Risca, Viviana; Chaudhuri, Ovijit; Chia, Jia-Jun; Geissler, Phillip; Fletcher, Daniel

2012-02-01

Actin filaments are key components of the cellular machinery, vital for a wide range of processes ranging from cell motility to endocytosis. Actin filaments can branch, and essential in this process is a protein complex known as the Arp2/3 complex, which nucleate new ``daughter'' filaments from pre-existing ``mother'' filaments by attaching itself to the mother filament. Though much progress has been made in understanding the Arp2/3-actin junction, some very interesting questions remain. In particular, F-actin is a dynamic polymer that undergoes a wide range of fluctuations. Prior studies of the Arp2/3-actin junction provides a very static notion of Arp2/3 binding. The question we ask is how differently does the Arp2/3 complex interact with a straight filament compared to a bent filament? In this study, we used Monte Carlo simulations of a surface-tethered worm-like chain to explore possible mechanisms underlying the experimental observation that there exists preferential branch formation by the Arp2/3 complex on the convex face of a curved filament. We show that a fluctuation gating model in which Arp2/3 binding to the actin filament is dependent upon a rare high-local-curvature shape fluctuation of the filament is consistent with the experimental data.

Path-Integration Computation of the Transport Properties of Polymers Nanoparticles and Complex Biological Structures

NASA Astrophysics Data System (ADS)

Douglas, Jack

2014-03-01

One of the things that puzzled me when I was a PhD student working under Karl Freed was the curious unity between the theoretical descriptions of excluded volume interactions in polymers, the hydrodynamic properties of polymers in solution, and the critical properties of fluid mixtures, gases and diverse other materials (magnets, superfluids,etc.) when these problems were formally expressed in terms of Wiener path integration and the interactions treated through a combination of epsilon expansion and renormalization group (RG) theory. It seemed that only the interaction labels changed from one problem to the other. What do these problems have in common? Essential clues to these interrelations became apparent when Karl Freed, myself and Shi-Qing Wang together began to study polymers interacting with hyper-surfaces of continuously variable dimension where the Feynman perturbation expansions could be performed through infinite order so that we could really understand what the RG theory was doing. It is evidently simply a particular method for resuming perturbation theory, and former ambiguities no longer existed. An integral equation extension of this type of exact calculation to ``surfaces'' of arbitrary fixed shape finally revealed the central mathematical object that links these diverse physical models- the capacity of polymer chains, whose value vanishes at the critical dimension of 4 and whose magnitude is linked to the friction coefficient of polymer chains, the virial coefficient of polymers and the 4-point function of the phi-4 field theory,...Once this central object was recognized, it then became possible solve diverse problems in material science through the calculation of capacity, and related ``virials'' properties, through Monte Carlo sampling of random walk paths. The essential ideas of this computational method are discussed and some applications given to non-trivial problems: nanotubes treated as either rigid rods or ensembles worm-like chains having finite cross-section, DNA, nanoparticles with grafted chain layers and knotted polymers. The path-integration method, which grew up from research in Karl Freed's group, is evidently a powerful tool for computing basic transport properties of complex-shaped objects and should find increasing application in polymer science, nanotechnological applications and biology.

Local site preference rationalizes disentangling by DNA topoisomerases

NASA Astrophysics Data System (ADS)

Liu, Zhirong; Zechiedrich, Lynn; Chan, Hue Sun

2010-03-01

To rationalize the disentangling action of type II topoisomerases, an improved wormlike DNA model was used to delineate the degree of unknotting and decatenating achievable by selective segment passage at specific juxtaposition geometries and to determine how these activities were affected by DNA circle size and solution ionic strength. We found that segment passage at hooked geometries can reduce knot populations as dramatically as seen in experiments. Selective segment passage also provided theoretical underpinning for an intriguing empirical scaling relation between unknotting and decatenating potentials.

Structural distributions from single-molecule measurements as a tool for molecular mechanics

PubMed Central

Hanson, Jeffrey A.; Brokaw, Jason; Hayden, Carl C.; Chu, Jhih-Wei; Yang, Haw

2011-01-01

A mechanical view provides an attractive alternative for predicting the behavior of complex systems since it circumvents the resource-intensive requirements of atomistic models; however, it remains extremely challenging to characterize the mechanical responses of a system at the molecular level. Here, the structural distribution is proposed to be an effective means to extracting the molecular mechanical properties. End-to-end distance distributions for a series of short poly-L-proline peptides with the sequence PnCG3K-biotin (n = 8, 12, 15 and 24) were used to experimentally illustrate this new approach. High-resolution single-molecule Förster-type resonance energy transfer (FRET) experiments were carried out and the conformation-resolving power was characterized and discussed in the context of the conventional constant-time binning procedure for FRET data analysis. It was shown that the commonly adopted theoretical polymer models—including the worm-like chain, the freely jointed chain, and the self-avoiding chain—could not be distinguished by the averaged end-to-end distances, but could be ruled out using the molecular details gained by conformational distribution analysis because similar polymers of different sizes could respond to external forces differently. Specifically, by fitting the molecular conformational distribution to a semi-flexible polymer model, the effective persistence lengths for the series of short poly-L-proline peptides were found to be size-dependent with values of ~190 Å, ~67 Å, ~51 Å, and ~76 Å for n = 8, 12, 15, and 24, respectively. A comprehensive computational modeling was carried out to gain further insights for this surprising discovery. It was found that P8 exists as the extended all-trans isomaer whereas P12 and P15 predominantly contained one proline residue in the cis conformation. P24 exists as a mixture of one-cis (75%) and two-cis (25%) isomers where each isomer contributes to an experimentally resolvable conformational mode. This work demonstrates the resolving power of the distribution-based approach, and the capacity of integrating high-resolution single-molecule FRET experiments with molecular modeling to reveal detailed structural information about the conformation of molecules on the length scales relevant to the study of biological molecules. PMID:22661822

Activation energy and entropy for viscosity of wormlike micelle solutions.

PubMed

Chandler, H D

2013-11-01

The viscosities of two surfactant solutions which form wormlike micelles (WLMs) were studied over a range of temperatures and strain rates. WLM solutions appear to differ from many other shear thinning systems in that, as the shear rate increases, stress-shear rate curves tend to converge with temperature rather than diverge and this can sometimes lead to higher temperature curves crossing those at lower. Behaviour was analysed in terms of activation kinetics. It is suggested that two mechanisms are involved: Newtonian flow, following an Arrhenius law superimposed on a non-Newtonian flow described by a stress assisted kinetic law, this being a more general form of the Arrhenius law. Anomalous flow is introduced into the kinetic equation via a stress dependent activation entropy term. Copyright © 2013 Elsevier Inc. All rights reserved.

Fabrication of Worm-Like Nanorods and Ultrafine Nanospheres of Silver Via Solid-State Photochemical Decomposition

PubMed Central

2009-01-01

Worm-like nanorods and nanospheres of silver have been synthesized by photochemical decomposition of silver oxalate in water by UV irradiation in the presence of CTAB and PVP, respectively. No external seeds have been employed for the synthesis of Ag nanorods. The synthesized Ag colloids have been characterized by UV-visible spectra, powder XRD, HRTEM, and selected area electron diffraction (SAED). Ag nanospheres of average size around 2 nm have been obtained in the presence of PVP. XRD and TEM analyses revealed that top and basal planes of nanorods are bound with {111} facets. Williamson–Hall plot has revealed the presence of defects in the Ag nanospheres and nanorods. Formation of defective Ag nanocrystals is attributed to the heating effect of UV-visible irradiation. PMID:20596513

Thermodynamic and dynamic behaviors of self-organizing polymeric systems

NASA Astrophysics Data System (ADS)

Zhao, Yiqiang

Two topics of self-organizing polymeric systems are explored in this work: thermodynamic and dynamic properties of liquid crystal polymers in solutions and rheological behaviors of self-organizing gels. For dilute nematic solutions of end-on side-chain liquid crystal polysiloxanes (SCLCP) dissolved in 5CB, the chain anisotropies R∥/R ⊥, obtained from electrorheological(ER) analysis based on the Brochard model, are consistent with independent measurements of Rg∥/R g⊥ via small-angle neutron scattering (SANS), which unambiguously demonstrating a slightly prolate SCLCP chain conformation. Dissolution of this prolate SCLCP in flow-aligning 5CB produces a tumbling flow, clearly indicating a discrepancy with the Brochard hydrodynamic theory which predicts such a transition only for oblate conformation. A numerical comparison using a modified version of the Brochard model leads to improved self-consistent agreement between SANS, ER and shear transient experiments. The molecular weight dependence of the chain conformational relaxation time it indicates an extended SCLCP chain conformation in 5CB. SANS analysis suggests that the SCLCP conformation is sensitive to the solvent interaction, i.e. a more extended conformation is observed in isotropic acetone-d6 than in nematic 5CB. A SANS conformational study of SCLCCs with methoxyphenylbenzoate mesogenic side group in CDC13 demonstrates that the form factor of a single comb-like SCLCP chain is well described by a wormlike chain model with finite cross-sectional thickness over the entire q range, taking into account the molecular weight polydispersity. Consistent with measurement of a large R g from low q analysis, the resulting persistence length lp is in the range 28˜32 A, substantially larger than that of unsubstituted polydimethylsiloxane (PDMS) chain (l p =5.8 A), which suggests a relatively rigid SCLCP chain due to the influence of densely attached mesogenic groups. For nematic mixtures of copolysiloxane SCLCP in 5OCB, a metastably extended miscible nematic range is observed at low SCLCP concentration upon cooling. Onset of an induced smectic phase occurs upon cooling at 60%wt SCLCP concentration which corresponds to 48:52 molar ratio of mesogens. Dielectric spectra of these mixtures over a wide concentration range exhibit two distinct regimes of relaxation behavior reflecting the crossover from dilute and semidilute to concentrated regime. Rheological behavior of a metallo-supramolecular gel with thixotropic feature is explored to understand the viscoelastic behaviors of self-assembling networks consisting of "living polymers". A well-defined yield point and non-linear viscoelasticity at small strain are probed via the controlled-stress and controlled-strain measurements, respectively. The self-assembled network is readily presheared into a Newtonian sol and displays a three-stage kinetic recovery process, closely associated with the metal ion-ligand binding kinetics and related phase behaviors. Finally, we investigate the viscoelastic properties of a novel colloidal gel in which macrocycles self-assemble into interconnected self-organized clusters. A series of rheological experiments are combined to reveal the shear responsive nature as well as linear and nonlinear viscoelasticity of this gel. Certain features of observed viscoelastic properties demonstrate the characteristics of the behavior of colloidal gels which show slow glassy dynamics. The negative temperature dependence of the storage modulus at low frequency suggests that enthalpic contributions to elasticity need to be considered, presumably due to internal energy changes upon deformation.

Ionic micelles and aromatic additives: a closer look at the molecular packing parameter.

PubMed

Lutz-Bueno, Viviane; Isabettini, Stéphane; Walker, Franziska; Kuster, Simon; Liebi, Marianne; Fischer, Peter

2017-08-16

Wormlike micellar aggregates formed from the mixture of ionic surfactants with aromatic additives result in solutions with impressive viscoelastic properties. These properties are of high interest for numerous industrial applications and are often used as model systems for soft matter physics. However, robust and simple models for tailoring the viscoelastic response of the solution based on the molecular structure of the employed additive are required to fully exploit the potential of these systems. We address this shortcoming with a modified packing parameter based model, considering the additive-surfactant pair. The role of charge neutralization on anisotropic micellar growth was investigated with derivatives of sodium salicylate. The impact of the additives on the morphology of the micellar aggregates is explained from the molecular level to the macroscopic viscoelasticity. Changes in the micelle's volume, headgroup area and additive structure are explored to redefine the packing parameter. Uncharged additives penetrated deeper into the hydrophobic region of the micelle, whilst charged additives remained trapped in the polar region, as revealed by a combination of 1 H-NMR, SAXS and rheological measurements. A deeper penetration of the additives densified the hydrophobic core of the micelle and induced anisotropic growth by increasing the effective volume of the additive-surfactant pair. This phenomenon largely influenced the viscosity of the solutions. Partially penetrating additives reduced the electrostatic repulsions between surfactant headgroups and neighboring micelles. The resulting increased network density governed the elasticity of the solutions. Considering a packing parameter composed of the additive-surfactant pair proved to be a facile means of engineering the viscoelastic response of surfactant solutions. The self-assembly of the wormlike micellar aggregates could be tailored to desired morphologies resulting in a specific and predictable rheological response.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ratto, T V; Rudd, R E; Langry, K C

We present evidence of multivalent interactions between a single protein molecule and multiple carbohydrates at a pH where the protein can bind four ligands. The evidence is based not only on measurements of the force required to rupture the bonds formed between ConcanavalinA (ConA) and {alpha}-D-mannose, but also on an analysis of the polymer-extension force curves to infer the polymer architecture that binds the protein to the cantilever and the ligands to the substrate. We find that although the rupture forces for multiple carbohydrate connections to a single protein are larger than the rupture force for a single connection, theymore » do not scale additively with increasing number. Specifically, the most common rupture forces are approximately 46, 66, and 85 pN, which we argue corresponds to 1, 2, and 3 ligands being pulled simultaneously from a single protein as corroborated by an analysis of the linkage architecture. As in our previous work polymer tethers allow us to discriminate between specific and non-specific binding. We analyze the binding configuration (i.e. serial versus parallel connections) through fitting the polymer stretching data with modified Worm-Like Chain (WLC) models that predict how the effective stiffness of the tethers is affected by multiple connections. This analysis establishes that the forces we measure are due to single proteins interacting with multiple ligands, the first force spectroscopy study that establishes single-molecule multivalent binding unambiguously.« less

Porous worm-like NiMoO4 coaxially decorated electrospun carbon nanofiber as binder-free electrodes for high performance supercapacitors and lithium-ion batteries

NASA Astrophysics Data System (ADS)

Tian, Xiaodong; Li, Xiao; Yang, Tao; Wang, Kai; Wang, Hongbao; Song, Yan; Liu, Zhanjun; Guo, Quangui

2018-03-01

The peculiar architectures consisting of electrospun carbon nanofibers coaxially decorated by porous worm-like NiMoO4 were successfully fabricated for the first time to address the poor cycling stability and inferior rate capability of the state-of-the-art NiMoO4-based electrodes caused by the insufficient structural stability, dense structure and low conductivity. The porous worm-like structure endows the electrode high capacitance/capacity due to large effective specific surface area and short electron/ion diffusion channels. Moreover, the robust integrated electrode with sufficient internal spaces can self-accommodate volume variation during charge/discharge processes, which is beneficial to the structural stability and integrity. By the virtue of rational design of the architecture, the hybrid electrode delivered high specific capacitance (1088.5 F g-1 at 1 A g-1), good rate capability (860.3 F g-1 at 20 A g-1) and long lifespan with a capacitance retention of 73.9% after 5000 cycles when used as supercapacitor electrode. For lithium-ion battery application, the electrode exhibited a high reversible capacity of 1132.1 mAh g-1 at 0.5 A g-1. Notably, 689.7 mAh g-1 can be achieved even after 150 continuous cycles at a current density of 1 A g-1. In the view of their outstanding electrochemical performance and the cost-effective fabrication process, the integrated nanostructure shows great promising applications in energy storage.

Predicting dynamics and rheology of blood flow: A comparative study of multiscale and low-dimensional models of red blood cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pan, Wenxiao; Fedosov, Dmitry A.; Caswell, Bruce

In this work we compare the predictive capability of two mathematical models for red blood cells (RBCs) focusing on blood flow in capillaries and arterioles. Both RBC models as well as their corresponding blood flows are based on the dissipative particle dynamics (DPD) method, a coarse-grained molecular dynamics approach. The first model employs a multiscale description of the RBC (MS-RBC), with its membrane represented by hundreds or even thousands of DPD-particles connected by springs into a triangular network in combination with out-of-plane elastic bending resistance. Extra dissipation within the network accounts for membrane viscosity, while the characteristic biconcave RBC shapemore » is achieved by imposition of constraints for constant membrane area and constant cell volume. The second model is based on a low-dimensional description (LD-RBC) constructed as a closed torus-like ring of only 10 large DPD colloidal particles. They are connected into a ring by worm-like chain (WLC) springs combined with bending resistance. The LD-RBC model can be fitted to represent the entire range of nonlinear elastic deformations as measured by optical-tweezers for healthy and for infected RBCs in malaria. MS-RBCs suspensions model the dynamics and rheology of blood flow accurately for any size vessel but this approach is computationally expensive above 100 microns. Surprisingly, the much more economical suspensions of LD-RBCs also capture the blood flow dynamics and rheology accurately except for vessels with sizes comparable to RBC diameter. In particular, the LD-RBC suspensions are shown to properly capture the experimental data for the apparent viscosity of blood and its cell-free layer (CFL) in tube flow. Taken together, these findings suggest a hierarchical approach in modeling blood flow in the arterial tree, whereby the MS-RBC model should be employed for capillaries and arterioles below 100 microns, the LD-RBC model for arterioles, and the continuum description for arteries.« less

Extracting physical chemistry from mechanics: a new approach to investigate DNA interactions with drugs and proteins in single molecule experiments.

PubMed

Rocha, M S

2015-09-01

In this review we focus on the idea of establishing connections between the mechanical properties of DNA-ligand complexes and the physical chemistry of DNA-ligand interactions. This type of connection is interesting because it opens the possibility of performing a robust characterization of such interactions by using only one experimental technique: single molecule stretching. Furthermore, it also opens new possibilities in comparing results obtained by very different approaches, in particular when comparing single molecule techniques to ensemble-averaging techniques. We start the manuscript reviewing important concepts of DNA mechanics, from the basic mechanical properties to the Worm-Like Chain model. Next we review the basic concepts of the physical chemistry of DNA-ligand interactions, revisiting the most important models used to analyze the binding data and discussing their binding isotherms. Then, we discuss the basic features of the single molecule techniques most used to stretch DNA-ligand complexes and to obtain "force × extension" data, from which the mechanical properties of the complexes can be determined. We also discuss the characteristics of the main types of interactions that can occur between DNA and ligands, from covalent binding to simple electrostatic driven interactions. Finally, we present a historical survey of the attempts to connect mechanics to physical chemistry for DNA-ligand systems, emphasizing a recently developed fitting approach useful to connect the persistence length of DNA-ligand complexes to the physicochemical properties of the interaction. Such an approach in principle can be used for any type of ligand, from drugs to proteins, even if multiple binding modes are present.

β-connectin studies by small-angle x-ray scattering and single-molecule force spectroscopy by atomic force microscopy

NASA Astrophysics Data System (ADS)

Marchetti, S.; Sbrana, F.; Toscano, A.; Fratini, E.; Carlà, M.; Vassalli, M.; Tiribilli, B.; Pacini, A.; Gambi, C. M. C.

2011-05-01

The three-dimensional structure and the mechanical properties of a β-connectin fragment from human cardiac muscle, belonging to the I band, from I27 to I34, were investigated by small-angle x-ray scattering (SAXS) and single-molecule force spectroscopy (SMFS). This molecule presents an entropic elasticity behavior, associated to globular domain unfolding, that has been widely studied in the last 10 years. In addition, atomic force microscopy based SMFS experiments suggest that this molecule has an additional elastic regime, for low forces, probably associated to tertiary structure remodeling. From a structural point of view, this behavior is a mark of the fact that the eight domains in the I27-I34 fragment are not independent and they organize in solution, assuming a well-defined three-dimensional structure. This hypothesis has been confirmed by SAXS scattering, both on a diluted and a concentrated sample. Two different models were used to fit the SAXS curves: one assuming a globular shape and one corresponding to an elongated conformation, both coupled with a Coulomb repulsion potential to take into account the protein-protein interaction. Due to the predominance of the structure factor, the effective shape of the protein in solution could not be clearly disclosed. By performing SMFS by atomic force microscopy, mechanical unfolding properties were investigated. Typical sawtooth profiles were obtained and the rupture force of each unfolding domain was estimated. By fitting a wormlike chain model to each peak of the sawtooth profile, the entropic elasticity of octamer was described.

Maier-Saupe model of polymer nematics: Comparing free energies calculated with Self Consistent Field theory and Monte Carlo simulations.

PubMed

Greco, Cristina; Jiang, Ying; Chen, Jeff Z Y; Kremer, Kurt; Daoulas, Kostas Ch

2016-11-14

Self Consistent Field (SCF) theory serves as an efficient tool for studying mesoscale structure and thermodynamics of polymeric liquid crystals (LC). We investigate how some of the intrinsic approximations of SCF affect the description of the thermodynamics of polymeric LC, using a coarse-grained model. Polymer nematics are represented as discrete worm-like chains (WLC) where non-bonded interactions are defined combining an isotropic repulsive and an anisotropic attractive Maier-Saupe (MS) potential. The range of the potentials, σ, controls the strength of correlations due to non-bonded interactions. Increasing σ (which can be seen as an increase of coarse-graining) while preserving the integrated strength of the potentials reduces correlations. The model is studied with particle-based Monte Carlo (MC) simulations and SCF theory which uses partial enumeration to describe discrete WLC. In MC simulations the Helmholtz free energy is calculated as a function of strength of MS interactions to obtain reference thermodynamic data. To calculate the free energy of the nematic branch with respect to the disordered melt, we employ a special thermodynamic integration (TI) scheme invoking an external field to bypass the first-order isotropic-nematic transition. Methodological aspects which have not been discussed in earlier implementations of the TI to LC are considered. Special attention is given to the rotational Goldstone mode. The free-energy landscape in MC and SCF is directly compared. For moderate σ the differences highlight the importance of local non-bonded orientation correlations between segments, which SCF neglects. Simple renormalization of parameters in SCF cannot compensate the missing correlations. Increasing σ reduces correlations and SCF reproduces well the free energy in MC simulations.

Response of cells on surface-induced nanopatterns: fibroblasts and mesenchymal progenitor cells.

PubMed

Khor, Hwei Ling; Kuan, Yujun; Kukula, Hildegard; Tamada, Kaoru; Knoll, Wolfgang; Moeller, Martin; Hutmacher, Dietmar W

2007-05-01

Ultrathin films of a poly(styrene)-block-poly(2-vinylpyrindine) diblock copolymer (PS-b-P2VP) and poly(styrene)-block-poly(4-vinylpyrindine) diblock copolymer (PS-b-P4VP) were used to form surface-induced nanopattern (SINPAT) on mica. Surface interaction controlled microphase separation led to the formation of chemically heterogeneous surface nanopatterns on dry ultrathin films. Two distinct nanopatterned surfaces, namely, wormlike and dotlike patterns, were used to investigate the influence of topography in the nanometer range on cell adhesion, proliferation, and migration. Atomic force microscopy was used to confirm that SINPAT was stable under cell culture conditions. Fibroblasts and mesenchymal progenitor cells were cultured on the nanopatterned surfaces. Phase contrast and confocal laser microscopy showed that fibroblasts and mesenchymal progenitor cells preferred the densely spaced wormlike patterns. Atomic force microscopy showed that the cells remodelled the extracellular matrix differently as they migrate over the two distinctly different nanopatterns.

Molten salt medium synthesis of wormlike platinum silver nanotubes without any organic surfactant or solvent for methanol and formic acid oxidation.

PubMed

Zhao, Haidong; Liu, Rui; Guo, Yong; Yang, Shengchun

2015-12-14

In the current research, the PtxAgy (x/y = 86/14, 79/21, 52/48, 21/79, 11/89) nanoparticles (NPs) are synthesized in the KNO3-LiNO3 molten salts without using any organic surfactant or solvent. The SEM results suggest that when the content of Ag is higher than 48%, the wormlike PtxAgy nanotubes (NTs) can be synthesized. The diameter of the PtxAgyNTs shows a slow decrease with the increase of Ag content. The TEM and HRTEM results indicate that the growth of hollow PtxAgy NTs undergoes an oriented attachment process and a Kirkendall effect approach. The results of cyclic voltammetry (CV) measurement indicate that the Pt52Ag48 catalyst presents a remarkable enhancement for methanol electrooxidation, while the Pt86Ag14 catalyst prefers electrochemically oxidizing formic acid compared with that of the commercially available Pt black.

Experimental and numerical studies of tethered DNA dynamics in shear flow

NASA Astrophysics Data System (ADS)

Lueth, Christopher A.

Polymer physics has a rich tradition spanning nearly two centuries. In the 1830s, Henri Braconnot and coworkers were perhaps the first to work on what is today known as polymer science when they derived semi-synthetic materials from naturally occurring cellulose. However, the true nature of polymers, as long chain molecules, had not been proposed until 1910 by Pickles. It was not until the 1950's when polymer models were developed using statistical mechanics. Recently, the field has been revitalized by the ability to study individual polymer molecules for the first time. The development of DNA single molecule fluorescence microscopy coupled with ever increasing computational power has opened the door to molecular level understanding of polymer physics, resolving old disputes and uncovering new interesting phenomena. In this work, we use a combination of theoretical predictions and lambda-phage DNA single molecule fluorescence microscopy to study the behavior of polymers tethered to surfaces. Brownian dynamics simulations of a number of coarse-grained polymer models---dynamic and equilibrium Kratky-Porod chains as well as bead-spring chains---were completed and compared with analytical and experimental results. First, an expression is developed for the entropic exclusion force experienced by a tethered polymer chain. We propose that, for a freely jointed chain, a modification to the free entropic force of kBT/y is needed in the direction normal to the surface. Analogously, we propose that for a wormlike chain, a modification of 2kBT/y is needed, due to the finite curvature of the model. Then, the reliability of discretized bead spring simulations containing this modified entropic force are analyzed using Kratky-Porod simulations and are found to reproduce most statistics, except for those very near the surface, such as end-wall contact. Next, experiments of tethered lambda-phage DNA in shear flow are presented for the first time in the flow-gradient plane. The tethering surface chemistry proved to be arduous work, but with the aide of contact angle and ellipsometry measurements, success was achieved. Extension behavior was shown to agree well with bead spring simulations, but deviations were discovered for weak flows in the extensional fluctuations, mean distance from the wall, and orientation angle. Cyclic dynamics---where the polymer continuously diffuses away from the wall, subsequently undergoes stretch in the flow direction, is then "entropically pulled back" towards the wall, and finally recoils---was observed and quantified through correlation and power spectral densities. Again, quantitative agreement was observed between experiments and bead spring simulations. The onset of cyclic dynamics was found to occur at Wi ≈ 3 and was found to decline with increasing Wi up to ≈ 200. Finally, a reliable procedure was developed utilizing Dip Pen Nanolithography to controllably tether DNA to gold surfaces. Preliminary experiments were performed and successful tethering was achieved, an important first step toward creating DNA scaffolds for molecular wires. However, further research is needed to fully develop the process and successfully double tether DNA molecules between gold electrodes.

Debranching and Crystallization of Waxy Maize Starch in Relation to Enzyme Digestibility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cai, L.; Shi, Y; Rong, L

Molecular and crystal structures as well as morphology during debranching and crystallization of waxy maize starch at a high solid content (25%, w/w) were investigated, and the results were related to the digestibility of debranched products. The starch was cooked at 115-120 C for 10 min, cooled to 50 C and debranched by isoamylase. After 1 h of debranching, wormlike objects with 5-10 nm width and ca. 30 nm length were observed by transmission electron microscopy. Further release of linear chains and crystallization led to assembly of semi-crystalline structures in the form of nano-particles and subsequent growth of nano-particles intomore » large aggregates. After 24 h at 50 C, a debranched starch product with an A-type X-ray diffraction pattern, a high melting temperature (90-140 C), and high resistant starch content (71.4%) was obtained. Small-angle X-ray scattering results indicated that all debranched products were surface fractal in a dry state (4% moisture) but had a mass fractal structure when hydrated (e.g. 45% moisture).« less

Aggregate-mediated charge transport in ionomeric electrolytes

NASA Astrophysics Data System (ADS)

Lu, Keran; Maranas, Janna; Milner, Scott

Polymers such PEO can conduct ions, and have been studied as possible replacements for organic liquid electrolytes in rechargeable metal-ion batteries. More generally, fast room-temperature ionic conduction has been reported for a variety of materials, from liquids to crystalline solids. Unfortunately, polymer electrolytes generally have limited conductivity; these polymers are too viscous to have fast ion diffusion like liquids, and too unstructured to promote cooperative transport like crystalline solids. Ionomers are polymer electrolytes in which ionic groups are covalently bound to the polymer backbone, neutralized by free counterions. These materials also conduct ions, and can exhibit strong ionic aggregation. Using coarse-grained molecular dynamics, we explore the forces driving ionic aggregation, and describe the role ion aggregates have in mediating charge transport. The aggregates are string-like such that ions typically have two neighbors. We find ion aggregates self-assemble like worm-like micelles. Excess charge, or free ions, occasionally coordinate with aggregates and are transported along the chain in a Grotthuss-like mechanism. We propose that controlling ionomer aggregate structure through materials design can enhance cooperative ion transport.

Cryo-TEM of morphology and kinetics of self-assembled nanostructures

NASA Astrophysics Data System (ADS)

Dong, Jingshan

Cryogenic Transmission Electron Microscopy (Cryo-TEM) is applied to study various structures in solutions and suspensions from micron to nanometer scale. By vitrifying the liquid samples at different moments, sequential stages of a dynamic process can be frozen and the structures occurring from about 30 sec to over 10 min can be imaged. Therefore a picture of how the structures evolve with time in the liquid systems can be established. This method has been proven to be a powerful technique in studying the morphology and kinetics of self-assembled nanostructures. Such a pseudo-in-situ technique is used to "watch" the crystallization process of silver stearate (AgSt) from sodium stearate (NaSt) dispersions. AgSt crystal is produced from a reaction of NaSt and silver nitrate. The reaction, as a AgSt crystallization process, starts from AgSt micelles, which aggregate and grow into hexagonal shaped crystals of about 10 microns. If silver bromide (AgBr) grains are present, the micelles do not prefer to aggregate, but rather deposit on the surface of the AgBr crystalline grains. Variation of the carboxylate chain length does not affect the crystallization process very much, although the morphology of both the reactant and the product is changed. Nanostructure transition in sodium lauryl ether sulfate (SLES) solutions is investigated as well. A micellar network structure can form if equal molar calcium chloride is added to 3 wt% SLES solution. The network can be broken into wormlike micelle segments such as spheres and rods by sonication. After about 10 min, these broken pieces can reassemble and reform the network through wormlike micelle growth and connection. Also by using Cryo-TEM, 100-200 nm casein micelles are observed at 1 wt% casein solution, but aggregated submicelles cannot be distinguished. However, individual submicelles of about 30 nm are indeed captured in a 0.03 wt% solution. By adding acid or EDTA, the casein micelles can be disrupted into small particles, the size of which is close to the estimated radius of gyration of single casein molecules.

Drug Combination Synergy in Worm-like Polymeric Micelles Improves Treatment Outcome for Small Cell and Non-Small Cell Lung Cancer.

PubMed

Wan, Xiaomeng; Min, Yuanzeng; Bludau, Herdis; Keith, Andrew; Sheiko, Sergei S; Jordan, Rainer; Wang, Andrew Z; Sokolsky-Papkov, Marina; Kabanov, Alexander V

2018-03-27

Nanoparticle-based systems for concurrent delivery of multiple drugs can improve outcomes of cancer treatments, but face challenges because of differential solubility and fairly low threshold for incorporation of many drugs. Here we demonstrate that this approach can be used to greatly improve the treatment outcomes of etoposide (ETO) and platinum drug combination ("EP/PE") therapy that is the backbone for treatment of prevalent and deadly small cell lung cancer (SCLC). A polymeric micelle system based on amphiphilic block copolymer poly(2-oxazoline)s (POx) poly(2-methyl-2-oxazoline- block-2-butyl-2-oxazoline- block-2-methyl-2-oxazoline) (P(MeOx- b-BuOx- b-MeOx) is used along with an alkylated cisplatin prodrug to enable co-formulation of EP/PE in a single high-capacity vehicle. A broad range of drug mixing ratios and exceptionally high two-drug loading of over 50% wt. drug in dispersed phase is demonstrated. The highly loaded POx micelles have worm-like morphology, unprecedented for drug loaded polymeric micelles reported so far, which usually form spheres upon drug loading. The drugs co-loading in the micelles result in a slowed-down release, improved pharmacokinetics, and increased tumor distribution of both drugs. A superior antitumor activity of co-loaded EP/PE drug micelles compared to single drug micelles or their combination as well as free drug combination was demonstrated using several animal models of SCLC and non-small cell lung cancer.

Sol-gel transition behavior of aqueous peptide-amphiphile (C16-W3K) solutions: effects of alkyl-tail length, mechanical shear, temperature, and salt

NASA Astrophysics Data System (ADS)

Yamamoto, Masashi; Otsuka, Takahiro; Orimo, Yoshinori; Maeda, Tomoki; Hotta, Atsushi

Peptide amphiphiles (PA) possess nanoscale micelle structures and excellent biocompatibility. In aqueous PA solution, PA molecules can self-assemble through various configurations into spherical and wormlike micelles, which can occasionally form hydrogels. C16-W3K is one of the unique PA, whose micelle configurations can transfer from spherical to wormlike structures in its aqueous solution over time, while the wormlike micelles could also lead to gelation. In our recent research, the effects of the length of the hydrophobic alkyl tail and other external factors of C16-W3K on the gelation behavior of the C16-W3K solution have been discussed. It has been revealed that longer alkyl-tails could facilitate the gelation of the C16-W3K solution, and that the external stimuli, such as mechanical shear and heat, could promote faster gelation of the C16-W3K solution. It was also found that salt could adjust the pH of the C16-W3K solution, having profound influence on the gelation behavior of the C16-W3K solution. In fact, the gelation of the C16-W3K with a higher storage modulus could be obtained from relatively acidic solutions, while the gelation of the C16-W3K solution was firmly suppressed in highly basic solutions. This work was supported by a Grant-in-Aid for Scientific Research (A) (No. 15H02298 to A.H.) and a Grant-in-Aid for Research Activity Start-up (No.15H06586 to T.M.) from JSPS: KAKENHI.

General Syntheses of Nanotubes Induced by Block Copolymer Self-Assembly.

PubMed

Zhao, Jianming; Huang, Wei; Si, Pengchao; Ulstrup, Jens; Diao, Fangyuan; Zhang, Jingdong

2018-06-01

Amphiphilic block copolymer templating strategies are extensively used for syntheses of mesoporous materials. However, monodisperse tubular nanostructures are limited. Here, a general method is developed to synthesize monodisperse nanotubes with narrow diameter distribution induced by self-assembly of block copolymer. 3-Aminophenol (AP) and formaldehyde (F) polymerize and self-assemble with cylindrical PS-b-PEO micelles into worm-like PS-b-PEO@APF composites with uniform diameter (49 ± 3 nm). After template extraction, worm-like APF polymer nanotubes are formed. The structure and morphology of the polymer nanotubes can be tuned by regulating the synthesis conditions. Furthermore, PS-b-PEO@APF composites are uniformly converted to isomorphic carbon nanotubes with large surface area of 662 m 2 g -1 , abundant hierarchical porous frameworks and nitrogen doping. The synthesis can be extended to silica nanotubes. These findings open an avenue to the design of porous materials with controlled structural framework, composition, and properties for a wide range of applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Facile fabrication of BiVO4 nanofilms with controlled pore size and their photoelectrochemical performances

NASA Astrophysics Data System (ADS)

Feng, Chenchen; Jiao, Zhengbo; Li, Shaopeng; Zhang, Yan; Bi, Yingpu

2015-12-01

We demonstrate a facile method for the rational fabrication of pore-size controlled nanoporous BiVO4 photoanodes, and confirmed that the optimum pore-size distributions could effectively absorb visible light through light diffraction and confinement functions. Furthermore, in situ X-ray photoelectron spectroscopy (XPS) reveals more efficient photoexcited electron-hole separation than conventional particle films, induced by light confinement and rapid charge transfer in the inter-crossed worm-like structures.We demonstrate a facile method for the rational fabrication of pore-size controlled nanoporous BiVO4 photoanodes, and confirmed that the optimum pore-size distributions could effectively absorb visible light through light diffraction and confinement functions. Furthermore, in situ X-ray photoelectron spectroscopy (XPS) reveals more efficient photoexcited electron-hole separation than conventional particle films, induced by light confinement and rapid charge transfer in the inter-crossed worm-like structures. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr06584d

Interacting Multiscale Acoustic Vortices as Coherent Excitations in Dust Acoustic Wave Turbulence

NASA Astrophysics Data System (ADS)

Lin, Po-Cheng; I, Lin

2018-03-01

In this work, using three-dimensional intermittent dust acoustic wave turbulence in a dusty plasma as a platform and multidimensional empirical mode decomposition into different-scale modes in the 2 +1 D spatiotemporal space, we demonstrate the experimental observation of the interacting multiscale acoustic vortices, winding around wormlike amplitude hole filaments coinciding with defect filaments, as the basic coherent excitations for acoustic-type wave turbulence. For different decomposed modes, the self-similar rescaled stretched exponential lifetime histograms of amplitude hole filaments, and the self-similar power spectra of dust density fluctuations, indicate that similar dynamical rules are followed over a wide range of scales. In addition to the intermode acoustic vortex pair generation, propagation, or annihilation, the intra- and intermode interactions of acoustic vortices with the same or opposite helicity, their entanglement and synchronization, are found to be the key dynamical processes in acoustic wave turbulence, akin to the interacting multiscale vortices around wormlike cores observed in hydrodynamic turbulence.

Synthesis of platinum nanowire networks using a soft template.

PubMed

Song, Yujiang; Garcia, Robert M; Dorin, Rachel M; Wang, Haorong; Qiu, Yan; Coker, Eric N; Steen, William A; Miller, James E; Shelnutt, John A

2007-12-01

Platinum nanowire networks have been synthesized by chemical reduction of a platinum complex using sodium borohydride in the presence of a soft template formed by cetyltrimethylammonium bromide in a two-phase water-chloroform system. The interconnected polycrystalline nanowires possess the highest surface area (53 +/- 1 m2/g) and electroactive surface area (32.4 +/- 3.6 m2/g) reported for unsupported platinum nanomaterials; the high surface area results from the small average diameter of the nanowires (2.2 nm) and the 2-10 nm pores determined by nitrogen adsorption measurements. Synthetic control over the network was achieved simply by varying the stirring rate and reagent concentrations, in some cases leading to other types of nanostructures including wormlike platinum nanoparticles. Similarly, substitution of a palladium complex for platinum gives palladium nanowire networks. A mechanism of formation of the metal nanowire networks is proposed based on confined metal growth within a soft template consisting of a network of swollen inverse wormlike micelles.

Flow of wormlike micellar solutions around confined microfluidic cylinders.

PubMed

Zhao, Ya; Shen, Amy Q; Haward, Simon J

2016-10-26

Wormlike micellar (WLM) solutions are frequently used in enhanced oil and gas recovery applications in porous rock beds where complex microscopic geometries result in mixed flow kinematics with strong shear and extensional components. Experiments with WLM solutions through model microfluidic porous media have revealed a variety of complex flow phenomena, including the formation of stable gel-like structures known as a Flow-Induced Structured Phase (FISP), which undoubtedly play an important role in applications of WLM fluids, but are still poorly understood. A first step in understanding flows of WLM fluids through porous media can be made by examining the flow around a single micro-scale cylinder aligned on the flow axis. Here we study flow behavior of an aqueous WLM solution consisting of cationic surfactant cetyltrimethylammonium bromide (CTAB) and a stable hydrotropic salt 3-hydroxy naphthalene-2-carboxylate (SHNC) in microfluidic devices with three different cylinder blockage ratios, β. We observe a rich sequence of flow instabilities depending on β as the Weissenberg number (Wi) is increased to large values while the Reynolds number (Re) remains low. Instabilities upstream of the cylinder are associated with high stresses in fluid that accelerates into the narrow gap between the cylinder and the channel wall; vortex growth upstream is reminiscent of that seen in microfluidic contraction geometries. Instability downstream of the cylinder is associated with stresses generated at the trailing stagnation point and the resulting flow modification in the wake, coupled with the onset of time-dependent flow upstream and the asymmetric division of flow around the cylinder.

Local conformation and intermolecular interaction of rigid ring polymers are not always the same as the linear analogue: cyclic amylose tris(phenylcarbamate) in Θ solvents.

PubMed

Asano, Natsuki; Kitamura, Shinichi; Terao, Ken

2013-08-15

Small-angle X-ray scattering and static and dynamic light scattering measurements were made for cyclic amylose tris(phenylcarbamate) (cATPC) of which weight-average molar mass M(w) ranges from 1.3 × 10(4) to 1.5 × 10(5) to determine their z-average mean square radius of gyration z, particle scattering function P(q), hydrodynamic radius R(H), and second virial coefficient A2 in methyl acetate (MEA), ethyl acetate (EA), and 4-methyl-2-pentanone (MIBK). The obtained z, P(q), and R(H) data were analyzed in terms of the wormlike ring to estimate the helix pitch per residue h and the Kuhn segment length λ(-1) (the stiffness parameter, twice the persistence length). Both h and λ(-1) for cATPC in MEA, EA, and MIBK are smaller than those for linear amylose tris(phenylcarbamate) (ATPC) in the corresponding solvent and the discrepancy becomes more significant with increasing the molar volume of the solvent. This indicates that not every rigid ring has the same local helical structure and chain stiffness as that for the linear polymer in the M(w) range investigated while infinitely long ring chains should have the same local conformation. This conformational difference also affects A2. In actuality, negative A2 was observed for cATPC in MIBK at the Θ temperature of linear ATPC whereas intermolecular topological interaction of ring polymers increases A2.

Surgical extraction of intraocular Parelaphostrongylus tenuis (Nematoda: Metastrongyloidea) in a horse

USDA-ARS?s Scientific Manuscript database

Case Description – A 4-year-old Hanoverian horse from Wisconsin presented for evaluation of a worm-like structure in the anterior chamber of the right eye. Clinical Findings – Ophthalmic examination of the right eye revealed a white, thin, mobile parasite, presumably a nematode, present in the ventr...

Fluctuations of wormlike micelle fluids in capillary flow

NASA Astrophysics Data System (ADS)

Salipante, Paul; Meek, Stephen; Hudson, Steven; Polymers; Complex Fluids Group Team

2017-11-01

We investigate the effect of entrance geometry on the flow stability of wormlike micelles solutions in capillary flow. These solutions exhibit strong shear thinning behavior resulting from micelle breakage and have been observed to undergo large flow rate fluctuations. We investigate these fluctuations using simultaneous measurements of flow rate and pressure drop across a capillary, and we adjust entrance geometry. With a tapered constriction, we observe large persistent fluctuations above a critical flow rate, characterized by rapid decreases in the pressure drop with corresponding increase in flow rate followed by a period of recovery where pressure increases and flow rate decreases. Flow field observations in the tapered entrance show large flow circulations. An abrupt contraction produces smaller transient fluidized jets forming upstream of the constriction and the magnitude of the fluctuations are significantly diminished. The effect of fluid properties is studied by comparing the magnitude and timescales of the fluctuations for surfactant systems with different relaxation times. The onset of fluctuations is compared to a criterion for the onset of elastic instabilities and the magnitude is compared to estimates for changes in channel resistance. NIST on a Chip.

Synthesis of Mesoporous α-Fe2O3 Nanoparticles by Non-ionic Soft Template and Their Applications to Heavy Oil Upgrading

NASA Astrophysics Data System (ADS)

Park, Chulwoo; Jung, Jinhwan; Lee, Chul Wee; Cho, Joungmo

2016-12-01

This paper reports the synthetic route of 3-D network shape α-Fe2O3 from aqueous solutions of iron precursor using a non-ionic polymeric soft-template, Pluronic P123. During the synthesis of α-Fe2O3, particle sizes, crystal phases and morphologies were significantly influenced by pH, concentrations of precursor and template. The unique shape of worm-like hematite was obtained only when a starting solution was prepared by a weakly basic pH condition and a very specific composition of constituents. The synthesized nanocrystal at this condition had a narrow pore size distribution and high surface area compared to the bulk α-Fe2O3 or the one synthesized from lower pH conditions. The hydrocracking performance was tested over the synthesized iron oxide catalysts with different morphologies. The worm-like shape of iron oxide showed a superior performance, including overall yield of liquid fuel product and coke formation, over the hydrocracking of heavy petroleum oil.

Synthesis of Mesoporous α-Fe2O3 Nanoparticles by Non-ionic Soft Template and Their Applications to Heavy Oil Upgrading

PubMed Central

Park, Chulwoo; Jung, Jinhwan; Lee, Chul Wee; Cho, Joungmo

2016-01-01

This paper reports the synthetic route of 3-D network shape α-Fe2O3 from aqueous solutions of iron precursor using a non-ionic polymeric soft-template, Pluronic P123. During the synthesis of α-Fe2O3, particle sizes, crystal phases and morphologies were significantly influenced by pH, concentrations of precursor and template. The unique shape of worm-like hematite was obtained only when a starting solution was prepared by a weakly basic pH condition and a very specific composition of constituents. The synthesized nanocrystal at this condition had a narrow pore size distribution and high surface area compared to the bulk α-Fe2O3 or the one synthesized from lower pH conditions. The hydrocracking performance was tested over the synthesized iron oxide catalysts with different morphologies. The worm-like shape of iron oxide showed a superior performance, including overall yield of liquid fuel product and coke formation, over the hydrocracking of heavy petroleum oil. PMID:27966663

Synthesis of Mesoporous α-Fe2O3 Nanoparticles by Non-ionic Soft Template and Their Applications to Heavy Oil Upgrading.

PubMed

Park, Chulwoo; Jung, Jinhwan; Lee, Chul Wee; Cho, Joungmo

2016-12-14

This paper reports the synthetic route of 3-D network shape α-Fe 2 O 3 from aqueous solutions of iron precursor using a non-ionic polymeric soft-template, Pluronic P123. During the synthesis of α-Fe 2 O 3 , particle sizes, crystal phases and morphologies were significantly influenced by pH, concentrations of precursor and template. The unique shape of worm-like hematite was obtained only when a starting solution was prepared by a weakly basic pH condition and a very specific composition of constituents. The synthesized nanocrystal at this condition had a narrow pore size distribution and high surface area compared to the bulk α-Fe 2 O 3 or the one synthesized from lower pH conditions. The hydrocracking performance was tested over the synthesized iron oxide catalysts with different morphologies. The worm-like shape of iron oxide showed a superior performance, including overall yield of liquid fuel product and coke formation, over the hydrocracking of heavy petroleum oil.

Manipulation of Liquid Metals on a Graphite Surface.

PubMed

Hu, Liang; Wang, Lei; Ding, Yujie; Zhan, Shihui; Liu, Jing

2016-11-01

Liquid metals (LMs) in an alkaline electrolyte, when placed on a graphite surface, are able to be manipulated into desired flat, stable shapes with sharp angles, like triangles. Unique transformations and worm-like anti-gravity upslope LM locomotion under a low-voltage electric field are also revealed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High performance aqueous symmetric supercapacitors based on advanced carbon electrodes and hydrophilic poly(vinylidene fluoride) porous separator

NASA Astrophysics Data System (ADS)

Xie, Qinxing; Huang, Xiaolin; Zhang, Yufeng; Wu, Shihua; Zhao, Peng

2018-06-01

The main components of a supercapacitor include two electrodes, electrolyte, and a separator, which are all essential to specify the energy storage capability of the device. In this work, two kinds of porous carbon materials have been fabricated via different routes using pomelo peel as raw material. The specific surface area are 1187 m2 g-1 for the nanosized worm-like carbon, and 1744 m2 g-1 for the nitrogen-enriched microsized carbon. Both carbon materials demonstrate excellent energy storage capability as electrodes for aqueous supercapacitors. According to the three-electrode measurements, the worm-like carbon exhibits a high specific capacitance of 316 F g-1 at 0.2 A g-1 in 6 M KOH, while the other exhibits 471 F g-1 due to the highly enriched nitrogen atoms in structure. In addition, two-electrode coin-type cells have been assembled with the carbon materials as electrodes and hydrophilic poly(vinylidene fluoride) porous membrane as the separator. The assembled cells exhibit high specific capacitances, excellent rate performance and superior cycling durability because of a synergistic effect of the high performance carbon electrodes and hydrophilic porous separator.

Sampling the kinetic pathways of a micelle fusion and fission transition.

PubMed

Pool, René; Bolhuis, Peter G

2007-06-28

The mechanism and kinetics of micellar breakup and fusion in a dilute solution of a model surfactant are investigated by path sampling techniques. Analysis of the path ensemble gives insight in the mechanism of the transition. For larger, less stable micelles the fission/fusion occurs via a clear neck formation, while for smaller micelles the mechanism is more direct. In addition, path analysis yields an appropriate order parameter to evaluate the fusion and fission rate constants using stochastic transition interface sampling. For the small, stable micelle (50 surfactants) the computed fission rate constant is a factor of 10 lower than the fusion rate constant. The procedure opens the way for accurate calculation of free energy and kinetics for, e.g., membrane fusion, and wormlike micelle endcap formation.

Extremely fast and highly selective detection of nitroaromatic explosive vapours using fluorescent polymer thin films.

PubMed

Demirel, Gokcen Birlik; Daglar, Bihter; Bayindir, Mehmet

2013-07-14

A novel sensing material based on pyrene doped polyethersulfone worm-like structured thin film is developed using a facile technique for detection of nitroaromatic explosive vapours. The formation of π-π stacking in the thin fluorescent film allows a highly sensitive fluorescence quenching which is detectable by the naked eye in a response time of a few seconds.

Nonlinear viscoelasticity of entangled wormlike micellar fluid under large-amplitude oscillatory shear: Role of elastic Taylor-Couette instability

NASA Astrophysics Data System (ADS)

Majumdar, Sayantan; Sood, A. K.

2014-06-01

The role of elastic Taylor-Couette flow instabilities in the dynamic nonlinear viscoelastic response of an entangled wormlike micellar fluid is studied by large-amplitude oscillatory shear (LAOS) rheology and in situ polarized light scattering over a wide range of strain and angular frequency values, both above and below the linear crossover point. Well inside the nonlinear regime, higher harmonic decomposition of the resulting stress signal reveals that the normalized third harmonic I3/I1 shows a power-law behavior with strain amplitude. In addition, I3/I1 and the elastic component of stress amplitude σ0E show a very prominent maximum at the strain value where the number density (nv) of the Taylor vortices is maximum. A subsequent increase in applied strain (γ) results in the distortions of the vortices and a concomitant decrease in nv, accompanied by a sharp drop in I3 and σ0E. The peak position of the spatial correlation function of the scattered intensity along the vorticity direction also captures the crossover. Lissajous plots indicate an intracycle strain hardening for the values of γ corresponding to the peak of I3, similar to that observed for hard-sphere glasses.

Origin of shear thickening in semidilute wormlike micellar solutions and evidence of elastic turbulence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marín-Santibáñez, Benjamín M.; Pérez-González, José, E-mail: jpg@esfm.ipn.mx; Rodríguez-González, Francisco

2014-11-01

The origin of shear thickening in an equimolar semidilute wormlike micellar solution of cetylpyridinium chloride and sodium salicylate was investigated in this work by using Couette rheometry, flow visualization, and capillary Rheo-particle image velocimetry. The use of the combined methods allowed the discovery of gradient shear banding flow occurring from a critical shear stress and consisting of two main bands, one isotropic (transparent) of high viscosity and one structured (turbid) of low viscosity. Mechanical rheometry indicated macroscopic shear thinning behavior in the shear banding regime. However, local velocimetry showed that the turbid band increased its viscosity along with the shearmore » stress, even though barely reached the value of the viscosity of the isotropic phase. This shear band is the precursor of shear induced structures that subsequently give rise to the average increase in viscosity or apparent shear thickening of the solution. Further increase in the shear stress promoted the growing of the turbid band across the flow region and led to destabilization of the shear banding flow independently of the type of rheometer used, as well as to vorticity banding in Couette flow. At last, vorticity banding disappeared and the flow developed elastic turbulence with chaotic dynamics.« less

Diffusing wave spectroscopy in Maxwellian fluids.

PubMed

Galvan-Miyoshi, J; Delgado, J; Castillo, R

2008-08-01

We present a critical assessment of the diffusing wave spectroscopy (DWS) technique for obtaining the characteristic lengths and for measuring the loss and storage moduli of a reasonable well-known wormlike micelle (WM) system. For this purpose, we tracked the Brownian motion of particles using DWS embedded in a Maxwellian fluid constituted by a wormlike micellar solution made of cetyltrimethylammonium bromide (CTAB), sodium salicylate (NaSal), and water. We found that the motion of particles was governed by the viscosity of the solvent at short times and by the stress relaxation mechanisms of the giant micelles at longer times. From the time evolution of the mean square displacement of particles, we could obtain for the WM solution the cage size where each particle is harmonically bound at short times, the long-time diffusion coefficient, and experimental values for the exponent that accounts for the broad spectrum of relaxation times at the plateau onset time found in the (deltar2(t)) vs. time curves. In addition, from the (deltar2(t)) vs. time curves, we obtained G'(omega) and G"(omega) for the WM solutions. All the DWS microreological information allowed us to estimate the characteristic lengths of the WM network. We compare our DWS microrheological results and characteristic lengths with those obtained with mechanical rheometers at different NaSal/CTAB concentration ratios and temperatures.

Viscoelastic fluid-structure interactions between a flexible cylinder and wormlike micelle solution

NASA Astrophysics Data System (ADS)

Dey, Anita A.; Modarres-Sadeghi, Yahya; Rothstein, Jonathan P.

2018-06-01

It is well known that when a flexible or flexibly mounted structure is placed perpendicular to the flow of a Newtonian fluid, it can oscillate due to the shedding of separated vortices at high Reynolds numbers. Unlike Newtonian fluids, the flow of viscoelastic fluids can become unstable even at infinitesimal Reynolds numbers due to a purely elastic flow instability that can occur at large Weissenberg numbers. Recent work has shown that these elastic flow instabilities can drive the motion of flexible sheets. The fluctuating fluid forces exerted on the structure from the elastic flow instabilities can lead to a coupling between an oscillatory structural motion and the state of stress in the fluid flow. In this paper, we present the results of an investigation into the flow of a viscoelastic wormlike micelle solution past a flexible circular cylinder. The time variation of the flow field and the state of stress in the fluid are shown using a combination of particle image tracking and flow-induced birefringence images. The static and dynamic responses of the flexible cylinder are presented for a range of flow velocities. The nonlinear dynamics of the structural motion is studied to better understand an observed transition from a symmetric to an asymmetric structural deformation and oscillation behavior.

Effect of genomic long-range correlations on DNA persistence length: from theory to single molecule experiments.

PubMed

Moukhtar, Julien; Faivre-Moskalenko, Cendrine; Milani, Pascale; Audit, Benjamin; Vaillant, Cedric; Fontaine, Emeline; Mongelard, Fabien; Lavorel, Guillaume; St-Jean, Philippe; Bouvet, Philippe; Argoul, Françoise; Arneodo, Alain

2010-04-22

Sequence dependency of DNA intrinsic bending properties has been emphasized as a possible key ingredient to in vivo chromatin organization. We use atomic force microscopy (AFM) in air and liquid to image intrinsically straight (synthetic), uncorrelated (hepatitis C RNA virus) and persistent long-range correlated (human) DNA fragments in various ionic conditions such that the molecules freely equilibrate on the mica surface before being captured in a particular conformation. 2D thermodynamic equilibrium is experimentally verified by a detailed statistical analysis of the Gaussian nature of the DNA bend angle fluctuations. We show that the worm-like chain (WLC) model, commonly used to describe the average conformation of long semiflexible polymers, reproduces remarkably well the persistence length estimates for the first two molecules as consistently obtained from (i) mean square end-to-end distance measurement and (ii) mean projection of the end-to-end vector on the initial orientation. Whatever the operating conditions (air or liquid, concentration of metal cations Mg(2+) and/or Ni(2+)), the persistence length found for the uncorrelated viral DNA underestimates the value obtained for the straight DNA. We show that this systematic difference is the signature of the presence of an uncorrelated structural intrinsic disorder in the hepatitis C virus (HCV) DNA fragment that superimposes on local curvatures induced by thermal fluctuations and that only the entropic disorder depends upon experimental conditions. In contrast, the WLC model fails to describe the human DNA conformations. We use a mean-field extension of the WLC model to account for the presence of long-range correlations (LRC) in the intrinsic curvature disorder of human genomic DNA: the stronger the LRC, the smaller the persistence length. The comparison of AFM imaging of human DNA with LRC DNA simulations confirms that the rather small mean square end-to-end distance observed, particularly for G+C-rich human DNA molecules, more likely results from a large-scale intrinsic curvature due to a persistent distribution of DNA curvature sites than from some increased flexibility.

Novel Hydrogels from Telechelic Polymers

NASA Astrophysics Data System (ADS)

Taribagil, Rajiv R.

The last two decades have seen telechelic polymers support an increasing number of applications as stabilizers and flow modifiers in fields as varied as pharmaceutics, paints and oil recovery. Mainly consisting of a long hydrophilic block end-capped with hydrophobic blocks, these polymers form gels at modest concentrations, comprising hydrophobic junctions with hydrophilic blocks bridging these junctions. This thesis examines two different types of telechelic polymer hydrogels: concentrated dispersions of telechelic triblock copolymers and dilute solutions of wormlike micelles cross-linked by hydrophobically end-capped polymers. Aqueous gels of telechelic poly(ethylene oxide) (PEO)-based triblock polymers, with homo and hetero combinations of 1,2-polybutadiene (PB) and poly(perfluoropropylene oxide) (PFPO) as hydrophobic end-blocks, were investigated using a combination of cryogenic scanning electron microscopy and small-angle neutron scattering. The PB-b-PEO-b-PB copolymers formed networks of spherical micelles at all concentrations as expected, albeit with significant spatial heterogeneity that diminished with increasing concentration. The PFPO-b-PEO-b-PFPO copolymers also formed networks by aggregation of the end-blocks, but the PFPO blocks tended to adopt disk-like or even sheet-like structures. This is attributed to the extremely high interfacial tension of PFPO with water and is consistent with the "super-strong" segregation regime behavior. The heterotelechelic PB-b-PEO- b-PFPO terpolymers adopted a quite different structure, namely an intricate bicontinuous open-cell foam, with cells on the order of 500 nm in size and cell walls composed of PFPO disks embedded in PB sheets. These various network structures illustrate the potential of using end-block chemistry to manipulate both the morphology and the physical properties of polymer gels. Dilute aqueous solutions containing 1 wt% cetyltrimethylammonium tosylate, a surfactant well recognized to form wormlike micelles, and low concentrations of hydrophobically end-capped poly(ethylene oxide), were investigated using dynamic mechanical spectroscopy and small-angle neutron scattering. The detailed examination shows that addition of as little as 0.1 wt% of the polymer to the dilute wormlike micelle solution leads to a massive enhancement in its viscoelastic response. This phenomenon raises the possibility of significantly reducing the amount of additive required to achieve a desired rheological profile, with concomitant advantages in both cost and environmental impact.

Facile fabrication of BiVO4 nanofilms with controlled pore size and their photoelectrochemical performances.

PubMed

Feng, Chenchen; Jiao, Zhengbo; Li, Shaopeng; Zhang, Yan; Bi, Yingpu

2015-12-28

We demonstrate a facile method for the rational fabrication of pore-size controlled nanoporous BiVO(4) photoanodes, and confirmed that the optimum pore-size distributions could effectively absorb visible light through light diffraction and confinement functions. Furthermore, in situ X-ray photoelectron spectroscopy (XPS) reveals more efficient photoexcited electron-hole separation than conventional particle films, induced by light confinement and rapid charge transfer in the inter-crossed worm-like structures.

Mixtures of lecithin and bile salt can form highly viscous wormlike micellar solutions in water.

PubMed

Cheng, Chih-Yang; Oh, Hyuntaek; Wang, Ting-Yu; Raghavan, Srinivasa R; Tung, Shih-Huang

2014-09-02

The self-assembly of biological surfactants in water is an important topic for study because of its relevance to physiological processes. Two common types of biosurfactants are lecithin (phosphatidylcholine) and bile salts, which are both present in bile and involved in digestion. Previous studies on lecithin-bile salt mixtures have reported the formation of short, rodlike micelles. Here, we show that lecithin-bile salt micelles can be further induced to grow into long, flexible wormlike structures. The formation of long worms and their resultant entanglement into transient networks is reflected in the rheology: the fluids become viscoelastic and exhibit Maxwellian behavior, and their zero-shear viscosity can be up to a 1000-fold higher than that of water. The presence of worms is further confirmed by data from small-angle neutron and X-ray scattering and from cryo-transmission electron microscopy (cryo-TEM). We find that micellar growth peaks at a specific molar ratio (near equimolar) of bile salt:lecithin, which suggests a strong binding interaction between the two species. In addition, micellar growth also requires a sufficient concentration of background electrolyte such as NaCl or sodium citrate that serves to screen the electrostatic repulsion of the amphiphiles and to "salt out" the amphiphiles. We postulate a mechanism based on changes in the molecular geometry caused by bile salts and electrolytes to explain the micellar growth.

pH-Responsive Wormlike Micelles with Sequential Metastasis Targeting Inhibit Lung Metastasis of Breast Cancer.

PubMed

He, Xinyu; Yu, Haijun; Bao, Xiaoyue; Cao, Haiqiang; Yin, Qi; Zhang, Zhiwen; Li, Yaping

2016-02-18

Cancer metastasis is the main cause for the high mortality in breast cancer patients. Herein, we first report succinobucol-loaded pH-responsive wormlike micelles (PWMs) with sequential targeting capability to inhibit lung metastasis of breast cancer. PWMs can in a first step be delivered specifically to the sites of metastases in the lungs and then enable the intracellular pH-stimulus responsive drug release in cancer cells to improve the anti-metastatic effect. PWMs are identified as nanofibrillar assemblies with a diameter of 19.9 ± 1.9 nm and a length within the 50-200 nm range, and exhibited pH-sensitive drug release behavior in response to acidic intracellular environments. Moreover, PWMs can obviously inhibit the migration and invasion abilities of metastatic 4T1 breast cancer cells, and reduce the expression of the metastasis-associated vascular cell adhesion molecule-1 (VCAM-1) at 400 ng mL(-1) of succinobucol. In particular, PWMs can induce a higher specific accumulation in lung and be specifically delivered to the sites of metastases in lung, thereby leading to an 86.6% inhibition on lung metastasis of breast cancer. Therefore, the use of sequentially targeting PWMs can become an encouraging strategy for specific targeting and effective treatment of cancer metastasis. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Finger-like pattern formation in dilute surfactant pentaethylene glycol monododecyl ether solutions.

PubMed

Kubo, Yoshihide; Yokoyama, Yasuhiro; Tanaka, Shinpei

2013-04-07

We report here peculiar finger-like patterns observed during the phase separation process of dilute micellar pentaethylene glycol monododecyl ether solutions. The patterns were composed of parallel and periodic threads of micelle-rich domains. Prior to this pattern formation, the phase separation always started with the appearance of water-rich domains rimmed by the micelle-rich domains. It was found that these rims played a significant role in the pattern formation. We explain this pattern formation using a simple simulation model with disconnectable springs. The simulation results suggested that the spatially inhomogeneous elasticity or connectivity of a transient gel of worm-like micelles was responsible for the rim formation. The rims thus formed lead rim-induced nucleation, growth, and elongation of the domains owing to their small mobility and the elastic frustration around them. These rim-induced processes eventually produce the observed finger-like patterns.

On the properties of a bundle of flexible actin filaments in an optical trap.

PubMed

Perilli, Alessia; Pierleoni, Carlo; Ciccotti, Giovanni; Ryckaert, Jean-Paul

2016-06-28

We establish the statistical mechanics framework for a bundle of Nf living and uncrosslinked actin filaments in a supercritical solution of free monomers pressing against a mobile wall. The filaments are anchored normally to a fixed planar surface at one of their ends and, because of their limited flexibility, they grow almost parallel to each other. Their growing ends hit a moving obstacle, depicted as a second planar wall, parallel to the previous one and subjected to a harmonic compressive force. The force constant is denoted as the trap strength while the distance between the two walls as the trap length to make contact with the experimental optical trap apparatus. For an ideal solution of reactive filaments and free monomers at fixed free monomer chemical potential μ1, we obtain the general expression for the grand potential from which we derive averages and distributions of relevant physical quantities, namely, the obstacle position, the bundle polymerization force, and the number of filaments in direct contact with the wall. The grafted living filaments are modeled as discrete Wormlike chains, with F-actin persistence length ℓp, subject to discrete contour length variations ±d (the monomer size) to model single monomer (de)polymerization steps. Rigid filaments (ℓp = ∞), either isolated or in bundles, all provide average values of the stalling force in agreement with Hill's predictions Fs (H)=NfkBTln(ρ1/ρ1c)/d, independent of the average trap length. Here ρ1 is the density of free monomers in the solution and ρ1c its critical value at which the filament does not grow nor shrink in the absence of external forces. Flexible filaments (ℓp < ∞) instead, for values of the trap strength suitable to prevent their lateral escape, provide an average bundle force and an average trap length slightly larger than the corresponding rigid cases (few percents). Still the stalling force remains nearly independent on the average trap length, but results from the product of two strongly L-dependent contributions: the fraction of touching filaments ∝〈L〉(O.T.) (2) and the single filament buckling force ∝〈L〉(O.T.) (-2).

Single molecule force measurements of perlecan/HSPG2: A key component of the osteocyte pericellular matrix.

PubMed

Wijeratne, Sithara S; Martinez, Jerahme R; Grindel, Brian J; Frey, Eric W; Li, Jingqiang; Wang, Liyun; Farach-Carson, Mary C; Kiang, Ching-Hwa

2016-03-01

Perlecan/HSPG2, a large, monomeric heparan sulfate proteoglycan (HSPG), is a key component of the lacunar canalicular system (LCS) of cortical bone, where it is part of the mechanosensing pericellular matrix (PCM) surrounding the osteocytic processes and serves as a tethering element that connects the osteocyte cell body to the bone matrix. Within the pericellular space surrounding the osteocyte cell body, perlecan can experience physiological fluid flow drag force and in that capacity function as a sensor to relay external stimuli to the osteocyte cell membrane. We previously showed that a reduction in perlecan secretion alters the PCM fiber composition and interferes with bone's response to a mechanical loading in vivo. To test our hypothesis that perlecan core protein can sustain tensile forces without unfolding under physiological loading conditions, atomic force microscopy (AFM) was used to capture images of perlecan monomers at nanoscale resolution and to perform single molecule force measurement (SMFMs). We found that the core protein of purified full-length human perlecan is of suitable size to span the pericellular space of the LCS, with a measured end-to-end length of 170±20 nm and a diameter of 2-4 nm. Force pulling revealed a strong protein core that can withstand over 100 pN of tension well over the drag forces that are estimated to be exerted on the individual osteocyte tethers. Data fitting with an extensible worm-like chain model showed that the perlecan protein core has a mean elastic constant of 890 pN and a corresponding Young's modulus of 71 MPa. We conclude that perlecan has physical properties that would allow it to act as a strong but elastic tether in the LCS. Copyright © 2015 International Society of Matrix Biology. Published by Elsevier B.V. All rights reserved.

Characterization of the biomechanical properties of T4 pili expressed by Streptococcus pneumoniae--a comparison between helix-like and open coil-like pili.

PubMed

Castelain, Mickaël; Koutris, Efstratios; Andersson, Magnus; Wiklund, Krister; Björnham, Oscar; Schedin, Staffan; Axner, Ove

2009-07-13

Bacterial adhesion organelles, known as fimbria or pili, are expressed by gram-positive as well as gram-negative bacteria families. These appendages play a key role in the first steps of the invasion and infection processes, and they therefore provide bacteria with pathogenic abilities. To improve the knowledge of pili-mediated bacterial adhesion to host cells and how these pili behave under the presence of an external force, we first characterize, using force measuring optical tweezers, open coil-like T4 pili expressed by gram-positive Streptococcus pneumoniae with respect to their biomechanical properties. It is shown that their elongation behavior can be well described by the worm-like chain model and that they possess a large degree of flexibility. Their properties are then compared with those of helix-like pili expressed by gram-negative uropathogenic Escherichia coli (UPEC), which have different pili architecture. The differences suggest that these two types of pili have distinctly dissimilar mechanisms to adhere and sustain external forces. Helix-like pili expressed by UPEC bacteria adhere to host cells by single adhesins located at the distal end of the pili while their helix-like structures act as shock absorbers to dampen the irregularly shear forces induced by urine flow and to increase the cooperativity of the pili ensemble, whereas open coil-like pili expressed by S. pneumoniae adhere to cells by a multitude of adhesins distributed along the pili. It is hypothesized that these two types of pili represent different strategies of adhering to host cells in the presence of external forces. When exposed to significant forces, bacteria expressing helix-like pili remain attached by distributing the external force among a multitude of pili, whereas bacteria expressing open coil-like pili sustain large forces primarily by their multitude of binding adhesins which presumably detach sequentially.

ABC Triblock Copolymer Worms: Synthesis, Characterization, and Evaluation as Pickering Emulsifiers for Millimeter-Sized Droplets

PubMed Central

2016-01-01

Polymerization-induced self-assembly (PISA) is used to prepare linear poly(glycerol monomethacrylate)–poly(2-hydroxypropyl methacrylate)–poly(benzyl methacrylate) [PGMA–PHPMA–PBzMA] triblock copolymer nano-objects in the form of a concentrated aqueous dispersion via a three-step synthesis based on reversible addition–fragmentation chain transfer (RAFT) polymerization. First, GMA is polymerized via RAFT solution polymerization in ethanol, then HPMA is polymerized via RAFT aqueous solution polymerization, and finally BzMA is polymerized via “seeded” RAFT aqueous emulsion polymerization. For certain block compositions, highly anisotropic worm-like particles are obtained, which are characterized by small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM). The design rules for accessing higher order morphologies (i.e., worms or vesicles) are briefly explored. Surprisingly, vesicular morphologies cannot be accessed by targeting longer PBzMA blocks—instead, only spherical nanoparticles are formed. SAXS is used to rationalize these counterintuitive observations, which are best explained by considering subtle changes in the relative enthalpic incompatibilities between the three blocks during the growth of the PBzMA block. Finally, the PGMA–PHPMA–PBzMA worms are evaluated as Pickering emulsifiers for the stabilization of oil-in-water emulsions. Millimeter-sized oil droplets can be obtained using low-shear homogenization (hand-shaking) in the presence of 20 vol % n-dodecane. In contrast, control experiments performed using PGMA–PHPMA diblock copolymer worms indicate that these more delicate nanostructures do not survive even these mild conditions. PMID:27795581

Mechanistic insights for block copolymer morphologies: how do worms form vesicles?

PubMed

Blanazs, Adam; Madsen, Jeppe; Battaglia, Giuseppe; Ryan, Anthony J; Armes, Steven P

2011-10-19

Amphiphilic diblock copolymers composed of two covalently linked, chemically distinct chains can be considered to be biological mimics of cell membrane-forming lipid molecules, but with typically more than an order of magnitude increase in molecular weight. These macromolecular amphiphiles are known to form a wide range of nanostructures (spheres, worms, vesicles, etc.) in solvents that are selective for one of the blocks. However, such self-assembly is usually limited to dilute copolymer solutions (<1%), which is a significant disadvantage for potential commercial applications such as drug delivery and coatings. In principle, this problem can be circumvented by polymerization-induced block copolymer self-assembly. Here we detail the synthesis and subsequent in situ self-assembly of amphiphilic AB diblock copolymers in a one pot concentrated aqueous dispersion polymerization formulation. We show that spherical micelles, wormlike micelles, and vesicles can be predictably and efficiently obtained (within 2 h of polymerization, >99% monomer conversion) at relatively high solids in purely aqueous solution. Furthermore, careful monitoring of the in situ polymerization by transmission electron microscopy reveals various novel intermediate structures (including branched worms, partially coalesced worms, nascent bilayers, "octopi", "jellyfish", and finally pure vesicles) that provide important mechanistic insights regarding the evolution of the particle morphology during the sphere-to-worm and worm-to-vesicle transitions. This environmentally benign approach (which involves no toxic solvents, is conducted at relatively high solids, and requires no additional processing) is readily amenable to industrial scale-up, since it is based on commercially available starting materials.

Phase diagrams of block copolymer melts by dissipative particle dynamics simulations

NASA Astrophysics Data System (ADS)

Gavrilov, Alexey A.; Kudryavtsev, Yaroslav V.; Chertovich, Alexander V.

2013-12-01

Phase diagrams for monodisperse and polydisperse diblock copolymer melts and a random multiblock copolymer melt are constructed using dissipative particle dynamics simulations. A thorough visual analysis and calculation of the static structure factor in several hundreds of points at each of the diagrams prove the ability of mesoscopic molecular dynamics to predict the phase behavior of polymer systems as effectively as the self-consistent field-theory and Monte Carlo simulations do. It is demonstrated that the order-disorder transition (ODT) curve for monodisperse diblocks can be precisely located by a spike in the dependence of the mean square pressure fluctuation on χN, where χ is the Flory-Huggins parameter and N is the chain length. For two other copolymer types, the continuous ODTs are observed. Large polydispersity of both blocks obeying the Flory distribution in length does not shift the ODT curve but considerably narrows the domains of the cylindrical and lamellar phases partially replacing them with the wormlike micelle and perforated lamellar phases, respectively. Instead of the pure 3d-bicontinuous phase in monodisperse diblocks, which could be identified as the gyroid, a coexistence of the 3d phase and cylindrical micelles is detected in polydisperse diblocks. The lamellar domain spacing D in monodisperse diblocks follows the strong-segregation theory prediction, D/N1/2 ˜ (χN)1/6, whereas in polydisperse diblocks it is almost independent of χN at χN < 100. Completely random multiblock copolymers cannot form ordered microstructures other than lamellas at any composition.

Viscoelastic diamine surfactant for stable carbon dioxide/water foams over a wide range in salinity and temperature.

PubMed

Elhag, Amro S; Da, Chang; Chen, Yunshen; Mukherjee, Nayan; Noguera, Jose A; Alzobaidi, Shehab; Reddy, Prathima P; AlSumaiti, Ali M; Hirasaki, George J; Biswal, Sibani L; Nguyen, Quoc P; Johnston, Keith P

2018-07-15

The viscosity and stability of CO 2 /water foams at elevated temperature can be increased significantly with highly viscoelastic aqueous lamellae. The slow thinning of these viscoelastic lamellae leads to greater foam stability upon slowing down Ostwald ripening and coalescence. In the aqueous phase, the viscoelasticity may be increased by increasing the surfactant tail length to form more entangled micelles even at high temperatures and salinity. Systematic measurements of the steady state shear viscosity of aqueous solutions of the diamine surfactant (C 16-18 N(CH 3 )C 3 N(CH 3 ) 2 ) were conducted at varying surfactant concentrations and salinity to determine the parameters for formation of entangled wormlike micelles. The apparent viscosity and stability of CO 2 /water foams were compared for systems with viscoelastic entangled micellar aqueous phases relative to those with much less viscous spherical micelles. We demonstrated for the first time stable CO 2 /water foams at temperatures up to 120 °C and CO 2 volumetric fractions up to 0.98 with a single diamine surfactant, C 16-18 N(CH 3 )C 3 N(CH 3 ) 2 . The foam stability was increased by increasing the packing parameter of the surfactant with a long tail and methyl substitution on the amine to form entangled viscoelastic wormlike micelles in the aqueous phase. The foam was more viscous and stable compared to foams with spherical micelles in the aqueous lamellae as seen with C 12-14 N(EO) 2 and C 16-18 N(EO)C 3 N(EO) 2 . Copyright © 2018. Published by Elsevier Inc.

Conservation education and habitat restoration for the endangered Sagalla caecilian (Boulengerula niedeni) in Sagalla Hill, Kenya.

PubMed

K Malonza, Patrick

2016-05-18

The Sagalla caecilian (Boulengerula niedeni) is an endangered amphibian endemic to Sagalla Hill in the Taita Hills. This burrowing worm-like species prefers soft soil with high moisture and organic matter. The major threats to the Sagalla caecilian are soil erosion caused by steep slopes, bare ground and water siphoning/soil hardening from exotic eucalyptus trees. The purpose of this study was to get a better understanding of the local people's attitude towards this species and how they can contribute to its continued conservation through restoration of its remaining habitat. In this study, it was found that 96% of Sagalla people are aware of the species, its habits and its association with soils high in organic matter. It was also found that 96% of Sagalla people use organic manure from cow dung in their farms. Habitat restoration through planting of indigenous plants was found to be ongoing, especially on compounds of public institutions as well as on private lands. Although drought was found to be a challenge for seedlings development especially on the low elevation sites, destruction by livestock especially during the dry season is also a major threat. In this study, it was recommended that any future habitat restoration initiative should include strong chain-link fencing to protect the seedlings from livestock activity. Recognizing that the preferred habitats for the species are in the valleys, systematic planting of keystone plant species such as fig trees (Ficus) creates the best microhabitats. These are better than general woodlots of indigenous trees.

Phospholipid Nonwoven Electrospun Membranes

NASA Astrophysics Data System (ADS)

McKee, Matthew G.; Layman, John M.; Cashion, Matthew P.; Long, Timothy E.

2006-01-01

Nonwoven fibrous membranes were formed from electrospinning lecithin solutions in a single processing step. As the concentration of lecithin increased, the micellar morphology evolved from spherical to cylindrical, and at higher concentrations the cylindrical micelles overlapped and entangled in a fashion similar to polymers in semi-dilute or concentrated solutions. At concentrations above the onset of entanglements of the wormlike micelles, electrospun fibers were fabricated with diameters on the order of 1 to 5 micrometers. The electrospun phospholipid fibers offer the potential for direct fabrication of biologically based, high-surface-area membranes without the use of multiple synthetic steps, complicated electrospinning designs, or postprocessing surface treatments.

Statistical-Mechanical Studies of the Collective Binding of Proteins to DNA

NASA Astrophysics Data System (ADS)

Zhang, Houyin

My dissertation work focuses on the microscopic statistical-mechanical studies of DNA-protein interactions and mainly comprises of three projects. In living cells, binding of proteins to DNA controls gene expression and packaging of the genome. Single-DNA stretching and twisting experiments provide a powerful tool to detect binding of proteins, via detection of their modification of DNA mechanical properties. However, it is often difficult or impossible to determine the numbers of proteins bound in such experiments, especially when the proteins interact nonspecifically with DNA. In the first project, we developed single-molecule versions of classical thermodynamic Maxwell relations and proposed that these relations could be used to measure DNA-bound protein numbers, changes in DNA double-helix torque with force, and many other quantities which are hard to directly measure. This approach does not need any theoretical assumptions beyond the existence of thermodynamic equilibrium and has been used in single-DNA experiments. Many single-molecule experiments associated with DNA-bending proteins suggest the existence of cooperative interactions between adjacent DNA-bound proteins. In the second project, we studied a statistical-mechanical worm-like chain model including binding cooperativity effects and found that the intrinsic cooperativity of binding sharpens force-extension curves and causes enhancement of fluctuation of extension and protein occupation. This model also allows us to estimate the intrinsic cooperativity in experiments. We also analyzed force-generated cooperativity and found that the related interaction between proteins is always attractive. This suggests that tension in DNA in vivo could alter the distribution of proteins bound along DNA, causing chromosome refolding, or changes in gene expression. In the third project, we investigated the correlations along DNA-protein complexes. We found there are two different correlation lengths corrected to the geometry of DNA bending - the shorter “longitudinal” correlation length ξ∥(f, μ) and the longer “transverse” correlation length ξ⊥( f, μ). In the high-force limit, ξ∥(f, μ) = ξ⊥(f, μ)/2 = A/4bf . Surprisingly, the range of the interaction between DNA-bending proteins is controlled by the second-longest correlation length. The effect arises from the protein-bend contribution to the Hamiltonian having an axial rotational symmetry which eliminates its coupling to the transverse bending fluctuations.

On the properties of a bundle of flexible actin filaments in an optical trap

NASA Astrophysics Data System (ADS)

Perilli, Alessia; Pierleoni, Carlo; Ciccotti, Giovanni; Ryckaert, Jean-Paul

2016-06-01

We establish the statistical mechanics framework for a bundle of Nf living and uncrosslinked actin filaments in a supercritical solution of free monomers pressing against a mobile wall. The filaments are anchored normally to a fixed planar surface at one of their ends and, because of their limited flexibility, they grow almost parallel to each other. Their growing ends hit a moving obstacle, depicted as a second planar wall, parallel to the previous one and subjected to a harmonic compressive force. The force constant is denoted as the trap strength while the distance between the two walls as the trap length to make contact with the experimental optical trap apparatus. For an ideal solution of reactive filaments and free monomers at fixed free monomer chemical potential μ1, we obtain the general expression for the grand potential from which we derive averages and distributions of relevant physical quantities, namely, the obstacle position, the bundle polymerization force, and the number of filaments in direct contact with the wall. The grafted living filaments are modeled as discrete Wormlike chains, with F-actin persistence length ℓp, subject to discrete contour length variations ±d (the monomer size) to model single monomer (de)polymerization steps. Rigid filaments (ℓp = ∞), either isolated or in bundles, all provide average values of the stalling force in agreement with Hill's predictions Fs H = N f k B T ln ( ρ 1 / ρ 1 c) / d , independent of the average trap length. Here ρ1 is the density of free monomers in the solution and ρ1c its critical value at which the filament does not grow nor shrink in the absence of external forces. Flexible filaments (ℓp < ∞) instead, for values of the trap strength suitable to prevent their lateral escape, provide an average bundle force and an average trap length slightly larger than the corresponding rigid cases (few percents). Still the stalling force remains nearly independent on the average trap length, but results from the product of two strongly L-dependent contributions: the fraction of touching filaments ∝ (" separators=" < L >O . T .) 2 and the single filament buckling force ∝ (" separators=" < L >O . T .) - 2 .

A constitutive rheological model for agglomerating blood derived from nonequilibrium thermodynamics

NASA Astrophysics Data System (ADS)

Tsimouri, Ioanna Ch.; Stephanou, Pavlos S.; Mavrantzas, Vlasis G.

2018-03-01

Red blood cells tend to aggregate in the presence of plasma proteins, forming structures known as rouleaux. Here, we derive a constitutive rheological model for human blood which accounts for the formation and dissociation of rouleaux using the generalized bracket formulation of nonequilibrium thermodynamics. Similar to the model derived by Owens and co-workers ["A non-homogeneous constitutive model for human blood. Part 1. Model derivation and steady flow," J. Fluid Mech. 617, 327-354 (2008)] through polymer network theory, each rouleau in our model is represented as a dumbbell; the corresponding structural variable is the conformation tensor of the dumbbell. The kinetics of rouleau formation and dissociation is treated as in the work of Germann et al. ["Nonequilibrium thermodynamic modeling of the structure and rheology of concentrated wormlike micellar solutions," J. Non-Newton. Fluid Mech. 196, 51-57 (2013)] by assuming a set of reversible reactions, each characterized by a forward and a reverse rate constant. The final set of evolution equations for the microstructure of each rouleau and the expression for the stress tensor turn out to be very similar to those of Owens and co-workers. However, by explicitly considering a mechanism for the formation and breakage of rouleaux, our model further provides expressions for the aggregation and disaggregation rates appearing in the final transport equations, which in the kinetic theory-based network model of Owens were absent and had to be specified separately. Despite this, the two models are found to provide similar descriptions of experimental data on the size distribution of rouleaux.

In vivo evaluation of folate decorated cross-linked micelles for the delivery of platinum anticancer drugs.

PubMed

Eliezar, Jeaniffer; Scarano, Wei; Boase, Nathan R B; Thurecht, Kristofer J; Stenzel, Martina H

2015-02-09

The biodistribution of micelles with and without folic acid targeting ligands were studied using a block copolymer consisting of acrylic acid (AA) and polyethylene glycol methyl ether acrylate (PEGMEA) blocks. The polymers were prepared using RAFT polymerization in the presence of a folic acid functionalized RAFT agent. Oxoplatin was conjugated onto the acrylic acid block to form amphiphilic polymers which, when diluted in water, formed stable micelles. In order to probe the in vivo stability, a selection of micelles were cross-linked using 1,8-diamino octane. The sizes of the micelles used in this study range between 75 and 200 nm, with both spherical and worm-like conformation. The effects of cross-linking, folate conjugation and different conformation on the biodistribution were studied in female nude mice (BALB/c) following intravenous injection into the tail vein. Using optical imaging to monitor the fluorophore-labeled polymer, the in vivo biodistribution of the micelles was monitored over a 48 h time-course after which the organs were removed and evaluated ex vivo. These experiments showed that both cross-linking and conjugation with folic acid led to increased fluorescence intensities in the organs, especially in the liver and kidneys, while micelles that are not conjugated with folate and not cross-linked are cleared rapidly from the body. Higher accumulation in the spleen, liver, and kidneys was also observed for micelles with worm-like shapes compared to the spherical micelles. While the various factors of cross-linking, micelle shape, and conjugation with folic acid all contribute separately to prolong the circulation time of the micelle, optimization of these parameters for drug delivery devices could potentially overcome adverse effects such as liver and kidney toxicity.

Developing Structure-Property Relationships in Branched Wormlike Micelles via Advanced Rheological and Neutron Scattering Techniques

NASA Astrophysics Data System (ADS)

Calabrese, Michelle A.

Surfactant wormlike micelles (WLMs) are of particular scientific interest due to their ability to branch, break, and reform under shear, which can lead to shear banding flow instabilities. The tunable self-assembly of WLMs makes them ubiquitous in applications ranging from consumer products to energy recovery fluids. Altering the topology of WLMs by inducing branching provides a microstructural pathway to design and optimize the flow properties for such targeted applications. The goal of this thesis is to understand the role of micellar branching on the resulting equilibrium and non-equilibrium properties, while advancing instrumentation and analysis methods in rheology and neutron scattering. The degree of branching in the mixed cationic/anionic surfactant solutions is controlled by the addition of sodium tosylate. The equilibrium properties are characterized via small angle neutron scattering (SANS), linear viscoelastic rheology, neutron spin echo, and dynamic light scattering. Combining rheology with spatiotemporally-resolved SANS enables unambiguous identification of non-equilibrium rheological and scattering signatures of branching and shear banding. The nonlinear WLM response is characterized via flow-SANS under steady shear, shear startup, and large amplitude oscillatory shear. New methods of time-resolved data analysis are developed, which improve experimental resolution by several-fold. Shear-induced orientation is a complex function of branching level, radial position, and deformation type. The structural mechanisms behind shear band formation are elucidated for steady and dynamic flows, which depend on branching level. Shear banding disappears at high branching levels for all deformation types. These responses are used to validate constitutive modeling predictions of dynamic shear banding for the first time. Finally, quantitative metrics to predict shear banding from rheology or flow-induced orientation are developed. Together, advanced rheological and neutron techniques provide a platform for creating structure-property relationships that predict flow and structural phenomena in WLMs and other soft materials. These methods have enabled characteristic differences in linear versus branched WLMs to be determined. This research is part of a broader effort to characterize branching in polymers and self-assembled systems, and may aid in the formulation of WLMs for specific applications. Finally, this work provides a basis for testing and developing microstructure-based constitutive equations that incorporate micellar breakage and branching.

Accurate and fast creep test for viscoelastic fluids using disk-probe-type and quadrupole-arrangement-type electromagnetically spinning systems

NASA Astrophysics Data System (ADS)

Hirano, Taichi; Sakai, Keiji

2017-07-01

Viscoelasticity is a unique characteristic of soft materials and describes its dynamic response to mechanical stimulations. A creep test is an experimental method for measuring the strain ratio/rate against an applied stress, thereby assessing the viscoelasticity of the materials. We propose two advanced experimental systems suitable for the creep test, adopting our original electromagnetically spinning (EMS) technique. This technique can apply a constant torque by a noncontact mechanism, thereby allowing more sensitive and rapid measurements. The viscosity and elasticity of a semidilute wormlike micellar solution were determined using two setups, and the consistency between the results was assessed.

Controlling self-assembly of diphenylalanine peptides at high pH using heterocyclic capping groups.

PubMed

Martin, Adam D; Wojciechowski, Jonathan P; Robinson, Andrew B; Heu, Celine; Garvey, Christopher J; Ratcliffe, Julian; Waddington, Lynne J; Gardiner, James; Thordarson, Pall

2017-03-08

Using small angle neutron scattering (SANS), it is shown that the existence of pre-assembled structures at high pH for a capped diphenylalanine hydrogel is controlled by the selection of N-terminal heterocyclic capping group, namely indole or carbazole. At high pH, changing from a somewhat hydrophilic indole capping group to a more hydrophobic carbazole capping group results in a shift from a high proportion of monomers to self-assembled fibers or wormlike micelles. The presence of these different self-assembled structures at high pH is confirmed through NMR and circular dichroism spectroscopy, scanning probe microscopy and cryogenic transmission electron microscopy.

A symmetrical method to obtain shear moduli from microrheology.

PubMed

Nishi, Kengo; Kilfoil, Maria L; Schmidt, Christoph F; MacKintosh, F C

2018-05-16

Passive microrheology typically deduces shear elastic loss and storage moduli from displacement time series or mean-squared displacements (MSD) of thermally fluctuating probe particles in equilibrium materials. Common data analysis methods use either Kramers-Kronig (KK) transformation or functional fitting to calculate frequency-dependent loss and storage moduli. We propose a new analysis method for passive microrheology that avoids the limitations of both of these approaches. In this method, we determine both real and imaginary components of the complex, frequency-dependent response function χ(ω) = χ'(ω) + iχ''(ω) as direct integral transforms of the MSD of thermal particle motion. This procedure significantly improves the high-frequency fidelity of χ(ω) relative to the use of KK transformation, which has been shown to lead to artifacts in χ'(ω). We test our method on both model and experimental data. Experiments were performed on solutions of worm-like micelles and dilute collagen solutions. While the present method agrees well with established KK-based methods at low frequencies, we demonstrate significant improvement at high frequencies using our symmetric analysis method, up to almost the fundamental Nyquist limit.

Analysis of supply chain management of shallots in Medan

NASA Astrophysics Data System (ADS)

Alam, M. C.; Supriana, T.

2018-02-01

Supply chain is important for business. One of supply chain that needs to be studied is the shallots supply chain. Medan have high demand while the supply of shallots is limited. This study aims to analyze the flow of shallots supply chain distribution in Medan. The method used was survey by using questionnaires to shallots producers, collecting traders, distributors, traders as well as government involved in shallots supply chain. Descriptive analysis was used to explain the shallots supply chain distribution flow. The results showed that there are two shallots supply chain model in Medan that was local shallots model and imported shallots model. Local shallots model could be distinguished based on three producer area, those were models of Medan Marelan, Samosir, and Simalungun. Medan Marelan and Simalungun models have seven supply chains, while the Samosir Model has eight supply chains. This condition indicates that the local shallots supply chain management in Medan was not efficient because of the length of the distribution channel. Supply chain imported shallots was more efficient because it had a shorter distribution flow with five supply chains.

Nano-assembly of Surfactants with Interfacial Drug-Interactive Motifs as Tailor-Designed Drug Carriers

PubMed Central

Gao, Xiang; Huang, Yixian; Makhov, Alexander M.; Epperly, Michael; Lu, Jianqin; Grab, Sheila; Zhang, Peijun; Rohan, Lisa; Xie, Xiang-qun (Sean); Wipf, Peter; Greenberger, Joel; Li, Song

2012-01-01

PEGylated lipopeptide surfactants carrying drug-interactive motifs specific for a peptide-nitroxide antioxidant, JP4-039, were designed and constructed to facilitate the solubilization of this drug candidate as micelles and emulsion nanoparticles. A simple screening process based on the ability that prevents the formation of crystals of JP4-039 in aqueous solution was used to identify agents that have potential drug-interactive activities. Several protected lysine derivatives possessing this activity were identified, of which α-Fmoc-ε-tBoc lysine is the most potent, followed by α-Cbz- and α-iso-butyloxycarbonyl-ε-tBoc-lysine. Using polymer-supported liquid-phase synthesis approach, a series of synthetic lipopeptide surfactants with PEG head group, varied numbers and geometries of α-Fmoc or α-Cbz-lysyl groups located at interfacial region as the drug-interactive domains, and oleoyl chains as the hydrophobic tails were synthesized. All α-Fmoc-lysyl-containing lipopeptide surfactants were able to solubilize JP4-039 as micelles, with enhanced solubilizing activity for surfactants with increased numbers of α-Fmoc groups. The PEGylated lipopeptide surfactants with α-Fmoc-lysyl groups alone tend to form filamentous or worm-like micelles. The presence of JP4-039 transformed α-Fmoc-containing filamentous micelles into dots and bar-like mixed micelles with substantially reduced sizes. Fluorescence quenching and NMR studies revealed that the drug and surfactant molecules were in a close proximity in the complex. JP4-039-loaded emulsion carrying α-Cbz-containing surfactants demonstrated enhanced stability over drug loaded emulsion without lipopeptide surfactants. JP4-039-emulsion showed significant mitigation effect on mice exposed to a lethal dose of radiation. PEGylated lipopeptides with an interfacially located drug-interactive domain are therefore tailor-designed formulation materials potentially useful for drug development. PMID:23244299

Phase separation in solution of worm-like micelles: a dilute ? spin-vector model

NASA Astrophysics Data System (ADS)

Panizza, Pascal; Cristobal, Galder; Curély, Jacques

1998-12-01

We show how the dilute 0953-8984/10/50/006/img2 spin vector model introduced originally by Wheeler and co-workers for describing the polymerization phenomenon in solutions of liquid sulphur and of living polymers may be conveniently adapted for studying phase separation in systems containing long flexible micelles. We draw an isomorphism between the coupling constant appearing in the exchange Hamiltonian and the surfactant energies in the micellar problem. We solve this problem within the mean-field approximation and compare the main results we have obtained with respect to polymer theory and previous theories of phase separation in micellar solutions. We show that the attractive interaction term 0953-8984/10/50/006/img3 between monomers renormalizes the aggregation energy and subsequently the corresponding size distribution. Under these conditions, we observe that the general aspect of the phase diagram in the 0953-8984/10/50/006/img4 plane (where 0953-8984/10/50/006/img5 is the surfactant concentration) is different from previous results. The spinodal line shows a re-entrant behaviour and, at low concentrations, we point out the possibility of specific nucleation phenomena related to the existence of a metastable transition line between a region composed of spherical micelles and another one corresponding to a dilute solution of long flexible micelles.

Remarks towards the spectrum of the Heisenberg spin chain type models

NASA Astrophysics Data System (ADS)

Burdík, Č.; Fuksa, J.; Isaev, A. P.; Krivonos, S. O.; Navrátil, O.

2015-05-01

The integrable close and open chain models can be formulated in terms of generators of the Hecke algebras. In this review paper, we describe in detail the Bethe ansatz for the XXX and the XXZ integrable close chain models. We find the Bethe vectors for two-component and inhomogeneous models. We also find the Bethe vectors for the fermionic realization of the integrable XXX and XXZ close chain models by means of the algebraic and coordinate Bethe ansatz. Special modification of the XXZ closed spin chain model ("small polaron model") is considered. Finally, we discuss some questions relating to the general open Hecke chain models.

Multi-chain Markov chain Monte Carlo methods for computationally expensive models

NASA Astrophysics Data System (ADS)

Huang, M.; Ray, J.; Ren, H.; Hou, Z.; Bao, J.

2017-12-01

Markov chain Monte Carlo (MCMC) methods are used to infer model parameters from observational data. The parameters are inferred as probability densities, thus capturing estimation error due to sparsity of the data, and the shortcomings of the model. Multiple communicating chains executing the MCMC method have the potential to explore the parameter space better, and conceivably accelerate the convergence to the final distribution. We present results from tests conducted with the multi-chain method to show how the acceleration occurs i.e., for loose convergence tolerances, the multiple chains do not make much of a difference. The ensemble of chains also seems to have the ability to accelerate the convergence of a few chains that might start from suboptimal starting points. Finally, we show the performance of the chains in the estimation of O(10) parameters using computationally expensive forward models such as the Community Land Model, where the sampling burden is distributed over multiple chains.

Graphene saturable absorber mirror for ultra-fast-pulse solid-state laser.

PubMed

Xu, Jin-Long; Li, Xian-Lei; Wu, Yong-Zhong; Hao, Xiao-Peng; He, Jing-Liang; Yang, Ke-Jian

2011-05-15

High-quality graphene sheets with lateral size over 20 μm have been obtained by bath sonicating after subjecting the wormlike graphite marginally to mixed oxidizer. To date, to our knowledge, they are the largest graphene sheets prepared by exfoliation in the liquid phase. A saturable absorber mirror was fabricated based on these sheets. We exploited it to realize mode-locking operation in a diode-pumped Nd:GdVO(4) laser. A pulse duration of 16 ps was produced with an average power of 360 mW and a highest pulse energy of 8.4 nJ for a graphene mode-locked laser. © 2011 Optical Society of America

Controlling self-assembly of diphenylalanine peptides at high pH using heterocyclic capping groups

PubMed Central

Martin, Adam D.; Wojciechowski, Jonathan P.; Robinson, Andrew B.; Heu, Celine; Garvey, Christopher J.; Ratcliffe, Julian; Waddington, Lynne J.; Gardiner, James; Thordarson, Pall

2017-01-01

Using small angle neutron scattering (SANS), it is shown that the existence of pre-assembled structures at high pH for a capped diphenylalanine hydrogel is controlled by the selection of N-terminal heterocyclic capping group, namely indole or carbazole. At high pH, changing from a somewhat hydrophilic indole capping group to a more hydrophobic carbazole capping group results in a shift from a high proportion of monomers to self-assembled fibers or wormlike micelles. The presence of these different self-assembled structures at high pH is confirmed through NMR and circular dichroism spectroscopy, scanning probe microscopy and cryogenic transmission electron microscopy. PMID:28272523

System Dynamics Modeling for Supply Chain Information Sharing

NASA Astrophysics Data System (ADS)

Feng, Yang

In this paper, we try to use the method of system dynamics to model supply chain information sharing. Firstly, we determine the model boundaries, establish system dynamics model of supply chain before information sharing, analyze the model's simulation results under different changed parameters and suggest improvement proposal. Then, we establish system dynamics model of supply chain information sharing and make comparison and analysis on the two model's simulation results, to show the importance of information sharing in supply chain management. We wish that all these simulations would provide scientific supports for enterprise decision-making.

Proactive Supply Chain Performance Management with Predictive Analytics

PubMed Central

Stefanovic, Nenad

2014-01-01

Today's business climate requires supply chains to be proactive rather than reactive, which demands a new approach that incorporates data mining predictive analytics. This paper introduces a predictive supply chain performance management model which combines process modelling, performance measurement, data mining models, and web portal technologies into a unique model. It presents the supply chain modelling approach based on the specialized metamodel which allows modelling of any supply chain configuration and at different level of details. The paper also presents the supply chain semantic business intelligence (BI) model which encapsulates data sources and business rules and includes the data warehouse model with specific supply chain dimensions, measures, and KPIs (key performance indicators). Next, the paper describes two generic approaches for designing the KPI predictive data mining models based on the BI semantic model. KPI predictive models were trained and tested with a real-world data set. Finally, a specialized analytical web portal which offers collaborative performance monitoring and decision making is presented. The results show that these models give very accurate KPI projections and provide valuable insights into newly emerging trends, opportunities, and problems. This should lead to more intelligent, predictive, and responsive supply chains capable of adapting to future business environment. PMID:25386605

Proactive supply chain performance management with predictive analytics.

PubMed

Stefanovic, Nenad

2014-01-01

Today's business climate requires supply chains to be proactive rather than reactive, which demands a new approach that incorporates data mining predictive analytics. This paper introduces a predictive supply chain performance management model which combines process modelling, performance measurement, data mining models, and web portal technologies into a unique model. It presents the supply chain modelling approach based on the specialized metamodel which allows modelling of any supply chain configuration and at different level of details. The paper also presents the supply chain semantic business intelligence (BI) model which encapsulates data sources and business rules and includes the data warehouse model with specific supply chain dimensions, measures, and KPIs (key performance indicators). Next, the paper describes two generic approaches for designing the KPI predictive data mining models based on the BI semantic model. KPI predictive models were trained and tested with a real-world data set. Finally, a specialized analytical web portal which offers collaborative performance monitoring and decision making is presented. The results show that these models give very accurate KPI projections and provide valuable insights into newly emerging trends, opportunities, and problems. This should lead to more intelligent, predictive, and responsive supply chains capable of adapting to future business environment.

Automated side-chain model building and sequence assignment by template matching.

PubMed

Terwilliger, Thomas C

2003-01-01

An algorithm is described for automated building of side chains in an electron-density map once a main-chain model is built and for alignment of the protein sequence to the map. The procedure is based on a comparison of electron density at the expected side-chain positions with electron-density templates. The templates are constructed from average amino-acid side-chain densities in 574 refined protein structures. For each contiguous segment of main chain, a matrix with entries corresponding to an estimate of the probability that each of the 20 amino acids is located at each position of the main-chain model is obtained. The probability that this segment corresponds to each possible alignment with the sequence of the protein is estimated using a Bayesian approach and high-confidence matches are kept. Once side-chain identities are determined, the most probable rotamer for each side chain is built into the model. The automated procedure has been implemented in the RESOLVE software. Combined with automated main-chain model building, the procedure produces a preliminary model suitable for refinement and extension by an experienced crystallographer.

Network evolution model for supply chain with manufactures as the core.

PubMed

Fang, Haiyang; Jiang, Dali; Yang, Tinghong; Fang, Ling; Yang, Jian; Li, Wu; Zhao, Jing

2018-01-01

Building evolution model of supply chain networks could be helpful to understand its development law. However, specific characteristics and attributes of real supply chains are often neglected in existing evolution models. This work proposes a new evolution model of supply chain with manufactures as the core, based on external market demand and internal competition-cooperation. The evolution model assumes the external market environment is relatively stable, considers several factors, including specific topology of supply chain, external market demand, ecological growth and flow conservation. The simulation results suggest that the networks evolved by our model have similar structures as real supply chains. Meanwhile, the influences of external market demand and internal competition-cooperation to network evolution are analyzed. Additionally, 38 benchmark data sets are applied to validate the rationality of our evolution model, in which, nine manufacturing supply chains match the features of the networks constructed by our model.

Network evolution model for supply chain with manufactures as the core

PubMed Central

Jiang, Dali; Fang, Ling; Yang, Jian; Li, Wu; Zhao, Jing

2018-01-01

Building evolution model of supply chain networks could be helpful to understand its development law. However, specific characteristics and attributes of real supply chains are often neglected in existing evolution models. This work proposes a new evolution model of supply chain with manufactures as the core, based on external market demand and internal competition-cooperation. The evolution model assumes the external market environment is relatively stable, considers several factors, including specific topology of supply chain, external market demand, ecological growth and flow conservation. The simulation results suggest that the networks evolved by our model have similar structures as real supply chains. Meanwhile, the influences of external market demand and internal competition-cooperation to network evolution are analyzed. Additionally, 38 benchmark data sets are applied to validate the rationality of our evolution model, in which, nine manufacturing supply chains match the features of the networks constructed by our model. PMID:29370201

Jetting of a shear banding fluid in rectangular ducts

PubMed Central

Salipante, Paul F.; Little, Charles A. E.; Hudson, Steven D.

2017-01-01

Non-Newtonian fluids are susceptible to flow instabilities such as shear banding, in which the fluid may exhibit a markedly discontinuous viscosity at a critical stress. Here we report the characteristics and causes of a jetting flow instability of shear banding wormlike micelle solutions in microfluidic channels with rectangular cross sections over an intermediate volumetric flow regime. Particle-tracking methods are used to measure the three-dimensional flow field in channels of differing aspect ratios, sizes, and wall materials. When jetting occurs, it is self-contained within a portion of the channel where the flow velocity is greater than the surroundings. We observe that the instability forms in channels with aspect ratio greater than 5, and that the location of the high-velocity jet appears to be sensitive to stress localizations. Jetting is not observed in a lower concentration solution without shear banding. Simulations using the Johnson-Segalman viscoelastic model show a qualitatively similar behavior to the experimental observations and indicate that compressive normal stresses in the cross-stream directions support the development of the jetting flow. Our results show that nonuniform flow of shear thinning fluids can develop across the wide dimension in rectangular microfluidic channels, with implications for microfluidic rheometry. PMID:28691108

Nonlinear dynamics of coiling, and mounding in viscoelastic jets

NASA Astrophysics Data System (ADS)

Majmudar, Trushant; Ober, Thomas; McKinley, Gareth

2009-11-01

Free surface continuous jets of non-Newtonian fluids, although relevant for many industrial processes like bottle filling, remain poorly understood in terms of fundamental fluid dynamics. Here we present a systematic study of the effect of viscoelasticity on the dynamics of continuous jets of worm-like micellar surfactant solutions of varying viscosities and elasticities, and model yield-stress fluids. We systematically vary the height of the drop and the flow rate in order to study the effects of varying geometric and kinematic parameters. We observe that for fluids with higher elastic relaxation times, folding is the preferred mode. In contrast, for low elasticity fluids we observe complex nonlinear dynamics consisting of coiling, folding, and irregular meandering as the height of the fall increases. Beyond this regime, the jet dynamics smoothly crosses over to exhibit the ``leaping shampoo" or the Kaye effect. Upon increasing the flow rate to very high values, the ``leaping shampoo" state disappears and is replaced by a pronounced mounding or ``heaping". A subsequent increase in the flow rate results in finger-like protrusions to emerge out of the mound and climb up towards the nozzle. This novel transition is currently under investigation and remains a theoretical challenge.

Mathematical supply-chain modelling: Product analysis of cost and time

NASA Astrophysics Data System (ADS)

Easters, D. J.

2014-03-01

Establishing a mathematical supply-chain model is a proposition that has received attention due to its inherent benefits of evolving global supply-chain efficiencies. This paper discusses the prevailing relationships found within apparel supply-chain environments, and contemplates the complex issues indicated for constituting a mathematical model. Principal results identified within the data suggest, that the multifarious nature of global supply-chain activities require a degree of simplification in order to fully dilate the necessary factors which affect, each sub-section of the chain. Subsequently, the research findings allowed the division of supply-chain components into sub-sections, which amassed a coherent method of product development activity. Concurrently, the supply-chain model was found to allow systematic mathematical formulae analysis, of cost and time, within the multiple contexts of each subsection encountered. The paper indicates the supply-chain model structure, the mathematics, and considers how product analysis of cost and time can improve the comprehension of product lifecycle management.

The zoonotic implications of pentastomiasis in the royal python (python regius).

PubMed

Ayinmode, Ab; Adedokun, Ao; Aina, A; Taiwo, V

2010-09-01

Pentastomes are worm-like endoparasites of the phylum Pentastomida found principally in the respiratory tract of reptiles, birds, and mammals. They cause a zoonotic disease known as pentastomiasis in humans and other mammals. The autopsy of a Nigerian royal python (Python regius) revealed two yellowish-white parasites in the lungs, tissue necrosis and inflammatory lesions. The parasite was confirmed to be Armillifer spp (Pentastomid); this is the first recorded case of pentastomiasis in the royal python (Python regius) in Nigeria. This report may be an alert of the possibility of on-going zoonotic transmission of pentastomiasis from snake to man, especially in the sub-urban/rural areas of Nigeria and other West African countries where people consume snake meat.

Amorphous-silicon module intercell corrosion

NASA Astrophysics Data System (ADS)

Mon, G. R.; Ross, R. G.

1987-06-01

Three non-electrochemical, moisture-induced a-Si module degradation modes have been observed and their mechanisms studied: (1) the formation and growth of pinholes in the thin-film layers; (2) the directional interfusion of pinholes along process scribe lines to form metallization-free regions that tend to open-circuit the module; and (3) worm-like filiform corrosion in the aluminum layer. The dependency on time-of-exposure to moist environments of the amount of material erosion in the module intercell zone has been quantified by two methods—directly by EDS analysis, and indirectly by sheet resistivity measurements on fully aluminized back surface modules. In addition, changes in maximum power output, series resistance, and open circuit voltage have been documented. Consequences for fielded modules are discussed.

Structure formation of lipid membranes: Membrane self-assembly and vesicle opening-up to octopus-like micelles

NASA Astrophysics Data System (ADS)

Noguchi, Hiroshi

2013-02-01

We briefly review our recent studies on self-assembly and vesicle rupture of lipid membranes using coarse-grained molecular simulations. For single component membranes, lipid molecules self-assemble from random gas states to vesicles via disk-shaped clusters. Clusters aggregate into larger clusters, and subsequently the large disks close into vesicles. The size of vesicles are determined by kinetics than by thermodynamics. When a vesicle composed of lipid and detergent types of molecules is ruptured, a disk-shaped micelle called bicelle can be formed. When both surfactants have negligibly low critical micelle concentration, it is found that bicelles connected with worm-like micelles are also formed depending on the surfactant ratio and spontaneous curvature of the membrane monolayer.

Thin-Film Module Reverse-Bias Breakdown Sites Identified by Thermal Imaging: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnston, Steven; Sulas, Dana; Guthrey, Harvey L

Thin-film module sections are stressed under reverse bias to simulate partial shading conditions. Such stresses can cause permanent damage in the form of 'wormlike' defects due to thermal runaway. When large reverse biases with limited current are applied to the cells, dark lock-in thermography (DLIT) can detect where spatially-localized breakdown initiates before thermal runaway leads to permanent damage. Predicted breakdown defect sites have been identified in both CIGS and CdTe modules using DLIT. These defects include small pinholes, craters, or voids in the absorber layer of the film that lead to built-in areas of weakness where high current densities maymore » cause thermal damage in a partial-shading event.« less

Thin-Film Module Reverse-Bias Breakdown Sites Identified by Thermal Imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnston, Steven; Sulas, Dana; Guthrey, Harvey L

Thin-film module sections are stressed under reverse bias to simulate partial shading conditions. Such stresses can cause permanent damage in the form of 'wormlike' defects due to thermal runaway. When large reverse biases with limited current are applied to the cells, dark lock-in thermography (DLIT) can detect where spatially-localized breakdown initiates before thermal runaway leads to permanent damage. Predicted breakdown defect sites have been identified in both CIGS and CdTe modules using DLIT. These defects include small pinholes, craters, or voids in the absorber layer of the film that lead to built-in areas of weakness where high current densities maymore » cause thermal damage in a partial-shading event.« less

Self-assembly of nanocomposite materials

DOEpatents

Brinker, C. Jeffrey; Sellinger, Alan; Lu, Yunfeng

2001-01-01

A method of making a nanocomposite self-assembly is provided where at least one hydrophilic compound, at least one hydrophobic compound, and at least one amphiphilic surfactant are mixed in an aqueous solvent with the solvent subsequently evaporated to form a self-assembled liquid crystalline mesophase material. Upon polymerization of the hydrophilic and hydrophobic compounds, a robust nanocomposite self-assembled material is formed. Importantly, in the reaction mixture, the amphiphilic surfactant has an initial concentration below the critical micelle concentration to allow formation of the liquid-phase micellar mesophase material. A variety of nanocomposite structures can be formed, depending upon the solvent evaporazation process, including layered mesophases, tubular mesophases, and a hierarchical composite coating composed of an isotropic worm-like micellar overlayer bonded to an oriented, nanolaminated underlayer.

Snap-through instability analysis of dielectric elastomers with consideration of chain entanglements

NASA Astrophysics Data System (ADS)

Zhu, Jiakun; Luo, Jun; Xiao, Zhongmin

2018-06-01

It is widely recognized that the extension limit of polymer chains has a significant effect on the snap-through instability of dielectric elastomers (DEs). The snap-through instability performance of DEs has been extensively studied by two limited-stretch models, i.e., the eight-chain model and Gent model. However, the real polymer networks usually have many entanglements due to the impenetrability of the network chains as well as a finite extensibility resulting from the full stretching of the polymer chains. The effects of entanglements on the snap-through instability of DEs cannot be captured by the previous two limited-stretch models. In this paper, the nonaffine model proposed by Davidson and Goulbourne is adopted to characterize the influence of entanglements and extension limit of the polymer chains. It is demonstrated that the nonaffine model is almost identical to the eight-chain model and is close to the Gent model if we ignore the effects of chain entanglements and adopt the affine assumption. The suitability of the nonaffine model to characterize the mechanical behavior of elastomers is validated by fitting the experimental results reported in the open literature. After that, the snap-through stability performance of an ideal DE membrane under equal-biaxial prestretches is studied with the nonaffine model. It is revealed that besides the prestretch and chain extension limit, the chain entanglements can markedly influence the snap-through instability and the path to failure of DEs. These results provide a more comprehensive understanding on the snap-through instability of a DE and may be helpful to guide the design of DE devices.

Long-distance entanglement and quantum teleportation in XX spin chains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Campos Venuti, L.; Giampaolo, S. M.; CNR-INFM Coherentia, Napoli

2007-11-15

Isotropic XX models of one-dimensional spin-1/2 chains are investigated with the aim to elucidate the formal structure and the physical properties that allow these systems to act as channels for long-distance, high-fidelity quantum teleportation. We introduce two types of models: (i) open, dimerized XX chains, and (ii) open XX chains with small end bonds. For both models we obtain the exact expressions for the end-to-end correlations and the scaling of the energy gap with the length of the chain. We determine the end-to-end concurrence and show that model (i) supports true long-distance entanglement at zero temperature, while model (ii) supportsmore » 'quasi-long-distance' entanglement that slowly falls off with the size of the chain. Due to the different scalings of the gaps, respectively exponential for model (i) and algebraic in model (ii), we demonstrate that the latter allows for efficient qubit teleportation with high fidelity in sufficiently long chains even at moderately low temperatures.« less

A 10-A spectroscopic ruler applied to short polyprolines.

PubMed

Sahoo, Harekrushna; Roccatano, Danilo; Hennig, Andreas; Nau, Werner M

2007-08-08

Fluorescence resonance energy transfer (FRET) from the amino acid tryptophan (Trp) as donor and a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine (Dbo) as acceptor in peptides of the general structure Trp-(Pro)n-Dbo-NH2 (n = 1-6) was investigated by steady-state and time-resolved fluorescence, CD, and NMR spectroscopy as well as by molecular dynamics (MD) simulations (GROMOS96 force field). The Trp/Dbo FRET pair is characterized by a very short Förster radius (R0 ca. 9 A), which allowed distance determinations in such short peptides. Water and propylene glycol were investigated as solvents. The peptides were designed to show an early nucleation of the poly(Pro)II (PPII) secondary helix structure for n > or = 2, which was confirmed by their CD spectra. The shortest peptide (n = 1) adopts preferentially the trans conformation about the Trp-Pro bond, as confirmed by NMR spectra. The FRET efficiencies ranged 2-72% and were found to depend sensitively on the peptide length, i.e., the number of intervening proline residues. The analysis of the FRET data at different levels of theory (assuming either a fixed distance or distance distributions according to a wormlike chain or Gaussian model) afforded donor-acceptor distances between ca. 8 A (n = 1) and ca. 16 A (n = 6) in water, which were found to be similar or slightly higher in propylene glycol. The distances afforded by the Trp/Dbo FRET pair were found to be reasonable in comparison to literature data, expectations from the PPII helix structure, and the results from MD simulations. The persistence lengths for the longer peptides were found to lie at 30-70 A in water and 220 +/- 40 A in propylene glycol, suggesting a more rigid PPII helical structure in propylene glycol. A detailed comparison with literature data on FRET in polyprolines demonstrates that the donor-acceptor distances extracted by FRET are correlated with the Förster radii of the employed FRET pairs. This demonstrates the limitations of using FRET as a spectroscopic ruler for short polyprolines, which is presumably due to the breakdown of the point dipole approximation in Förster theory, when the size of the chromophores becomes comparable or larger than the distances under investigation.

Simple model of inhibition of chain-branching combustion processes

NASA Astrophysics Data System (ADS)

Babushok, Valeri I.; Gubernov, Vladimir V.; Minaev, Sergei S.; Miroshnichenko, Taisia P.

2017-11-01

A simple kinetic model has been suggested to describe the inhibition and extinction of flame propagation in reaction systems with chain-branching reactions typical for hydrocarbon systems. The model is based on the generalised model of the combustion process with chain-branching reaction combined with the one-stage reaction describing the thermal mode of flame propagation with the addition of inhibition reaction steps. Inhibitor addition suppresses the radical overshoot in flame and leads to the change of reaction mode from the chain-branching reaction to a thermal mode of flame propagation. With the increase of inhibitor the transition of chain-branching mode of reaction to the reaction with straight-chains (non-branching chain reaction) is observed. The inhibition part of the model includes a block of three reactions to describe the influence of the inhibitor. The heat losses are incorporated into the model via Newton cooling. The flame extinction is the result of the decreased heat release of inhibited reaction processes and the suppression of radical overshoot with the further decrease of the reaction rate due to the temperature decrease and mixture dilution. A comparison of the results of modelling laminar premixed methane/air flames inhibited by potassium bicarbonate (gas phase model, detailed kinetic model) with the results obtained using the suggested simple model is presented. The calculations with the detailed kinetic model demonstrate the following modes of combustion process: (1) flame propagation with chain-branching reaction (with radical overshoot, inhibitor addition decreases the radical overshoot down to the equilibrium level); (2) saturation of chemical influence of inhibitor, and (3) transition to thermal mode of flame propagation (non-branching chain mode of reaction). The suggested simple kinetic model qualitatively reproduces the modes of flame propagation with the addition of the inhibitor observed using detailed kinetic models.

Teaching Supply Chain Management Complexities: A SCOR Model Based Classroom Simulation

ERIC Educational Resources Information Center

Webb, G. Scott; Thomas, Stephanie P.; Liao-Troth, Sara

2014-01-01

The SCOR (Supply Chain Operations Reference) Model Supply Chain Classroom Simulation is an in-class experiential learning activity that helps students develop a holistic understanding of the processes and challenges of supply chain management. The simulation has broader learning objectives than other supply chain related activities such as the…

A BENCHMARKING ANALYSIS FOR FIVE RADIONUCLIDE VADOSE ZONE MODELS (CHAIN, MULTIMED_DP, FECTUZ, HYDRUS, AND CHAIN 2D) IN SOIL SCREENING LEVEL CALCULATIONS

EPA Science Inventory

Five radionuclide vadose zone models with different degrees of complexity (CHAIN, MULTIMED_DP, FECTUZ, HYDRUS, and CHAIN 2D) were selected for use in soil screening level (SSL) calculations. A benchmarking analysis between the models was conducted for a radionuclide (99Tc) rele...

Thermodynamic perturbation theory for fused sphere hard chain fluids using nonadditive interactions

NASA Astrophysics Data System (ADS)

Abu-Sharkh, Basel F.; Sunaidi, Abdallah; Hamad, Esam Z.

2004-03-01

A model is developed for the equation of state of fused chains based on Wertheim thermodynamic perturbation theory and nonadditive size interactions. The model also assumes that the structure (represented by the radial distribution function) of the fused chain fluid is the same as that of the touching hard sphere chain fluid. The model is completely based on spherical additive and nonadditive size interactions. The model has the advantage of offering good agreement with simulation data while at the same time being independent of fitted parameters. The model is most accurate for short chains, small values of Δ (slightly fused spheres) and at intermediate (liquidlike) densities.

Computational modelling of cell chain migration reveals mechanisms that sustain follow-the-leader behaviour

PubMed Central

Wynn, Michelle L.; Kulesa, Paul M.; Schnell, Santiago

2012-01-01

Follow-the-leader chain migration is a striking cell migratory behaviour observed during vertebrate development, adult neurogenesis and cancer metastasis. Although cell–cell contact and extracellular matrix (ECM) cues have been proposed to promote this phenomenon, mechanisms that underlie chain migration persistence remain unclear. Here, we developed a quantitative agent-based modelling framework to test mechanistic hypotheses of chain migration persistence. We defined chain migration and its persistence based on evidence from the highly migratory neural crest model system, where cells within a chain extend and retract filopodia in short-lived cell contacts and move together as a collective. In our agent-based simulations, we began with a set of agents arranged as a chain and systematically probed the influence of model parameters to identify factors critical to the maintenance of the chain migration pattern. We discovered that chain migration persistence requires a high degree of directional bias in both lead and follower cells towards the target. Chain migration persistence was also promoted when lead cells maintained cell contact with followers, but not vice-versa. Finally, providing a path of least resistance in the ECM was not sufficient alone to drive chain persistence. Our results indicate that chain migration persistence depends on the interplay of directional cell movement and biased cell–cell contact. PMID:22219399

How to fold a spin chain: Integrable boundaries of the Heisenberg XXX and Inozemtsev hyperbolic models

NASA Astrophysics Data System (ADS)

De La Rosa Gomez, Alejandro; MacKay, Niall; Regelskis, Vidas

2017-04-01

We present a general method of folding an integrable spin chain, defined on a line, to obtain an integrable open spin chain, defined on a half-line. We illustrate our method through two fundamental models with sl2 Lie algebra symmetry: the Heisenberg XXX and the Inozemtsev hyperbolic spin chains. We obtain new long-range boundary Hamiltonians and demonstrate that they exhibit Yangian symmetries, thus ensuring integrability of the models we obtain. The method presented provides a ;bottom-up; approach for constructing integrable boundaries and can be applied to any spin chain model.

Molecular modeling of calmodulin: a comparison with crystallographic data

NASA Technical Reports Server (NTRS)

McDonald, J. J.; Rein, R.

1989-01-01

Two methods of side-chain placement on a modeled protein have been examined. Two molecular models of calmodulin were constructed that differ in the treatment of side chains prior to optimization of the molecule. A virtual bond analysis program developed by Purisima and Scheraga was used to determine the backbone conformation based on 2.2 angstroms resolution C alpha coordinates for the molecules. In the first model, side chains were initially constructed in an extended conformation. In the second model, a conformational grid search technique was employed. Calcium ions were treated explicitly during energy optimization using CHARMM. The models are compared to a recently published refined crystal structure of calmodulin. The results indicate that the initial choices for side-chains, but also significant effects on the main-chain conformation and supersecondary structure. The conformational differences are discussed. Analysis of these and other methods makes possible the formulation of a methodology for more appropriate side-chain placement in modeled proteins.

Modeling methodology for supply chain synthesis and disruption analysis

NASA Astrophysics Data System (ADS)

Wu, Teresa; Blackhurst, Jennifer

2004-11-01

The concept of an integrated or synthesized supply chain is a strategy for managing today's globalized and customer driven supply chains in order to better meet customer demands. Synthesizing individual entities into an integrated supply chain can be a challenging task due to a variety of factors including conflicting objectives, mismatched incentives and constraints of the individual entities. Furthermore, understanding the effects of disruptions occurring at any point in the system is difficult when working toward synthesizing supply chain operations. Therefore, the goal of this research is to present a modeling methodology to manage the synthesis of a supply chain by linking hierarchical levels of the system and to model and analyze disruptions in the integrated supply chain. The contribution of this research is threefold: (1) supply chain systems can be modeled hierarchically (2) the performance of synthesized supply chain system can be evaluated quantitatively (3) reachability analysis is used to evaluate the system performance and verify whether a specific state is reachable, allowing the user to understand the extent of effects of a disruption.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Amy Cha-Tien; Downes, Paula Sue; Heinen, Russell

Analysis of chemical supply chains is an inherently complex task, given the dependence of these supply chains on multiple infrastructure systems (e.g., the petroleum sector, transportation, etc.). This effort requires data and information at various levels of resolution, ranging from network-level distribution systems to individual chemical reactions. Sandia National Laboratories (Sandia) has integrated its existing simulation and infrastructure analysis capabilities with chemical data models to analyze the chemical supply chains of several nationally critical chemical commodities. This paper describes how Sandia models the ethylene supply chain; that is, the supply chain for the most widely used raw material for plasticsmore » production including a description of the types of data and modeling capabilities that are required to represent the ethylene supply chain. The paper concludes with a description of Sandia's use the model to project how the supply chain would be affected by and adapt to a disruptive scenario hurricane.« less

Research on BIM-based building information value chain reengineering

NASA Astrophysics Data System (ADS)

Hui, Zhao; Weishuang, Xie

2017-04-01

The achievement of value and value-added factor to the building engineering information is accomplished through a chain-flow, that is, building the information value chain. Based on the deconstruction of the information chain on the construction information in the traditional information mode, this paper clarifies the value characteristics and requirements of each stage of the construction project. In order to achieve building information value-added, the paper deconstructs the traditional building information value chain, reengineer the information value chain model on the basis of the theory and techniques of BIM, to build value-added management model and analyse the value of the model.

The formation of Cr2O3 nanoclusters over graphene sheet and carbon nanotubes

NASA Astrophysics Data System (ADS)

Dabaghmanesh, Samira; Neek-Amal, Mehdi; Partoens, Bart; Neyts, Erik C.

2017-11-01

Carbon supported metal oxide nanoparticles hold promise for various future applications in diverse areas including spintronics, catalysis and biomedicine. These applications, however, typically depend on the structure and morphology of the nanoparticles. In this contribution, we employ classical molecular dynamic simulations based on a recently developed force field to study the structural properties of Cr2O3 nanoclusters over graphene and carbon nanotubes. We observe that Cr2O3 nanoclusters tend to aggregate over both freestanding graphene and carbon nanotubes and form larger nanoclusters. These large nanoclusters are characterized by their worm-like shape with a lattice constant similar to that of bulk Cr2O3. We also investigate the structural deformation induced in graphene due to the presence of Cr2O3 nanoclusters.

Single- and multi-pulse formation of surface structures under static femtosecond irradiation

NASA Astrophysics Data System (ADS)

Guillermin, M.; Garrelie, F.; Sanner, N.; Audouard, E.; Soder, H.

2007-07-01

Femtosecond surface structure modifications are investigated under irradiation with laser pulses of 150 fs at 800 nm, on copper and silicon. We report sub-wavelength periodic structures formation (ripples) with a periodicity of 500 nm for both materials. These ripples are perpendicular to the laser polarization and can be obtained with only one pulse. The formation of these ripples corresponds to a fluence threshold of 1 J/cm 2 for copper and 0.15 J/cm 2 for silicon. We find several morphologies when more pulses are applied: larger ripples parallel to the polarization are formed with a periodicity of 1 μm and degenerate into a worm-like morphology with a higher number of pulses. In addition, walls of deep holes also show sub-wavelength and large ripples.

Flexibility evaluation of multiechelon supply chains.

PubMed

Almeida, João Flávio de Freitas; Conceição, Samuel Vieira; Pinto, Luiz Ricardo; de Camargo, Ricardo Saraiva; Júnior, Gilberto de Miranda

2018-01-01

Multiechelon supply chains are complex logistics systems that require flexibility and coordination at a tactical level to cope with environmental uncertainties in an efficient and effective manner. To cope with these challenges, mathematical programming models are developed to evaluate supply chain flexibility. However, under uncertainty, supply chain models become complex and the scope of flexibility analysis is generally reduced. This paper presents a unified approach that can evaluate the flexibility of a four-echelon supply chain via a robust stochastic programming model. The model simultaneously considers the plans of multiple business divisions such as marketing, logistics, manufacturing, and procurement, whose goals are often conflicting. A numerical example with deterministic parameters is presented to introduce the analysis, and then, the model stochastic parameters are considered to evaluate flexibility. The results of the analysis on supply, manufacturing, and distribution flexibility are presented. Tradeoff analysis of demand variability and service levels is also carried out. The proposed approach facilitates the adoption of different management styles, thus improving supply chain resilience. The model can be extended to contexts pertaining to supply chain disruptions; for example, the model can be used to explore operation strategies when subtle events disrupt supply, manufacturing, or distribution.

Flexibility evaluation of multiechelon supply chains

PubMed Central

Conceição, Samuel Vieira; Pinto, Luiz Ricardo; de Camargo, Ricardo Saraiva; Júnior, Gilberto de Miranda

2018-01-01

Multiechelon supply chains are complex logistics systems that require flexibility and coordination at a tactical level to cope with environmental uncertainties in an efficient and effective manner. To cope with these challenges, mathematical programming models are developed to evaluate supply chain flexibility. However, under uncertainty, supply chain models become complex and the scope of flexibility analysis is generally reduced. This paper presents a unified approach that can evaluate the flexibility of a four-echelon supply chain via a robust stochastic programming model. The model simultaneously considers the plans of multiple business divisions such as marketing, logistics, manufacturing, and procurement, whose goals are often conflicting. A numerical example with deterministic parameters is presented to introduce the analysis, and then, the model stochastic parameters are considered to evaluate flexibility. The results of the analysis on supply, manufacturing, and distribution flexibility are presented. Tradeoff analysis of demand variability and service levels is also carried out. The proposed approach facilitates the adoption of different management styles, thus improving supply chain resilience. The model can be extended to contexts pertaining to supply chain disruptions; for example, the model can be used to explore operation strategies when subtle events disrupt supply, manufacturing, or distribution. PMID:29584755

Primitive-path statistics of entangled polymers: mapping multi-chain simulations onto single-chain mean-field models

NASA Astrophysics Data System (ADS)

Steenbakkers, Rudi J. A.; Tzoumanekas, Christos; Li, Ying; Liu, Wing Kam; Kröger, Martin; Schieber, Jay D.

2014-01-01

We present a method to map the full equilibrium distribution of the primitive-path (PP) length, obtained from multi-chain simulations of polymer melts, onto a single-chain mean-field ‘target’ model. Most previous works used the Doi-Edwards tube model as a target. However, the average number of monomers per PP segment, obtained from multi-chain PP networks, has consistently shown a discrepancy of a factor of two with respect to tube-model estimates. Part of the problem is that the tube model neglects fluctuations in the lengths of PP segments, the number of entanglements per chain and the distribution of monomers among PP segments, while all these fluctuations are observed in multi-chain simulations. Here we use a recently proposed slip-link model, which includes fluctuations in all these variables as well as in the spatial positions of the entanglements. This turns out to be essential to obtain qualitative and quantitative agreement with the equilibrium PP-length distribution obtained from multi-chain simulations. By fitting this distribution, we are able to determine two of the three parameters of the model, which govern its equilibrium properties. This mapping is executed for four different linear polymers and for different molecular weights. The two parameters are found to depend on chemistry, but not on molecular weight. The model predicts a constant plateau modulus minus a correction inversely proportional to molecular weight. The value for well-entangled chains, with the parameters determined ab initio, lies in the range of experimental data for the materials investigated.

Steric interactions determine side-chain conformations in protein cores.

PubMed

Caballero, D; Virrueta, A; O'Hern, C S; Regan, L

2016-09-01

We investigate the role of steric interactions in defining side-chain conformations in protein cores. Previously, we explored the strengths and limitations of hard-sphere dipeptide models in defining sterically allowed side-chain conformations and recapitulating key features of the side-chain dihedral angle distributions observed in high-resolution protein structures. Here, we show that modeling residues in the context of a particular protein environment, with both intra- and inter-residue steric interactions, is sufficient to specify which of the allowed side-chain conformations is adopted. This model predicts 97% of the side-chain conformations of Leu, Ile, Val, Phe, Tyr, Trp and Thr core residues to within 20°. Although the hard-sphere dipeptide model predicts the observed side-chain dihedral angle distributions for both Thr and Ser, the model including the protein environment predicts side-chain conformations to within 20° for only 60% of core Ser residues. Thus, this approach can identify the amino acids for which hard-sphere interactions alone are sufficient and those for which additional interactions are necessary to accurately predict side-chain conformations in protein cores. We also show that our approach can predict alternate side-chain conformations of core residues, which are supported by the observed electron density. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Modeling sustainability in renewable energy supply chain systems

NASA Astrophysics Data System (ADS)

Xie, Fei

This dissertation aims at modeling sustainability of renewable fuel supply chain systems against emerging challenges. In particular, the dissertation focuses on the biofuel supply chain system design, and manages to develop advanced modeling framework and corresponding solution methods in tackling challenges in sustaining biofuel supply chain systems. These challenges include: (1) to integrate "environmental thinking" into the long-term biofuel supply chain planning; (2) to adopt multimodal transportation to mitigate seasonality in biofuel supply chain operations; (3) to provide strategies in hedging against uncertainty from conversion technology; and (4) to develop methodologies in long-term sequential planning of the biofuel supply chain under uncertainties. All models are mixed integer programs, which also involves multi-objective programming method and two-stage/multistage stochastic programming methods. In particular for the long-term sequential planning under uncertainties, to reduce the computational challenges due to the exponential expansion of the scenario tree, I also developed efficient ND-Max method which is more efficient than CPLEX and Nested Decomposition method. Through result analysis of four independent studies, it is found that the proposed modeling frameworks can effectively improve the economic performance, enhance environmental benefits and reduce risks due to systems uncertainties for the biofuel supply chain systems.

Chemically Realistic Tetrahedral Lattice Models for Polymer Chains: Application to Polyethylene Oxide.

PubMed

Dietschreit, Johannes C B; Diestler, Dennis J; Knapp, Ernst W

2016-05-10

To speed up the generation of an ensemble of poly(ethylene oxide) (PEO) polymer chains in solution, a tetrahedral lattice model possessing the appropriate bond angles is used. The distance between noncovalently bonded atoms is maintained at realistic values by generating chains with an enhanced degree of self-avoidance by a very efficient Monte Carlo (MC) algorithm. Potential energy parameters characterizing this lattice model are adjusted so as to mimic realistic PEO polymer chains in water simulated by molecular dynamics (MD), which serves as a benchmark. The MD data show that PEO chains have a fractal dimension of about two, in contrast to self-avoiding walk lattice models, which exhibit the fractal dimension of 1.7. The potential energy accounts for a mild hydrophobic effect (HYEF) of PEO and for a proper setting of the distribution between trans and gauche conformers. The potential energy parameters are determined by matching the Flory radius, the radius of gyration, and the fraction of trans torsion angles in the chain. A gratifying result is the excellent agreement of the pair distribution function and the angular correlation for the lattice model with the benchmark distribution. The lattice model allows for the precise computation of the torsional entropy of the chain. The generation of polymer conformations of the adjusted lattice model is at least 2 orders of magnitude more efficient than MD simulations of the PEO chain in explicit water. This method of generating chain conformations on a tetrahedral lattice can also be applied to other types of polymers with appropriate adjustment of the potential energy function. The efficient MC algorithm for generating chain conformations on a tetrahedral lattice is available for download at https://github.com/Roulattice/Roulattice .

Calculation of single chain cellulose elasticity using fully atomistic modeling

Treesearch

Xiawa Wu; Robert J. Moon; Ashlie Martini

2011-01-01

Cellulose nanocrystals, a potential base material for green nanocomposites, are ordered bundles of cellulose chains. The properties of these chains have been studied for many years using atomic-scale modeling. However, model predictions are difficult to interpret because of the significant dependence of predicted properties on model details. The goal of this study is...

A Simulation Model Articulation of the REA Ontology

NASA Astrophysics Data System (ADS)

Laurier, Wim; Poels, Geert

This paper demonstrates how the REA enterprise ontology can be used to construct simulation models for business processes, value chains and collaboration spaces in supply chains. These models support various high-level and operational management simulation applications, e.g. the analysis of enterprise sustainability and day-to-day planning. First, the basic constructs of the REA ontology and the ExSpect modelling language for simulation are introduced. Second, collaboration space, value chain and business process models and their conceptual dependencies are shown, using the ExSpect language. Third, an exhibit demonstrates the use of value chain models in predicting the financial performance of an enterprise.

Modelling a flows in supply chain with analytical models: Case of a chemical industry

NASA Astrophysics Data System (ADS)

Benhida, Khalid; Azougagh, Yassine; Elfezazi, Said

2016-02-01

This study is interested on the modelling of the logistics flows in a supply chain composed on a production sites and a logistics platform. The contribution of this research is to develop an analytical model (integrated linear programming model), based on a case study of a real company operating in the phosphate field, considering a various constraints in this supply chain to resolve the planning problems for a better decision-making. The objectives of this model is to determine and define the optimal quantities of different products to route, to and from the various entities in the supply chain studied.

Analytical model of multi-planetary resonant chains and constraints on migration scenarios

NASA Astrophysics Data System (ADS)

Delisle, J.-B.

2017-09-01

Resonant chains are groups of planets for which each pair is in resonance, with an orbital period ratio locked at a rational value (2/1, 3/2, etc.). Such chains naturally form as a result of convergent migration of the planets in the proto-planetary disk. In this article, I present an analytical model of resonant chains of any number of planets. Using this model, I show that a system captured in a resonant chain can librate around several possible equilibrium configurations. The probability of capture around each equilibrium depends on how the chain formed, and especially on the order in which the planets have been captured in the chain. Therefore, for an observed resonant chain, knowing around which equilibrium the chain is librating allows for constraints to be put on the formation and migration scenario of the system. I apply this reasoning to the four planets orbiting Kepler-223 in a 3:4:6:8 resonant chain. I show that the system is observed around one of the six equilibria predicted by the analytical model. Using N-body integrations, I show that the most favorable scenario to reproduce the observed configuration is to first capture the two intermediate planets, then the outermost, and finally the innermost.

Nonlinear oscillatory rheology and structure of wormlike micellar solutions and colloidal suspensions

NASA Astrophysics Data System (ADS)

Gurnon, Amanda Kate

The complex, nonlinear flow behavior of soft materials transcends industrial applications, smart material design and non-equilibrium thermodynamics. A long-standing, fundamental challenge in soft-matter science is establishing a quantitative connection between the deformation field, local microstructure and macroscopic dynamic flow properties i.e., the rheology. Soft materials are widely used in consumer products and industrial processes including energy recovery, surfactants for personal healthcare (e.g. soap and shampoo), coatings, plastics, drug delivery, medical devices and therapeutics. Oftentimes, these materials are processed by, used during, or exposed to non-equilibrium conditions for which the transient response of the complex fluid is critical. As such, designing new dynamic experiments is imperative to testing these materials and further developing micromechanical models to predict their transient response. Two of the most common classes of these soft materials stand as the focus of the present research; they are: solutions of polymer-like micelles (PLM or also known as wormlike micelles, WLM) and concentrated colloidal suspensions. In addition to their varied applications these two different classes of soft materials are also governed by different physics. In contrast, to the shear thinning behavior of the WLMs at high shear rates, the near hard-sphere colloidal suspensions are known to display increases, sometimes quite substantial, in viscosity (known as shear thickening). The stress response of these complex fluids derive from the shear-induced microstructure, thus measurements of the microstructure under flow are critical for understanding the mechanisms underlying the complex, nonlinear rheology of these complex fluids. A popular micromechanical model is reframed from its original derivation for predicting steady shear rheology of polymers and WLMs to be applicable to weakly nonlinear oscillatory shear flow. The validity, utility and limits of this constitutive model are tested by comparison with experiments on model WLM solutions. Further comparisons to the nonlinear oscillatory shear responses measured from colloidal suspensions establishes this analysis as a promising, quantitative method for understanding the underlying mechanisms responsible for the nonlinear dynamic response of complex fluids. A new experimental technique is developed to measure the microstructure of complex fluids during steady and transient shear flow using small-angle neutron scattering (SANS). The Flow-SANS experimental method is now available to the broader user communities at the NIST Center for Neutron Research, Gaithersburg, MD and the Institut Laue-Langevin, Grenoble, France. Using this new method, a model shear banding WLM solution is interrogated under steady and oscillatory shear. For the first time, the flow-SANS methods identify new metastable states for shear banding WLM solutions, thus establishing the method as capable of probing new states not accessible using traditional steady or linear oscillatory shear methods. The flow-induced three-dimensional microstructure of a colloidal suspension under steady and dynamic oscillatory shear is also measured using these rheo- and flow-SANS methods. A new structure state is identified in the shear thickening regime that proves critical for defining the "hydrocluster" microstructure state of the suspension that is responsible for shear thickening. For both the suspensions and the WLM solutions, stress-SANS rules with the measured microstructures define the individual stress components arising separately from conservative and hydrodynamic forces and these are compared with the macroscopic rheology. Analysis of these results defines the crucial length- and time-scales of the transient microstructure response. The novel dynamic microstructural measurements presented in this dissertation provide new insights into the complexities of shear thickening and shear banding flow phenomena, which are effects observed more broadly across many different types of soft materials. Consequently, the microstructure-rheology property relationships developed for these two classes of complex fluids will aid in the testing and advancement of micromechanical constitutive model development, smart material design, industrial processing and fundamental non-equilibrium thermodynamic research of a broad range of soft materials.

Using SCOR as a Supply Chain Management Framework for Government Agency Contract Requirements

NASA Technical Reports Server (NTRS)

Paxton, Joseph; Tucker, Brian

2010-01-01

This paper will present a model that uses the Supply-Chain Operations Reference (SCOR) model as a foundation for a framework to illustrate the information needed throughout a product lifecycle to support a healthy supply chain management function and the subsequent contract requirements to enable it. It will also show where in the supply chain the information must be extracted. The ongoing case study used to exemplify the model is NASA's (National Aeronautics and Space Administration) Ares I program for human spaceflight. Effective supply chain management and contract requirements are ongoing opportunities for continuous improvement within government agencies, specifically development of systems for human spaceflight operations. Multiple reports from the Government Accountability Office (GAO) reinforce this importance. The SCOR model is a framework for describing a supply chain with process building blocks and business activities. It provides a set of metrics for measuring supply chain performance and best practices for continuously improving. This paper expands the application of the SCOR to also provide the framework for defining information needed from different levels of the supply chain and at different phases of the lifecycle. These needs can be incorporated into contracts to enable more effective supply chain management. Depending on the phase of the lifecycle, effective supply chain management will require involvement from different levels of the organization and different levels of the supply chain.

Diy Geospatial Web Service Chains: Geochaining Make it Easy

NASA Astrophysics Data System (ADS)

Wu, H.; You, L.; Gui, Z.

2011-08-01

It is a great challenge for beginners to create, deploy and utilize a Geospatial Web Service Chain (GWSC). People in Computer Science are usually not familiar with geospatial domain knowledge. Geospatial practitioners may lack the knowledge about web services and service chains. The end users may lack both. However, integrated visual editing interfaces, validation tools, and oneclick deployment wizards may help to lower the learning curve and improve modelling skills so beginners will have a better experience. GeoChaining is a GWSC modelling tool designed and developed based on these ideas. GeoChaining integrates visual editing, validation, deployment, execution etc. into a unified platform. By employing a Virtual Globe, users can intuitively visualize raw data and results produced by GeoChaining. All of these features allow users to easily start using GWSC, regardless of their professional background and computer skills. Further, GeoChaining supports GWSC model reuse, meaning that an entire GWSC model created or even a specific part can be directly reused in a new model. This greatly improves the efficiency of creating a new GWSC, and also contributes to the sharing and interoperability of GWSC.

A symmetrical method to obtain shear moduli from microrheology† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sm02499a

PubMed Central

Nishi, Kengo

2018-01-01

Passive microrheology typically deduces shear elastic loss and storage moduli from displacement time series or mean-squared displacements (MSD) of thermally fluctuating probe particles in equilibrium materials. Common data analysis methods use either Kramers–Kronig (KK) transformation or functional fitting to calculate frequency-dependent loss and storage moduli. We propose a new analysis method for passive microrheology that avoids the limitations of both of these approaches. In this method, we determine both real and imaginary components of the complex, frequency-dependent response function χ(ω) = χ′(ω) + iχ′′(ω) as direct integral transforms of the MSD of thermal particle motion. This procedure significantly improves the high-frequency fidelity of χ(ω) relative to the use of KK transformation, which has been shown to lead to artifacts in χ′(ω). We test our method on both model and experimental data. Experiments were performed on solutions of worm-like micelles and dilute collagen solutions. While the present method agrees well with established KK-based methods at low frequencies, we demonstrate significant improvement at high frequencies using our symmetric analysis method, up to almost the fundamental Nyquist limit. PMID:29611576

Geometrically confined ultrasmall gadolinium oxide nanoparticles boost the T1 contrast ability

NASA Astrophysics Data System (ADS)

Ni, Kaiyuan; Zhao, Zhenghuan; Zhang, Zongjun; Zhou, Zijian; Yang, Li; Wang, Lirong; Ai, Hua; Gao, Jinhao

2016-02-01

High-performance magnetic resonance imaging (MRI) contrast agents and novel contrast enhancement strategies are urgently needed for sensitive and accurate diagnosis. Here we report a strategy to construct a new T1 contrast agent based on the Solomon-Bloembergen-Morgan (SBM) theory. We loaded the ultrasmall gadolinium oxide nanoparticles into worm-like interior channels of mesoporous silica nanospheres (Gd2O3@MSN nanocomposites). This unique structure endows the nanocomposites with geometrical confinement, high molecular tumbling time, and a large coordinated number of water molecules, which results in a significant enhancement of the T1 contrast with longitudinal proton relaxivity (r1) as high as 45.08 mM-1 s-1. Such a high r1 value of Gd2O3@MSN, compared to those of ultrasmall Gd2O3 nanoparticles and gadolinium-based clinical contrast agents, is mainly attributed to the strong geometrical confinement effect. This strategy provides new guidance for developing various high-performance T1 contrast agents for sensitive imaging and disease diagnosis.High-performance magnetic resonance imaging (MRI) contrast agents and novel contrast enhancement strategies are urgently needed for sensitive and accurate diagnosis. Here we report a strategy to construct a new T1 contrast agent based on the Solomon-Bloembergen-Morgan (SBM) theory. We loaded the ultrasmall gadolinium oxide nanoparticles into worm-like interior channels of mesoporous silica nanospheres (Gd2O3@MSN nanocomposites). This unique structure endows the nanocomposites with geometrical confinement, high molecular tumbling time, and a large coordinated number of water molecules, which results in a significant enhancement of the T1 contrast with longitudinal proton relaxivity (r1) as high as 45.08 mM-1 s-1. Such a high r1 value of Gd2O3@MSN, compared to those of ultrasmall Gd2O3 nanoparticles and gadolinium-based clinical contrast agents, is mainly attributed to the strong geometrical confinement effect. This strategy provides new guidance for developing various high-performance T1 contrast agents for sensitive imaging and disease diagnosis. Electronic supplementary information (ESI) available: Supplementary Fig. S1-S6. See DOI: 10.1039/c5nr08402d

Stochastic entangled chain dynamics of dense polymer solutions.

PubMed

Kivotides, Demosthenes; Wilkin, S Louise; Theofanous, Theo G

2010-10-14

We propose an adjustable-parameter-free, entangled chain dynamics model of dense polymer solutions. The model includes the self-consistent dynamics of molecular chains and solvent by describing the former via coarse-grained polymer dynamics that incorporate hydrodynamic interaction effects, and the latter via the forced Stokes equation. Real chain elasticity is modeled via the inclusion of a Pincus regime in the polymer's force-extension curve. Excluded volume effects are taken into account via the combined action of coarse-grained intermolecular potentials and explicit geometric tracking of chain entanglements. We demonstrate that entanglements are responsible for a new (compared to phantom chain dynamics), slow relaxation mode whose characteristic time scale agrees very well with experiment. Similarly good agreement between theory and experiment is also obtained for the equilibrium chain size. We develop methods for the solution of the model in periodic flow domains and apply them to the computation of entangled polymer solutions in equilibrium. We show that the number of entanglements Π agrees well with the number of entanglements expected on the basis of tube theory, satisfactorily reproducing the latter's scaling of Π with the polymer volume fraction φ. Our model predicts diminishing chain size with concentration, thus vindicating Flory's suggestion of excluded volume effects screening in dense solutions. The predicted scaling of chain size with φ is consistent with the heuristic, Flory theory based value.

A chain-retrieval model for voluntary task switching.

PubMed

Vandierendonck, André; Demanet, Jelle; Liefooghe, Baptist; Verbruggen, Frederick

2012-09-01

To account for the findings obtained in voluntary task switching, this article describes and tests the chain-retrieval model. This model postulates that voluntary task selection involves retrieval of task information from long-term memory, which is then used to guide task selection and task execution. The model assumes that the retrieved information consists of acquired sequences (or chains) of tasks, that selection may be biased towards chains containing more task repetitions and that bottom-up triggered repetitions may overrule the intended task. To test this model, four experiments are reported. In Studies 1 and 2, sequences of task choices and the corresponding transition sequences (task repetitions or switches) were analyzed with the help of dependency statistics. The free parameters of the chain-retrieval model were estimated on the observed task sequences and these estimates were used to predict autocorrelations of tasks and transitions. In Studies 3 and 4, sequences of hand choices and their transitions were analyzed similarly. In all studies, the chain-retrieval model yielded better fits and predictions than statistical models of event choice. In applications to voluntary task switching (Studies 1 and 2), all three parameters of the model were needed to account for the data. When no task switching was required (Studies 3 and 4), the chain-retrieval model could account for the data with one or two parameters clamped to a neutral value. Implications for our understanding of voluntary task selection and broader theoretical implications are discussed. Copyright © 2012 Elsevier Inc. All rights reserved.

How Can Students Generalize the Chain Rule? The Roles of Abduction in Mathematical Modeling

ERIC Educational Resources Information Center

Park, Jin Hyeong; Lee, Kyeong-Hwa

2016-01-01

The purpose of this study is to design a modeling task to facilitate students' inquiries into the chain rule in calculus and to analyze the results after implementation of the task. In this study, we take a modeling approach to the teaching and learning of the chain rule by facilitating the generalization of students' models and modeling…

Demand Activated Manufacturing Architecture (DAMA) model for supply chain collaboration

DOE Office of Scientific and Technical Information (OSTI.GOV)

CHAPMAN,LEON D.; PETERSEN,MARJORIE B.

The Demand Activated Manufacturing Architecture (DAMA) project during the last five years of work with the U.S. Integrated Textile Complex (retail, apparel, textile, and fiber sectors) has developed an inter-enterprise architecture and collaborative model for supply chains. This model will enable improved collaborative business across any supply chain. The DAMA Model for Supply Chain Collaboration is a high-level model for collaboration to achieve Demand Activated Manufacturing. The five major elements of the architecture to support collaboration are (1) activity or process, (2) information, (3) application, (4) data, and (5) infrastructure. These five elements are tied to the application of themore » DAMA architecture to three phases of collaboration - prepare, pilot, and scale. There are six collaborative activities that may be employed in this model: (1) Develop Business Planning Agreements, (2) Define Products, (3) Forecast and Plan Capacity Commitments, (4) Schedule Product and Product Delivery, (5) Expedite Production and Delivery Exceptions, and (6) Populate Supply Chain Utility. The Supply Chain Utility is a set of applications implemented to support collaborative product definition, forecast visibility, planning, scheduling, and execution. The DAMA architecture and model will be presented along with the process for implementing this DAMA model.« less

Simulating the Afghanistan-Pakistan opium supply chain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Watkins, Jennifer H; MacKerrow, Edward P; Merritt, Terence M

2010-04-08

This paper outlines an opium supply chain using the Hilmand province of Afghanistan as exemplar. The opium supply chain model follows the transformation of opium poppy seed through cultivation and chemical alteration to brown heroin base. The purpose of modeling and simulating the Afghanistan-Pakistan opium supply chain is to discover and test strategies that will disrupt this criminal enterprise.

A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation.

PubMed

Li, Yongxiu; Gao, Ya; Zhang, Xuqiang; Wang, Xingyu; Mou, Lirong; Duan, Lili; He, Xiao; Mei, Ye; Zhang, John Z H

2013-09-01

Main chain torsions of alanine dipeptide are parameterized into coupled 2-dimensional Fourier expansions based on quantum mechanical (QM) calculations at M06 2X/aug-cc-pvtz//HF/6-31G** level. Solvation effect is considered by employing polarizable continuum model. Utilization of the M06 2X functional leads to precise potential energy surface that is comparable to or even better than MP2 level, but with much less computational demand. Parameterization of the 2D expansions is against the full main chain torsion space instead of just a few low energy conformations. This procedure is similar to that for the development of AMBER03 force field, except unique weighting factor was assigned to all the grid points. To avoid inconsistency between quantum mechanical calculations and molecular modeling, the model peptide is further optimized at molecular mechanics level with main chain dihedral angles fixed before the calculation of the conformational energy on molecular mechanical level at each grid point, during which generalized Born model is employed. Difference in solvation models at quantum mechanics and molecular mechanics levels makes this parameterization procedure less straightforward. All force field parameters other than main chain torsions are taken from existing AMBER force field. With this new main chain torsion terms, we have studied the main chain dihedral distributions of ALA dipeptide and pentapeptide in aqueous solution. The results demonstrate that 2D main chain torsion is effective in delineating the energy variation associated with rotations along main chain dihedrals. This work is an implication for the necessity of more accurate description of main chain torsions in the future development of ab initio force field and it also raises a challenge to the development of quantum mechanical methods, especially the quantum mechanical solvation models.

Phasic Triplet Markov Chains.

PubMed

El Yazid Boudaren, Mohamed; Monfrini, Emmanuel; Pieczynski, Wojciech; Aïssani, Amar

2014-11-01

Hidden Markov chains have been shown to be inadequate for data modeling under some complex conditions. In this work, we address the problem of statistical modeling of phenomena involving two heterogeneous system states. Such phenomena may arise in biology or communications, among other fields. Namely, we consider that a sequence of meaningful words is to be searched within a whole observation that also contains arbitrary one-by-one symbols. Moreover, a word may be interrupted at some site to be carried on later. Applying plain hidden Markov chains to such data, while ignoring their specificity, yields unsatisfactory results. The Phasic triplet Markov chain, proposed in this paper, overcomes this difficulty by means of an auxiliary underlying process in accordance with the triplet Markov chains theory. Related Bayesian restoration techniques and parameters estimation procedures according to the new model are then described. Finally, to assess the performance of the proposed model against the conventional hidden Markov chain model, experiments are conducted on synthetic and real data.

The development of a green supply chain dual-objective facility by considering different levels of uncertainty

NASA Astrophysics Data System (ADS)

Khorasani, Sasan Torabzadeh; Almasifard, Maryam

2017-11-01

This paper presents a dual-objective facility programming model for a green supply chain network. The main objectives of the presented model are minimizing overall expenditure and negative environmental impacts of the supply chain. This study contributes to the existing literature by incorporating uncertainty in customer demand, suppliers, production, and casting capacity. An industrial case study is also analyzed to reveal the feasibility of the proposed model and its application. A fuzzy approach which is known as TH is used to solve the suggested dual-objective model. TH approach is integration of a max-min method (LH) and modified version of Werners' approach (MW). The outcome of this study reveals that the presented model can support green supply chain network in different levels of uncertainty. In presented model, cost and negative environmental impacts derived from the supply chain network will increase of higher levels of uncertainty.

Simulating the dynamic behavior of chain drive systems by advanced CAE programs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ross, J.; Meyer, J.

1996-09-01

Due to the increased requirements for chain drive systems of 4-stroke internal combustion engines CAE-tools are necessary to design the optimum dynamic system. In comparison to models used din the past the advantage of the new model CDD (Chain Drive Dynamics) is the capability of simulating the trajectory of each chain link around the drive system. Each chain link is represented by a mass with two degrees of freedom and is coupled to the next by a spring-damper element. The drive sprocket can be moved with a constant or non-constant speed. As in reality the other sprockets are driven bymore » the running chain and can be excited by torques. Due to these unique model features it is possible to calculate all vibration types of the chain, polygon effects and radial or angular vibrations of the sprockets very accurately. The model includes the detailed simulation of a mechanical or a hydraulic tensioner as well. The method is ready to be coupled to other detailed calculation models (e.g. valve train systems, crankshaft, etc.). The high efficiency of the tool predicting the dynamic and acoustic behavior of a chain drive system will be demonstrated in comparison to measurements.« less

Ising Model on Tangled Chain, Some Thermodynamic Properties

NASA Astrophysics Data System (ADS)

Mejdani, R.

1996-09-01

In this paper we consider an Ising model on tangled chain, where some additional bonds compared to a pure Ising chain are presented. To understand the behavior of this system and the competition between ferromagnetic bonds J along the chain and antiferromagnetic bonds J' across the chain, we have studied in detail analytically and iteratively some of the thermodynamic quantities. Particularly interesting is, in the zero-field and zero-temperature limit, the behavior of the magnetization and the susceptibility closely related to the ground-state configurations and their degeneracies. This degeneracy, presented at the condition J' ≤ -J between J and J', explains, also, the existence of nonzero entropy at zero temperature. This model applied as a lattice gas model defined on a tangled chain could be also useful for the experimental investigations in studying the saturation curves for the enzyme kinetics or the melting curves for DNA-denaturation.

Learning In networks

NASA Technical Reports Server (NTRS)

Buntine, Wray L.

1995-01-01

Intelligent systems require software incorporating probabilistic reasoning, and often times learning. Networks provide a framework and methodology for creating this kind of software. This paper introduces network models based on chain graphs with deterministic nodes. Chain graphs are defined as a hierarchical combination of Bayesian and Markov networks. To model learning, plates on chain graphs are introduced to model independent samples. The paper concludes by discussing various operations that can be performed on chain graphs with plates as a simplification process or to generate learning algorithms.

Hybrid modeling and empirical analysis of automobile supply chain network

NASA Astrophysics Data System (ADS)

Sun, Jun-yan; Tang, Jian-ming; Fu, Wei-ping; Wu, Bing-ying

2017-05-01

Based on the connection mechanism of nodes which automatically select upstream and downstream agents, a simulation model for dynamic evolutionary process of consumer-driven automobile supply chain is established by integrating ABM and discrete modeling in the GIS-based map. Firstly, the rationality is proved by analyzing the consistency of sales and changes in various agent parameters between the simulation model and a real automobile supply chain. Second, through complex network theory, hierarchical structures of the model and relationships of networks at different levels are analyzed to calculate various characteristic parameters such as mean distance, mean clustering coefficients, and degree distributions. By doing so, it verifies that the model is a typical scale-free network and small-world network. Finally, the motion law of this model is analyzed from the perspective of complex self-adaptive systems. The chaotic state of the simulation system is verified, which suggests that this system has typical nonlinear characteristics. This model not only macroscopically illustrates the dynamic evolution of complex networks of automobile supply chain but also microcosmically reflects the business process of each agent. Moreover, the model construction and simulation of the system by means of combining CAS theory and complex networks supplies a novel method for supply chain analysis, as well as theory bases and experience for supply chain analysis of auto companies.

Equilibriumizing all food chain chaos through reproductive efficiency.

PubMed

Deng, Bo

2006-12-01

The intraspecific interference of a top-predator is incorporated into a classical mathematical model for three-trophic food chains. All chaos types known to the classical model are shown to exist for this comprehensive model. It is further demonstrated that if the top-predator reproduces at high efficiency, then all chaotic dynamics will change to a stable coexisting equilibrium, a novel property not found in the classical model. This finding gives a mechanistic explanation to the question of why food chain chaos is rare in the field. It also suggests that high reproductive efficiency of top-predators tends to stabilize food chains.

Model systems for single molecule polymer dynamics

PubMed Central

Latinwo, Folarin

2012-01-01

Double stranded DNA (dsDNA) has long served as a model system for single molecule polymer dynamics. However, dsDNA is a semiflexible polymer, and the structural rigidity of the DNA double helix gives rise to local molecular properties and chain dynamics that differ from flexible chains, including synthetic organic polymers. Recently, we developed single stranded DNA (ssDNA) as a new model system for single molecule studies of flexible polymer chains. In this work, we discuss model polymer systems in the context of “ideal” and “real” chain behavior considering thermal blobs, tension blobs, hydrodynamic drag and force–extension relations. In addition, we present monomer aspect ratio as a key parameter describing chain conformation and dynamics, and we derive dynamical scaling relations in terms of this molecular-level parameter. We show that asymmetric Kuhn segments can suppress monomer–monomer interactions, thereby altering global chain dynamics. Finally, we discuss ssDNA in the context of a new model system for single molecule polymer dynamics. Overall, we anticipate that future single polymer studies of flexible chains will reveal new insight into the dynamic behavior of “real” polymers, which will highlight the importance of molecular individualism and the prevalence of non-linear phenomena. PMID:22956980

Effect of chain stiffness on the competition between crystallization and glass-formation in model unentangled polymers

NASA Astrophysics Data System (ADS)

Nguyen, Hong T.; Smith, Tyler B.; Hoy, Robert S.; Karayiannis, Nikos Ch.

2015-10-01

We map out the solid-state morphologies formed by model soft-pearl-necklace polymers as a function of chain stiffness, spanning the range from fully flexible to rodlike chains. The ratio of Kuhn length to bead diameter (lK/r0) increases monotonically with increasing bending stiffness kb and yields a one-parameter model that relates chain shape to bulk morphology. In the flexible limit, monomers occupy the sites of close-packed crystallites while chains retain random-walk-like order. In the rodlike limit, nematic chain ordering typical of lamellar precursors coexists with close-packing. At intermediate values of bending stiffness, the competition between random-walk-like and nematic chain ordering produces glass-formation; the range of kb over which this occurs increases with the thermal cooling rate | T ˙ | implemented in our molecular dynamics simulations. Finally, values of kb between the glass-forming and rodlike ranges produce complex ordered phases such as close-packed spirals. Our results should provide a useful initial step in a coarse-grained modeling approach to systematically determining the effect of chain stiffness on the crystallization-vs-glass-formation competition in both synthetic and colloidal polymers.

Influence of solvent on micellar morphologies of semifluorinated block copolymers.

PubMed

Lee, Min Young; Kim, Sang Jae; Jeong, Yeon Tae; Kim, Joo Hyun; Gal, Yeong-Soon; Lim, Kwon Taek

2009-12-01

The influence of solvents on micellar architectures of block copolymers composed of poly(1H,1H-dihydroperfluorooctyl methacrylate) and poly(ethylene oxide) was investigated. In this study, binary solvents with desired proportions were chosen, which had remarkable influence on the morphology of the resulting micelles. With simple adjusting the composition of the binary solvent of chloroform and trichlorofluoromethane, interesting shapes of micelle-like aggregates, such as core-shell, cylinder, worm-like and inverted micelles were formed with sizes of 15, 70, 30 and 250 nm, respectively. In the case of methanol/water system, core-shell spheres and vesicles were produced by varying the proportion of the contents. The morphologies were also tuned to honeycomb-like and bowl-shaped micelles as well as large planar lamellae with holes in DMF and water binary solvent.

Fast-slow asymptotics for a Markov chain model of fast sodium current

NASA Astrophysics Data System (ADS)

Starý, Tomáš; Biktashev, Vadim N.

2017-09-01

We explore the feasibility of using fast-slow asymptotics to eliminate the computational stiffness of discrete-state, continuous-time deterministic Markov chain models of ionic channels underlying cardiac excitability. We focus on a Markov chain model of fast sodium current, and investigate its asymptotic behaviour with respect to small parameters identified in different ways.

Polymer models of interphase chromosomes

PubMed Central

Vasquez, Paula A; Bloom, Kerry

2014-01-01

Clear organizational patterns on the genome have emerged from the statistics of population studies of fixed cells. However, how these results translate into the dynamics of individual living cells remains unexplored. We use statistical mechanics models derived from polymer physics to inquire into the effects that chromosome properties and dynamics have in the temporal and spatial behavior of the genome. Overall, changes in the properties of individual chains affect the behavior of all other chains in the domain. We explore two modifications of chain behavior: single chain motion and chain-chain interactions. We show that there is not a direct relation between these effects, as increase in motion, doesn’t necessarily translate into an increase on chain interaction. PMID:25482191

A novel approach for inventory problem in the pharmaceutical supply chain.

PubMed

Candan, Gökçe; Yazgan, Harun Reşit

2016-02-24

In pharmaceutical enterprises, keeping up with global market conditions is possible with properly selected supply chain management policies. Generally; demand-driven classical supply chain model is used in the pharmaceutical industry. In this study, a new mathematical model is developed to solve an inventory problem in the pharmaceutical supply chain. Unlike the studies in literature, the "shelf life and product transition times" constraints are considered, simultaneously, first time in the pharmaceutical production inventory problem. The problem is formulated as a mixed-integer linear programming (MILP) model with a hybrid time representation. The objective is to maximize total net profit. Effectiveness of the proposed model is illustrated considering a classical and a vendor managed inventory (VMI) supply chain on an experimental study. To show the effectiveness of the model, an experimental study is performed; which contains 2 different supply chain policy (Classical and VMI), 24 and 30 months planning horizon, 10 and 15 different cephalosporin products. Finally the mathematical model is compared to another model in literature and the results show that proposed model is superior. This study suggest a novel approach for solving pharmaceutical inventory problem. The developed model is maximizing total net profit while determining optimal production plan under shelf life and product transition constraints in the pharmaceutical industry. And we believe that the proposed model is much more closed to real life unlike the other studies in literature.

A mixed integer linear programming model for operational planning of a biodiesel supply chain network from used cooking oil

NASA Astrophysics Data System (ADS)

Jonrinaldi, Hadiguna, Rika Ampuh; Salastino, Rades

2017-11-01

Environmental consciousness has paid many attention nowadays. It is not only about how to recycle, remanufacture or reuse used end products but it is also how to optimize the operations of the reverse system. A previous research has proposed a design of reverse supply chain of biodiesel network from used cooking oil. However, the research focused on the design of the supply chain strategy not the operations of the supply chain. It only decided how to design the structure of the supply chain in the next few years, and the process of each stage will be conducted in the supply chain system in general. The supply chain system has not considered operational policies to be conducted by the companies in the supply chain. Companies need a policy for each stage of the supply chain operations to be conducted so as to produce the optimal supply chain system, including how to use all the resources that have been designed in order to achieve the objectives of the supply chain system. Therefore, this paper proposes a model to optimize the operational planning of a biodiesel supply chain network from used cooking oil. A mixed integer linear programming is developed to model the operational planning of biodiesel supply chain in order to minimize the total operational cost of the supply chain. Based on the implementation of the model developed, the total operational cost of the biodiesel supply chain incurred by the system is less than the total operational cost of supply chain based on the previous research during seven days of operational planning about amount of 2,743,470.00 or 0.186%. Production costs contributed to 74.6 % of total operational cost and the cost of purchasing the used cooking oil contributed to 24.1 % of total operational cost. So, the system should pay more attention to these two aspects as changes in the value of these aspects will cause significant effects to the change in the total operational cost of the supply chain.

Semiflexible macromolecules in quasi-one-dimensional confinement: Discrete versus continuous bond angles.

PubMed

Huang, Aiqun; Hsu, Hsiao-Ping; Bhattacharya, Aniket; Binder, Kurt

2015-12-28

The conformations of semiflexible polymers in two dimensions confined in a strip of width D are studied by computer simulations, investigating two different models for the mechanism by which chain stiffness is realized. One model (studied by molecular dynamics) is a bead-spring model in the continuum, where stiffness is controlled by a bond angle potential allowing for arbitrary bond angles. The other model (studied by Monte Carlo) is a self-avoiding walk chain on the square lattice, where only discrete bond angles (0° and ±90°) are possible, and the bond angle potential then controls the density of kinks along the chain contour. The first model is a crude description of DNA-like biopolymers, while the second model (roughly) describes synthetic polymers like alkane chains. It is first demonstrated that in the bulk the crossover from rods to self-avoiding walks for both models is very similar, when one studies average chain linear dimensions, transverse fluctuations, etc., despite their differences in local conformations. However, in quasi-one-dimensional confinement two significant differences between both models occur: (i) The persistence length (extracted from the average cosine of the bond angle) gets renormalized for the lattice model when D gets less than the bulk persistence length, while in the continuum model it stays unchanged. (ii) The monomer density near the repulsive walls for semiflexible polymers is compatible with a power law predicted for the Kratky-Porod model in the case of the bead-spring model, while for the lattice case it tends to a nonzero constant across the strip. However, for the density of chain ends, such a constant behavior seems to occur for both models, unlike the power law observed for flexible polymers. In the regime where the bulk persistence length ℓp is comparable to D, hairpin conformations are detected, and the chain linear dimensions are discussed in terms of a crossover from the Daoud/De Gennes "string of blobs"-picture to the flexible rod picture when D decreases and/or the chain stiffness increases. Introducing a suitable further coarse-graining of the chain contours of the continuum model, direct estimates for the deflection length and its distribution could be obtained.

Dynamics of global supply chain and electric power networks: Models, pricing analysis, and computations

NASA Astrophysics Data System (ADS)

Matsypura, Dmytro

In this dissertation, I develop a new theoretical framework for the modeling, pricing analysis, and computation of solutions to electric power supply chains with power generators, suppliers, transmission service providers, and the inclusion of consumer demands. In particular, I advocate the application of finite-dimensional variational inequality theory, projected dynamical systems theory, game theory, network theory, and other tools that have been recently proposed for the modeling and analysis of supply chain networks (cf. Nagurney (2006)) to electric power markets. This dissertation contributes to the extant literature on the modeling, analysis, and solution of supply chain networks, including global supply chains, in general, and electric power supply chains, in particular, in the following ways. It develops a theoretical framework for modeling, pricing analysis, and computation of electric power flows/transactions in electric power systems using the rationale for supply chain analysis. The models developed include both static and dynamic ones. The dissertation also adds a new dimension to the methodology of the theory of projected dynamical systems by proving that, irrespective of the speeds of adjustment, the equilibrium of the system remains the same. Finally, I include alternative fuel suppliers, along with their behavior into the supply chain modeling and analysis framework. This dissertation has strong practical implications. In an era in which technology and globalization, coupled with increasing risk and uncertainty, complicate electricity demand and supply within and between nations, the successful management of electric power systems and pricing become increasingly pressing topics with relevance not only for economic prosperity but also national security. This dissertation addresses such related topics by providing models, pricing tools, and algorithms for decentralized electric power supply chains. This dissertation is based heavily on the following coauthored papers: Nagurney, Cruz, and Matsypura (2003), Nagurney and Matsypura (2004, 2005, 2006), Matsypura and Nagurney (2005), Matsypura, Nagurney, and Liu (2006).

Modeling competitive substitution in a polyelectrolyte complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peng, B.; Muthukumar, M., E-mail: muthu@polysci.umass.edu

2015-12-28

We have simulated the invasion of a polyelectrolyte complex made of a polycation chain and a polyanion chain, by another longer polyanion chain, using the coarse-grained united atom model for the chains and the Langevin dynamics methodology. Our simulations reveal many intricate details of the substitution reaction in terms of conformational changes of the chains and competition between the invading chain and the chain being displaced for the common complementary chain. We show that the invading chain is required to be sufficiently longer than the chain being displaced for effecting the substitution. Yet, having the invading chain to be longermore » than a certain threshold value does not reduce the substitution time much further. While most of the simulations were carried out in salt-free conditions, we show that presence of salt facilitates the substitution reaction and reduces the substitution time. Analysis of our data shows that the dominant driving force for the substitution process involving polyelectrolytes lies in the release of counterions during the substitution.« less

A Case Study Using Modeling and Simulation to Predict Logistics Supply Chain Issues

NASA Technical Reports Server (NTRS)

Tucker, David A.

2007-01-01

Optimization of critical supply chains to deliver thousands of parts, materials, sub-assemblies, and vehicle structures as needed is vital to the success of the Constellation Program. Thorough analysis needs to be performed on the integrated supply chain processes to plan, source, make, deliver, and return critical items efficiently. Process modeling provides simulation technology-based, predictive solutions for supply chain problems which enable decision makers to reduce costs, accelerate cycle time and improve business performance. For example, United Space Alliance, LLC utilized this approach in late 2006 to build simulation models that recreated shuttle orbiter thruster failures and predicted the potential impact of thruster removals on logistics spare assets. The main objective was the early identification of possible problems in providing thruster spares for the remainder of the Shuttle Flight Manifest. After extensive analysis the model results were used to quantify potential problems and led to improvement actions in the supply chain. Similarly the proper modeling and analysis of Constellation parts, materials, operations, and information flows will help ensure the efficiency of the critical logistics supply chains and the overall success of the program.

Future supply chains enabled by continuous processing--opportunities and challenges. May 20-21, 2014 Continuous Manufacturing Symposium.

PubMed

Srai, Jagjit Singh; Badman, Clive; Krumme, Markus; Futran, Mauricio; Johnston, Craig

2015-03-01

This paper examines the opportunities and challenges facing the pharmaceutical industry in moving to a primarily "continuous processing"-based supply chain. The current predominantly "large batch" and centralized manufacturing system designed for the "blockbuster" drug has driven a slow-paced, inventory heavy operating model that is increasingly regarded as inflexible and unsustainable. Indeed, new markets and the rapidly evolving technology landscape will drive more product variety, shorter product life-cycles, and smaller drug volumes, which will exacerbate an already unsustainable economic model. Future supply chains will be required to enhance affordability and availability for patients and healthcare providers alike despite the increased product complexity. In this more challenging supply scenario, we examine the potential for a more pull driven, near real-time demand-based supply chain, utilizing continuous processing where appropriate as a key element of a more "flow-through" operating model. In this discussion paper on future supply chain models underpinned by developments in the continuous manufacture of pharmaceuticals, we have set out; The significant opportunities to moving to a supply chain flow-through operating model, with substantial opportunities in inventory reduction, lead-time to patient, and radically different product assurance/stability regimes. Scenarios for decentralized production models producing a greater variety of products with enhanced volume flexibility. Production, supply, and value chain footprints that are radically different from today's monolithic and centralized batch manufacturing operations. Clinical trial and drug product development cost savings that support more rapid scale-up and market entry models with early involvement of SC designers within New Product Development. The major supply chain and industrial transformational challenges that need to be addressed. The paper recognizes that although current batch operational performance in pharma is far from optimal and not necessarily an appropriate end-state benchmark for batch technology, the adoption of continuous supply chain operating models underpinned by continuous production processing, as full or hybrid solutions in selected product supply chains, can support industry transformations to deliver right-first-time quality at substantially lower inventory profiles. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

Comparison of Video and Live Modeling in Teaching Response Chains to Children with Autism

ERIC Educational Resources Information Center

Ergenekon, Yasemin; Tekin-Iftar, Elif; Kapan, Alper; Akmanoglu, Nurgul

2014-01-01

Research has shown that video and live modeling are both effective in teaching new skills to children with autism. An adapted alternating treatments design was used to compare the effectiveness and efficiency of video and live modeling in teaching response chains to three children with autism. Each child was taught two chained skills; one skill…

Wide-angle x-ray scattering and solid-state nuclear magnetic resonance data combined to test models for cellulose microfibrils in mung bean cell walls.

PubMed

Newman, Roger H; Hill, Stefan J; Harris, Philip J

2013-12-01

A synchrotron wide-angle x-ray scattering study of mung bean (Vigna radiata) primary cell walls was combined with published solid-state nuclear magnetic resonance data to test models for packing of (1→4)-β-glucan chains in cellulose microfibrils. Computer-simulated peak shapes, calculated for 36-chain microfibrils with perfect order or uncorrelated disorder, were sharper than those in the experimental diffractogram. Introducing correlated disorder into the models broaden the simulated peaks but only when the disorder was increased to unrealistic magnitudes. Computer-simulated diffractograms, calculated for 24- and 18-chain models, showed good fits to experimental data. Particularly good fits to both x-ray and nuclear magnetic resonance data were obtained for collections of 18-chain models with mixed cross-sectional shapes and occasional twinning. Synthesis of 18-chain microfibrils is consistent with a model for cellulose-synthesizing complexes in which three cellulose synthase polypeptides form a particle and six particles form a rosette.

Managing risks in the fisheries supply chain using House of Risk Framework (HOR) and Interpretive Structural Modeling (ISM)

NASA Astrophysics Data System (ADS)

Nguyen, T. L. T.; Tran, T. T.; Huynh, T. P.; Ho, T. K. D.; Le, A. T.; Do, T. K. H.

2018-04-01

One of the sectors which contributes importantly to the development of Vietnam economy is fishery industry. However, during recent year, it has been witnessed many difficulties on managing the performance of the fishery supply chain operations as a whole. In this paper, a framework for supply chain risk management (SCRM) is proposed. Initially, all the activities are mapped by using Supply Chain Operations Reference (SCOR) model. Next, the risk ranking is analyzed in House of Risk. Furthermore, interpretive structural modeling (ISM) is used to identify inter-relationships among supply chain risks and to visualize the risks according to their levels. For illustration, the model has been tested in several case studies with fishery companies in Can Tho, Mekong Delta. This study identifies 22 risk events and 20 risk agents through the supply chain. Also, the risk priority could be used for further House of Risk with proactive actions in future studies.

A review of agent-based modeling approach in the supply chain collaboration context

NASA Astrophysics Data System (ADS)

Arvitrida, N. I.

2018-04-01

Collaboration is considered as the key aspect of supply chain management (SCM) success. This issue has been addressed by many studies in recent years, but there are still few research employs agent-based modeling (ABM) approach to study business partnerships in SCM. This paper reviews the use of ABM in modeling collaboration in supply chains and inform the scope of ABM application in the existing literature. The review reveals that ABM can be an effective tool to address various aspects in supply chain relationships, but its applications in SCM studies are still limited. Moreover, where ABM is applied in the SCM context, most of the studies focus on software architecture rather than analyzing the supply chain issues. This paper also provides insights to SCM researchers about the opportunity uses of ABM in studying complexity in supply chain collaboration.

Multi-host model-based identification of Armillifer agkistrodontis (Pentastomida), a new zoonotic parasite from China.

PubMed

Chen, Shao-Hong; Liu, Qin; Zhang, Yong-Nian; Chen, Jia-Xu; Li, Hao; Chen, Ying; Steinmann, Peter; Zhou, Xiao-Nong

2010-04-06

Pentastomiasis is a rare parasitic infection of humans. Pentastomids are dioecious obligate parasites requiring multiple hosts to complete their lifecycle. Despite their worm-like appearance, they are commonly placed into a separate sub-class of the subphylum Crustacea, phylum Arthropoda. However, their systematic position is not uncontested and historically, they have been considered as a separate phylum. An appraisal of Armillifer agkistrodontis was performed in terms of morphology and genetic identification after its lifecycle had been established in a multi-host model, i.e., mice and rats as intermediate hosts, and snakes (Agkistrodon acutus and Python molurus) as definitive hosts. Different stages of the parasite, including eggs, larvae and adults, were isolated and examined morphologically using light and electron microscopes. Phylogenetic and cluster analysis were also undertaken, focusing on the 18S rRNA and the Cox1 gene. The time for lifecycle completion was about 14 months, including 4 months for the development of eggs to infectious larvae in the intermediate host and 10 months for infectious larvae to mature in the final host. The main morphological difference between A. armillatus and Linguatula serrata is the number of abdominal annuli. Based on the 18S rRNA sequence, the shortest hereditary distance was found between A. agkistrodontis and Raillietiella spp. The highest degree of homology in the Cox 1 nucleic acid sequences and predicted amino acid sequences was found between A. agkistrodontis and A. armillatus. This is the first time that a multi-host model of the entire lifecycle of A. agkistrodontis has been established. Morphologic and genetic analyses supported the notion that pentastomids should be placed into the phylum Arthropoda.

Stability of ecological industry chain: an entropy model approach.

PubMed

Wang, Qingsong; Qiu, Shishou; Yuan, Xueliang; Zuo, Jian; Cao, Dayong; Hong, Jinglan; Zhang, Jian; Dong, Yong; Zheng, Ying

2016-07-01

A novel methodology is proposed in this study to examine the stability of ecological industry chain network based on entropy theory. This methodology is developed according to the associated dissipative structure characteristics, i.e., complexity, openness, and nonlinear. As defined in the methodology, network organization is the object while the main focus is the identification of core enterprises and core industry chains. It is proposed that the chain network should be established around the core enterprise while supplementation to the core industry chain helps to improve system stability, which is verified quantitatively. Relational entropy model can be used to identify core enterprise and core eco-industry chain. It could determine the core of the network organization and core eco-industry chain through the link form and direction of node enterprises. Similarly, the conductive mechanism of different node enterprises can be examined quantitatively despite the absence of key data. Structural entropy model can be employed to solve the problem of order degree for network organization. Results showed that the stability of the entire system could be enhanced by the supplemented chain around the core enterprise in eco-industry chain network organization. As a result, the sustainability of the entire system could be further improved.

An integrated supply chain model for new products with imprecise production and supply under scenario dependent fuzzy random demand

NASA Astrophysics Data System (ADS)

Nagar, Lokesh; Dutta, Pankaj; Jain, Karuna

2014-05-01

In the present day business scenario, instant changes in market demand, different source of materials and manufacturing technologies force many companies to change their supply chain planning in order to tackle the real-world uncertainty. The purpose of this paper is to develop a multi-objective two-stage stochastic programming supply chain model that incorporates imprecise production rate and supplier capacity under scenario dependent fuzzy random demand associated with new product supply chains. The objectives are to maximise the supply chain profit, achieve desired service level and minimise financial risk. The proposed model allows simultaneous determination of optimum supply chain design, procurement and production quantities across the different plants, and trade-offs between inventory and transportation modes for both inbound and outbound logistics. Analogous to chance constraints, we have used the possibility measure to quantify the demand uncertainties and the model is solved using fuzzy linear programming approach. An illustration is presented to demonstrate the effectiveness of the proposed model. Sensitivity analysis is performed for maximisation of the supply chain profit with respect to different confidence level of service, risk and possibility measure. It is found that when one considers the service level and risk as robustness measure the variability in profit reduces.

Monte Carlo simulations of lattice models for single polymer systems

NASA Astrophysics Data System (ADS)

Hsu, Hsiao-Ping

2014-10-01

Single linear polymer chains in dilute solutions under good solvent conditions are studied by Monte Carlo simulations with the pruned-enriched Rosenbluth method up to the chain length N ˜ O(10^4). Based on the standard simple cubic lattice model (SCLM) with fixed bond length and the bond fluctuation model (BFM) with bond lengths in a range between 2 and sqrt{10}, we investigate the conformations of polymer chains described by self-avoiding walks on the simple cubic lattice, and by random walks and non-reversible random walks in the absence of excluded volume interactions. In addition to flexible chains, we also extend our study to semiflexible chains for different stiffness controlled by a bending potential. The persistence lengths of chains extracted from the orientational correlations are estimated for all cases. We show that chains based on the BFM are more flexible than those based on the SCLM for a fixed bending energy. The microscopic differences between these two lattice models are discussed and the theoretical predictions of scaling laws given in the literature are checked and verified. Our simulations clarify that a different mapping ratio between the coarse-grained models and the atomistically realistic description of polymers is required in a coarse-graining approach due to the different crossovers to the asymptotic behavior.

[Healthcare value chain: a model for the Brazilian healthcare system].

PubMed

Pedroso, Marcelo Caldeira; Malik, Ana Maria

2012-10-01

This article presents a model of the healthcare value chain which consists of a schematic representation of the Brazilian healthcare system. The proposed model is adapted for the Brazilian reality and has the scope and flexibility for use in academic activities and analysis of the healthcare sector in Brazil. It places emphasis on three components: the main activities of the value chain, grouped in vertical and horizontal links; the mission of each link and the main value chain flows. The proposed model consists of six vertical and three horizontal links, amounting to nine. These are: knowledge development; supply of products and technologies; healthcare services; financial intermediation; healthcare financing; healthcare consumption; regulation; distribution of healthcare products; and complementary and support services. Four flows can be used to analyze the value chain: knowledge and innovation; products and services; financial; and information.

Thermal conductivity of the Lennard-Jones chain fluid model.

PubMed

Galliero, Guillaume; Boned, Christian

2009-12-01

Nonequilibrium molecular dynamics simulations have been performed to estimate, analyze, and correlate the thermal conductivity of a fluid composed of short Lennard-Jones chains (up to 16 segments) over a large range of thermodynamic conditions. It is shown that the dilute gas contribution to the thermal conductivity decreases when the chain length increases for a given temperature. In dense states, simulation results indicate that the residual thermal conductivity of the monomer increases strongly with density, but is weakly dependent on the temperature. Compared to the monomer value, it has been noted that the residual thermal conductivity of the chain was slightly decreasing with its length. Using these results, an empirical relation, including a contribution due to the critical enhancement, is proposed to provide an accurate estimation of the thermal conductivity of the Lennard-Jones chain fluid model (up to 16 segments) over the domain 0.8

Optimizing bi-objective, multi-echelon supply chain model using particle swarm intelligence algorithm

NASA Astrophysics Data System (ADS)

Sathish Kumar, V. R.; Anbuudayasankar, S. P.; Rameshkumar, K.

2018-02-01

In the current globalized scenario, business organizations are more dependent on cost effective supply chain to enhance profitability and better handle competition. Demand uncertainty is an important factor in success or failure of a supply chain. An efficient supply chain limits the stock held at all echelons to the extent of avoiding a stock-out situation. In this paper, a three echelon supply chain model consisting of supplier, manufacturing plant and market is developed and the same is optimized using particle swarm intelligence algorithm.

Parallel Markov chain Monte Carlo - bridging the gap to high-performance Bayesian computation in animal breeding and genetics.

PubMed

Wu, Xiao-Lin; Sun, Chuanyu; Beissinger, Timothy M; Rosa, Guilherme Jm; Weigel, Kent A; Gatti, Natalia de Leon; Gianola, Daniel

2012-09-25

Most Bayesian models for the analysis of complex traits are not analytically tractable and inferences are based on computationally intensive techniques. This is true of Bayesian models for genome-enabled selection, which uses whole-genome molecular data to predict the genetic merit of candidate animals for breeding purposes. In this regard, parallel computing can overcome the bottlenecks that can arise from series computing. Hence, a major goal of the present study is to bridge the gap to high-performance Bayesian computation in the context of animal breeding and genetics. Parallel Monte Carlo Markov chain algorithms and strategies are described in the context of animal breeding and genetics. Parallel Monte Carlo algorithms are introduced as a starting point including their applications to computing single-parameter and certain multiple-parameter models. Then, two basic approaches for parallel Markov chain Monte Carlo are described: one aims at parallelization within a single chain; the other is based on running multiple chains, yet some variants are discussed as well. Features and strategies of the parallel Markov chain Monte Carlo are illustrated using real data, including a large beef cattle dataset with 50K SNP genotypes. Parallel Markov chain Monte Carlo algorithms are useful for computing complex Bayesian models, which does not only lead to a dramatic speedup in computing but can also be used to optimize model parameters in complex Bayesian models. Hence, we anticipate that use of parallel Markov chain Monte Carlo will have a profound impact on revolutionizing the computational tools for genomic selection programs.

Parallel Markov chain Monte Carlo - bridging the gap to high-performance Bayesian computation in animal breeding and genetics

PubMed Central

2012-01-01

Background Most Bayesian models for the analysis of complex traits are not analytically tractable and inferences are based on computationally intensive techniques. This is true of Bayesian models for genome-enabled selection, which uses whole-genome molecular data to predict the genetic merit of candidate animals for breeding purposes. In this regard, parallel computing can overcome the bottlenecks that can arise from series computing. Hence, a major goal of the present study is to bridge the gap to high-performance Bayesian computation in the context of animal breeding and genetics. Results Parallel Monte Carlo Markov chain algorithms and strategies are described in the context of animal breeding and genetics. Parallel Monte Carlo algorithms are introduced as a starting point including their applications to computing single-parameter and certain multiple-parameter models. Then, two basic approaches for parallel Markov chain Monte Carlo are described: one aims at parallelization within a single chain; the other is based on running multiple chains, yet some variants are discussed as well. Features and strategies of the parallel Markov chain Monte Carlo are illustrated using real data, including a large beef cattle dataset with 50K SNP genotypes. Conclusions Parallel Markov chain Monte Carlo algorithms are useful for computing complex Bayesian models, which does not only lead to a dramatic speedup in computing but can also be used to optimize model parameters in complex Bayesian models. Hence, we anticipate that use of parallel Markov chain Monte Carlo will have a profound impact on revolutionizing the computational tools for genomic selection programs. PMID:23009363

Statistical Analysis of Notational AFL Data Using Continuous Time Markov Chains

PubMed Central

Meyer, Denny; Forbes, Don; Clarke, Stephen R.

2006-01-01

Animal biologists commonly use continuous time Markov chain models to describe patterns of animal behaviour. In this paper we consider the use of these models for describing AFL football. In particular we test the assumptions for continuous time Markov chain models (CTMCs), with time, distance and speed values associated with each transition. Using a simple event categorisation it is found that a semi-Markov chain model is appropriate for this data. This validates the use of Markov Chains for future studies in which the outcomes of AFL matches are simulated. Key Points A comparison of four AFL matches suggests similarity in terms of transition probabilities for events and the mean times, distances and speeds associated with each transition. The Markov assumption appears to be valid. However, the speed, time and distance distributions associated with each transition are not exponential suggesting that semi-Markov model can be used to model and simulate play. Team identified events and directions associated with transitions are required to develop the model into a tool for the prediction of match outcomes. PMID:24357946

Statistical Analysis of Notational AFL Data Using Continuous Time Markov Chains.

PubMed

Meyer, Denny; Forbes, Don; Clarke, Stephen R

2006-01-01

Animal biologists commonly use continuous time Markov chain models to describe patterns of animal behaviour. In this paper we consider the use of these models for describing AFL football. In particular we test the assumptions for continuous time Markov chain models (CTMCs), with time, distance and speed values associated with each transition. Using a simple event categorisation it is found that a semi-Markov chain model is appropriate for this data. This validates the use of Markov Chains for future studies in which the outcomes of AFL matches are simulated. Key PointsA comparison of four AFL matches suggests similarity in terms of transition probabilities for events and the mean times, distances and speeds associated with each transition.The Markov assumption appears to be valid.However, the speed, time and distance distributions associated with each transition are not exponential suggesting that semi-Markov model can be used to model and simulate play.Team identified events and directions associated with transitions are required to develop the model into a tool for the prediction of match outcomes.

Ground-state energies of the nonlinear sigma model and the Heisenberg spin chains

NASA Technical Reports Server (NTRS)

Zhang, Shoucheng; Schulz, H. J.; Ziman, Timothy

1989-01-01

A theorem on the O(3) nonlinear sigma model with the topological theta term is proved, which states that the ground-state energy at theta = pi is always higher than the ground-state energy at theta = 0, for the same value of the coupling constant g. Provided that the nonlinear sigma model gives the correct description for the Heisenberg spin chains in the large-s limit, this theorem makes a definite prediction relating the ground-state energies of the half-integer and the integer spin chains. The ground-state energies obtained from the exact Bethe ansatz solution for the spin-1/2 chain and the numerical diagonalization on the spin-1, spin-3/2, and spin-2 chains support this prediction.

Profit Analysis Model of Smart Item Implementation in Integrated Supply Chain Process

NASA Astrophysics Data System (ADS)

Tritularsih, Yustina; Rinanto, Andhy; Prasetyo, Hoedi; Nur Rosyidi, Cucuk

2018-03-01

Nowadays all links of the entire supply chain need to integrate their different infrastructures and they have better control of them to drive better profits. This integration should offer the ability for companies in order to have an overall and transparent insight to its supply chain activities. An intelligent supply chain which is mainly supported by Smart Items technology can satisfy the need of those integration. By means of Smart Items, a company can benefit some advantages. Those are cost reduction and value creation. However, currently there is no comprehensive Smart Item infrastructure exists yet so it is difficult to calculate the true benefit information. This paper attempts to recommend a model for estimating the benefits of implementing Smart Items in a company which has an integrated supply chain process. The integrated supply chain means that three echelons (supplier, shipper and retailer) of supply chain are belonged to a company. The proposed model was used to determine the shrinkage value and RFID tag price which can give the maximum benefit of Smart Items implementation. A numerical example is also provided to give a better comprehension on model calculation.

Flory-type theories of polymer chains under different external stimuli

NASA Astrophysics Data System (ADS)

Budkov, Yu A.; Kiselev, M. G.

2018-01-01

In this Review, we present a critical analysis of various applications of the Flory-type theories to a theoretical description of the conformational behavior of single polymer chains in dilute polymer solutions under a few external stimuli. Different theoretical models of flexible polymer chains in the supercritical fluid are discussed and analysed. Different points of view on the conformational behavior of the polymer chain near the liquid-gas transition critical point of the solvent are presented. A theoretical description of the co-solvent-induced coil-globule transitions within the implicit-solvent-explicit-co-solvent models is discussed. Several explicit-solvent-explicit-co-solvent theoretical models of the coil-to-globule-to-coil transition of the polymer chain in a mixture of good solvents (co-nonsolvency) are analysed and compared with each other. Finally, a new theoretical model of the conformational behavior of the dielectric polymer chain under the external constant electric field in the dilute polymer solution with an explicit account for the many-body dipole correlations is discussed. The polymer chain collapse induced by many-body dipole correlations of monomers in the context of statistical thermodynamics of dielectric polymers is analysed.

Integrating biomass quality variability in stochastic supply chain modeling and optimization for large-scale biofuel production

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castillo-Villar, Krystel K.; Eksioglu, Sandra; Taherkhorsandi, Milad

The production of biofuels using second-generation feedstocks has been recognized as an important alternative source of sustainable energy and its demand is expected to increase due to regulations such as the Renewable Fuel Standard. However, the pathway to biofuel industry maturity faces unique, unaddressed challenges. Here, to address this challenges, this article presents an optimization model which quantifies and controls the impact of biomass quality variability on supply chain related decisions and technology selection. We propose a two-stage stochastic programming model and associated efficient solution procedures for solving large-scale problems to (1) better represent the random nature of the biomassmore » quality (defined by moisture and ash contents) in supply chain modeling, and (2) assess the impact of these uncertainties on the supply chain design and planning. The proposed model is then applied to a case study in the state of Tennessee. Results show that high moisture and ash contents negatively impact the unit delivery cost since poor biomass quality requires the addition of quality control activities. Experimental results indicate that supply chain cost could increase as much as 27%–31% when biomass quality is poor. We assess the impact of the biomass quality on the topological supply chain. Our case study indicates that biomass quality impacts supply chain costs; thus, it is important to consider the impact of biomass quality in supply chain design and management decisions.« less

Integrating biomass quality variability in stochastic supply chain modeling and optimization for large-scale biofuel production

DOE PAGES

Castillo-Villar, Krystel K.; Eksioglu, Sandra; Taherkhorsandi, Milad

2017-02-20

The production of biofuels using second-generation feedstocks has been recognized as an important alternative source of sustainable energy and its demand is expected to increase due to regulations such as the Renewable Fuel Standard. However, the pathway to biofuel industry maturity faces unique, unaddressed challenges. Here, to address this challenges, this article presents an optimization model which quantifies and controls the impact of biomass quality variability on supply chain related decisions and technology selection. We propose a two-stage stochastic programming model and associated efficient solution procedures for solving large-scale problems to (1) better represent the random nature of the biomassmore » quality (defined by moisture and ash contents) in supply chain modeling, and (2) assess the impact of these uncertainties on the supply chain design and planning. The proposed model is then applied to a case study in the state of Tennessee. Results show that high moisture and ash contents negatively impact the unit delivery cost since poor biomass quality requires the addition of quality control activities. Experimental results indicate that supply chain cost could increase as much as 27%–31% when biomass quality is poor. We assess the impact of the biomass quality on the topological supply chain. Our case study indicates that biomass quality impacts supply chain costs; thus, it is important to consider the impact of biomass quality in supply chain design and management decisions.« less

Respiratory chain inhibition: one more feature to propose MPTP intoxication as a Leigh syndrome model.

PubMed

Da Costa, Barbara; Dumon, Elodie; Le Moigno, Laurence; Bodard, Sylvie; Castelnau, Pierre; Letellier, Thierry; Rocher, Christophe

2016-10-01

1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) intoxicated mice have been widely used to model the loss of dopaminergic neurons. As this treatment leads to basal ganglia degeneration, it was proposed that MPTP mice could be used as a model of Leigh syndrome. However, this mitochondrial pathology is biochemically characterized by a respiratory chain dysfunction. To determine if MPTP can affect in vivo mitochondria function, we measured the activities of mitochondrial respiratory chain complexes in several tissues. Our results show that MPTP affects mainly mitochondrial respiratory chain complex IV, as found in Leigh Syndrome, confirming that acute MPTP intoxicated mice are a good model of Leigh Syndrome.

On the dynamics of chain systems. [applications in manipulator and human body models

NASA Technical Reports Server (NTRS)

Huston, R. L.; Passerello, C. E.

1974-01-01

A computer-oriented method for obtaining dynamical equations of motion for chain systems is presented. A chain system is defined as an arbitrarily assembled set of rigid bodies such that adjoining bodies have at least one common point and such that closed loops are not formed. The equations of motion are developed through the use of Lagrange's form of d'Alembert's principle. The method and procedure is illustrated with an elementary study of a tripod space manipulator. The method is designed for application with systems such as human body models, chains and cables, and dynamic finite-segment models.

Development of S-ARIMA Model for Forecasting Demand in a Beverage Supply Chain

NASA Astrophysics Data System (ADS)

Mircetic, Dejan; Nikolicic, Svetlana; Maslaric, Marinko; Ralevic, Nebojsa; Debelic, Borna

2016-11-01

Demand forecasting is one of the key activities in planning the freight flows in supply chains, and accordingly it is essential for planning and scheduling of logistic activities within observed supply chain. Accurate demand forecasting models directly influence the decrease of logistics costs, since they provide an assessment of customer demand. Customer demand is a key component for planning all logistic processes in supply chain, and therefore determining levels of customer demand is of great interest for supply chain managers. In this paper we deal with exactly this kind of problem, and we develop the seasonal Autoregressive IntegratedMoving Average (SARIMA) model for forecasting demand patterns of a major product of an observed beverage company. The model is easy to understand, flexible to use and appropriate for assisting the expert in decision making process about consumer demand in particular periods.

A Looping-Based Model for Quenching Repression

PubMed Central

Pollak, Yaroslav; Goldberg, Sarah; Amit, Roee

2017-01-01

We model the regulatory role of proteins bound to looped DNA using a simulation in which dsDNA is represented as a self-avoiding chain, and proteins as spherical protrusions. We simulate long self-avoiding chains using a sequential importance sampling Monte-Carlo algorithm, and compute the probabilities for chain looping with and without a protrusion. We find that a protrusion near one of the chain’s termini reduces the probability of looping, even for chains much longer than the protrusion–chain-terminus distance. This effect increases with protrusion size, and decreases with protrusion-terminus distance. The reduced probability of looping can be explained via an eclipse-like model, which provides a novel inhibitory mechanism. We test the eclipse model on two possible transcription-factor occupancy states of the D. melanogaster eve 3/7 enhancer, and show that it provides a possible explanation for the experimentally-observed eve stripe 3 and 7 expression patterns. PMID:28085884

Internal friction and mode relaxation in a simple chain model.

PubMed

Fugmann, S; Sokolov, I M

2009-12-21

We consider the equilibrium relaxation properties of the end-to-end distance and of the principal components in a one-dimensional polymer chain model with nonlinear interaction between the beads. While for the single-well potentials these properties are similar to the ones of a Rouse chain, for the double-well interaction potentials, modeling internal friction, they differ vastly from the ones of the harmonic chain at intermediate times and intermediate temperatures. This minimal description within a one-dimensional model mimics the relaxation properties found in much more complex polymer systems. Thus, the relaxation time of the end-to-end distance may grow by orders of magnitude at intermediate temperatures. The principal components (whose directions are shown to coincide with the normal modes of the harmonic chain, whatever interaction potential is assumed) not only display larger relaxation times but also subdiffusive scaling.

An equal force theory for network models of soft materials with arbitrary molecular weight distribution

NASA Astrophysics Data System (ADS)

Verron, E.; Gros, A.

2017-09-01

Most network models for soft materials, e.g. elastomers and gels, are dedicated to idealized materials: all chains admit the same number of Kuhn segments. Nevertheless, such standard models are not appropriate for materials involving multiple networks, and some specific constitutive equations devoted to these materials have been derived in the last few years. In nearly all cases, idealized networks of different chain lengths are assembled following an equal strain assumption; only few papers adopt an equal stress assumption, although some authors argue that such hypothesis would reflect the equilibrium of the different networks in contact. In this work, a full-network model with an arbitrary chain length distribution is derived by considering that chains of different lengths satisfy the equal force assumption in each direction of the unit sphere. The derivation is restricted to non-Gaussian freely jointed chains and to affine deformation of the sphere. Firstly, after a proper definition of the undeformed configuration of the network, we demonstrate that the equal force assumption leads to the equality of a normalized stretch in chains of different lengths. Secondly, we establish that the network with chain length distribution behaves as an idealized full-network of which both chain length and density of are provided by the chain length distribution. This approach is finally illustrated with two examples: the derivation of a new expression for the Young modulus of bimodal interpenetrated polymer networks, and the prediction of the change in fluorescence during deformation of mechanochemically responsive elastomers.

Optimal design of supply chain network under uncertainty environment using hybrid analytical and simulation modeling approach

NASA Astrophysics Data System (ADS)

Chiadamrong, N.; Piyathanavong, V.

2017-12-01

Models that aim to optimize the design of supply chain networks have gained more interest in the supply chain literature. Mixed-integer linear programming and discrete-event simulation are widely used for such an optimization problem. We present a hybrid approach to support decisions for supply chain network design using a combination of analytical and discrete-event simulation models. The proposed approach is based on iterative procedures until the difference between subsequent solutions satisfies the pre-determined termination criteria. The effectiveness of proposed approach is illustrated by an example, which shows closer to optimal results with much faster solving time than the results obtained from the conventional simulation-based optimization model. The efficacy of this proposed hybrid approach is promising and can be applied as a powerful tool in designing a real supply chain network. It also provides the possibility to model and solve more realistic problems, which incorporate dynamism and uncertainty.

The Analysis of Rush Orders Risk in Supply Chain: A Simulation Approach

NASA Technical Reports Server (NTRS)

Mahfouz, Amr; Arisha, Amr

2011-01-01

Satisfying customers by delivering demands at agreed time, with competitive prices, and in satisfactory quality level are crucial requirements for supply chain survival. Incidence of risks in supply chain often causes sudden disruptions in the processes and consequently leads to customers losing their trust in a company's competence. Rush orders are considered to be one of the main types of supply chain risks due to their negative impact on the overall performance, Using integrated definition modeling approaches (i.e. IDEF0 & IDEF3) and simulation modeling technique, a comprehensive integrated model has been developed to assess rush order risks and examine two risk mitigation strategies. Detailed functions sequence and objects flow were conceptually modeled to reflect on macro and micro levels of the studied supply chain. Discrete event simulation models were then developed to assess and investigate the mitigation strategies of rush order risks, the objective of this is to minimize order cycle time and cost.

Irreversible Markov chains in spin models: Topological excitations

NASA Astrophysics Data System (ADS)

Lei, Ze; Krauth, Werner

2018-01-01

We analyze the convergence of the irreversible event-chain Monte Carlo algorithm for continuous spin models in the presence of topological excitations. In the two-dimensional XY model, we show that the local nature of the Markov-chain dynamics leads to slow decay of vortex-antivortex correlations while spin waves decorrelate very quickly. Using a Fréchet description of the maximum vortex-antivortex distance, we quantify the contributions of topological excitations to the equilibrium correlations, and show that they vary from a dynamical critical exponent z∼ 2 at the critical temperature to z∼ 0 in the limit of zero temperature. We confirm the event-chain algorithm's fast relaxation (corresponding to z = 0) of spin waves in the harmonic approximation to the XY model. Mixing times (describing the approach towards equilibrium from the least favorable initial state) however remain much larger than equilibrium correlation times at low temperatures. We also describe the respective influence of topological monopole-antimonopole excitations and of spin waves on the event-chain dynamics in the three-dimensional Heisenberg model.

Developing a model for agile supply: an empirical study from Iranian pharmaceutical supply chain.

PubMed

Rajabzadeh Ghatari, Ali; Mehralian, Gholamhossein; Zarenezhad, Forouzandeh; Rasekh, Hamid Reza

2013-01-01

Agility is the fundamental characteristic of a supply chain needed for survival in turbulent markets, where environmental forces create additional uncertainty resulting in higher risk in the supply chain management. In addition, agility helps providing the right product, at the right time to the consumer. The main goal of this research is therefore to promote supplier selection in pharmaceutical industry according to the formative basic factors. Moreover, this paper can configure its supply network to achieve the agile supply chain. The present article analyzes the supply part of supply chain based on SCOR model, used to assess agile supply chains by highlighting their specific characteristics and applicability in providing the active pharmaceutical ingredient (API). This methodology provides an analytical modeling; the model enables potential suppliers to be assessed against the multiple criteria using both quantitative and qualitative measures. In addition, for making priority of critical factors, TOPSIS algorithm has been used as a common technique of MADM model. Finally, several factors such as delivery speed, planning and reorder segmentation, trust development and material quantity adjustment are identified and prioritized as critical factors for being agile in supply of API.

Developing a Model for Agile Supply: an Empirical Study from Iranian Pharmaceutical Supply Chain

PubMed Central

Rajabzadeh Ghatari, Ali; Mehralian, Gholamhossein; Zarenezhad, Forouzandeh; Rasekh, Hamid Reza

2013-01-01

Agility is the fundamental characteristic of a supply chain needed for survival in turbulent markets, where environmental forces create additional uncertainty resulting in higher risk in the supply chain management. In addition, agility helps providing the right product, at the right time to the consumer. The main goal of this research is therefore to promote supplier selection in pharmaceutical industry according to the formative basic factors. Moreover, this paper can configure its supply network to achieve the agile supply chain. The present article analyzes the supply part of supply chain based on SCOR model, used to assess agile supply chains by highlighting their specific characteristics and applicability in providing the active pharmaceutical ingredient (API). This methodology provides an analytical modeling; the model enables potential suppliers to be assessed against the multiple criteria using both quantitative and qualitative measures. In addition, for making priority of critical factors, TOPSIS algorithm has been used as a common technique of MADM model. Finally, several factors such as delivery speed, planning and reorder segmentation, trust development and material quantity adjustment are identified and prioritized as critical factors for being agile in supply of API. PMID:24250689

Twist-writhe partitioning in a coarse-grained DNA minicircle model

NASA Astrophysics Data System (ADS)

Sayar, Mehmet; Avşaroǧlu, Barış; Kabakçıoǧlu, Alkan

2010-04-01

Here we present a systematic study of supercoil formation in DNA minicircles under varying linking number by using molecular-dynamics simulations of a two-bead coarse-grained model. Our model is designed with the purpose of simulating long chains without sacrificing the characteristic structural properties of the DNA molecule, such as its helicity, backbone directionality, and the presence of major and minor grooves. The model parameters are extracted directly from full-atomistic simulations of DNA oligomers via Boltzmann inversion; therefore, our results can be interpreted as an extrapolation of those simulations to presently inaccessible chain lengths and simulation times. Using this model, we measure the twist/writhe partitioning in DNA minicircles, in particular its dependence on the chain length and excess linking number. We observe an asymmetric supercoiling transition consistent with experiments. Our results suggest that the fraction of the linking number absorbed as twist and writhe is nontrivially dependent on chain length and excess linking number. Beyond the supercoiling transition, chains of the order of one persistence length carry equal amounts of twist and writhe. For longer chains, an increasing fraction of the linking number is absorbed by the writhe.

Tuning the Morphology of Li2O2 by Noble and 3d metals: A Planar Model Electrode Study for Li-O2 Battery.

PubMed

Yang, Yao; Liu, Wei; Wu, Nian; Wang, Xiaochen; Zhang, Tao; Chen, Linfeng; Zeng, Rui; Wang, Yingming; Lu, Juntao; Fu, Lei; Xiao, Li; Zhuang, Lin

2017-06-14

In this work, a planar model electrode method has been used to investigate the structure-activity relationship of multiple noble and 3d metal catalysts for the cathode reaction of Li-O 2 battery. The result shows that the battery performance (discharge/charge overpotential) strongly depends not only on the type of catalysts but also on the morphology of the discharge product (Li 2 O 2 ). Specifically, according to electrochemical characterization and scanning electron microscopy (SEM) observation, noble metals (Pd, Pt, Ru, Ir, and Au) show excellent battery performance (smaller discharge/charge overpotential), with wormlike Li 2 O 2 particles with size less than 200 nm on their surfaces. On the other hand, 3d metals (Fe, Co, Ni, and Mn) offered poor battery performance (larger discharge/charge overpotential), with much larger Li 2 O 2 particles (1 μm to a few microns) on their surfaces after discharging. Further research shows that a "volcano plot" is found by correlating the discharging/charging plateau voltage with the adsorption energy of LiO 2 on different metals. The metals with better battery performance and worm-like-shaped Li 2 O 2 are closer to the top of the "volcano", indicating adsorption energy of LiO 2 is one of the key characters for the catalyst to reach a good performance for the oxygen electrode of Li-O 2 battery, and it has a strong influence on the morphology of the discharge product on the electrode surface.

Supply-Chain Optimization Template

NASA Technical Reports Server (NTRS)

Quiett, William F.; Sealing, Scott L.

2009-01-01

The Supply-Chain Optimization Template (SCOT) is an instructional guide for identifying, evaluating, and optimizing (including re-engineering) aerospace- oriented supply chains. The SCOT was derived from the Supply Chain Council s Supply-Chain Operations Reference (SCC SCOR) Model, which is more generic and more oriented toward achieving a competitive advantage in business.

Markov Chain Estimation of Avian Seasonal Fecundity

EPA Science Inventory

To explore the consequences of modeling decisions on inference about avian seasonal fecundity we generalize previous Markov chain (MC) models of avian nest success to formulate two different MC models of avian seasonal fecundity that represent two different ways to model renestin...

Quantum criticality and duality in the Sachdev-Ye-Kitaev/AdS2 chain

NASA Astrophysics Data System (ADS)

Jian, Shao-Kai; Xian, Zhuo-Yu; Yao, Hong

2018-05-01

We show that the quantum critical point (QCP) between a diffusive metal and ferromagnetic (or antiferromagnetic) phases in the SYK chain has a gravitational description corresponding to the double-trace deformation in an AdS2 chain. Specifically, by studying a double-trace deformation of a Z2 scalar in an AdS2 chain where the Z2 scalar is dual to the order parameter in the SYK chain, we find that the susceptibility and renormalization group equation describing the QCP in the SYK chain can be exactly reproduced in the holographic model. Our results suggest that the infrared geometry in the gravity theory dual to the diffusive metal of the SYK chain is also an AdS2 chain. We further show that the transition in SYK model captures universal information about double-trace deformation in generic black holes with near horizon AdS2 space-time.

A systems-based approach for integrated design of materials, products and design process chains

NASA Astrophysics Data System (ADS)

Panchal, Jitesh H.; Choi, Hae-Jin; Allen, Janet K.; McDowell, David L.; Mistree, Farrokh

2007-12-01

The concurrent design of materials and products provides designers with flexibility to achieve design objectives that were not previously accessible. However, the improved flexibility comes at a cost of increased complexity of the design process chains and the materials simulation models used for executing the design chains. Efforts to reduce the complexity generally result in increased uncertainty. We contend that a systems based approach is essential for managing both the complexity and the uncertainty in design process chains and simulation models in concurrent material and product design. Our approach is based on simplifying the design process chains systematically such that the resulting uncertainty does not significantly affect the overall system performance. Similarly, instead of striving for accurate models for multiscale systems (that are inherently complex), we rely on making design decisions that are robust to uncertainties in the models. Accordingly, we pursue hierarchical modeling in the context of design of multiscale systems. In this paper our focus is on design process chains. We present a systems based approach, premised on the assumption that complex systems can be designed efficiently by managing the complexity of design process chains. The approach relies on (a) the use of reusable interaction patterns to model design process chains, and (b) consideration of design process decisions using value-of-information based metrics. The approach is illustrated using a Multifunctional Energetic Structural Material (MESM) design example. Energetic materials store considerable energy which can be released through shock-induced detonation; conventionally, they are not engineered for strength properties. The design objectives for the MESM in this paper include both sufficient strength and energy release characteristics. The design is carried out by using models at different length and time scales that simulate different aspects of the system. Finally, by applying the method to the MESM design problem, we show that the integrated design of materials and products can be carried out more efficiently by explicitly accounting for design process decisions with the hierarchy of models.

Wide-Angle X-Ray Scattering and Solid-State Nuclear Magnetic Resonance Data Combined to Test Models for Cellulose Microfibrils in Mung Bean Cell Walls1

PubMed Central

Newman, Roger H.; Hill, Stefan J.; Harris, Philip J.

2013-01-01

A synchrotron wide-angle x-ray scattering study of mung bean (Vigna radiata) primary cell walls was combined with published solid-state nuclear magnetic resonance data to test models for packing of (1→4)-β-glucan chains in cellulose microfibrils. Computer-simulated peak shapes, calculated for 36-chain microfibrils with perfect order or uncorrelated disorder, were sharper than those in the experimental diffractogram. Introducing correlated disorder into the models broaden the simulated peaks but only when the disorder was increased to unrealistic magnitudes. Computer-simulated diffractograms, calculated for 24- and 18-chain models, showed good fits to experimental data. Particularly good fits to both x-ray and nuclear magnetic resonance data were obtained for collections of 18-chain models with mixed cross-sectional shapes and occasional twinning. Synthesis of 18-chain microfibrils is consistent with a model for cellulose-synthesizing complexes in which three cellulose synthase polypeptides form a particle and six particles form a rosette. PMID:24154621

Modelling inter-supply chain competition with resource limitation and demand disruption

NASA Astrophysics Data System (ADS)

Chen, Zhaobo; Teng, Chunxian; Zhang, Ding; Sun, Jiayi

2016-05-01

This paper proposes a comprehensive model for studying supply chain versus supply chain competition with resource limitation and demand disruption. We assume that there are supply chains with heterogeneous supply network structures that compete at multiple demand markets. Each supply chain is comprised of internal and external firms. The internal firms are coordinated in production and distribution and share some common but limited resources within the supply chain, whereas the external firms are independent and do not share the internal resources. The supply chain managers strive to develop optimal strategies in terms of production level and resource allocation in maximising their profit while facing competition at the end market. The Cournot-Nash equilibrium of this inter-supply chain competition is formulated as a variational inequality problem. We further study the case when there is demand disruption in the plan-execution phase. In such a case, the managers need to revise their planned strategy in order to maximise their profit with the new demand under disruption and minimise the cost of change. We present a bi-criteria decision-making model for supply chain managers and develop the optimal conditions in equilibrium, which again can be formulated by another variational inequality problem. Numerical examples are presented for illustrative purpose.

Propagation of the Hawaiian-Emperor volcano chain by Pacific plate cooling stress

USGS Publications Warehouse

Stuart, W.D.; Foulger, G.R.; Barall, M.

2007-01-01

The lithosphere crack model, the main alternative to the mantle plume model for age-progressive magma emplacement along the Hawaiian-Emperor volcano chain, requires the maximum horizontal tensile stress to be normal to the volcano chain. However, published stress fields calculated from Pacific lithosphere tractions and body forces (e.g., subduction pull, basal drag, lithosphere density) are not optimal for southeast propagation of a stress-free, vertical tensile crack coincident with the Hawaiian segment of the Hawaiian-Emperor chain. Here we calculate the thermoelastic stress rate for present-day cooling of the Pacific plate using a spherical shell finite element representation of the plate geometry. We use observed seafloor isochrons and a standard model for lithosphere cooling to specify the time dependence of vertical temperature profiles. The calculated stress rate multiplied by a time increment (e.g., 1 m.y.) then gives a thermoelastic stress increment for the evolving Pacific plate. Near the Hawaiian chain position, the calculated stress increment in the lower part of the shell is tensional, with maximum tension normal to the chain direction. Near the projection of the chain trend to the southeast beyond Hawaii, the stress increment is compressive. This incremental stress field has the form necessary to maintain and propagate a tensile crack or similar lithosphere flaw and is thus consistent with the crack model for the Hawaiian volcano chain.?? 2007 The Geological Society of America.

Future Supply Chains Enabled by Continuous Processing—Opportunities and Challenges. May 20–21, 2014 Continuous Manufacturing Symposium

PubMed Central

Srai, Jagjit Singh; Badman, Clive; Krumme, Markus; Futran, Mauricio; Johnston, Craig

2015-01-01

This paper examines the opportunities and challenges facing the pharmaceutical industry in moving to a primarily “continuous processing”-based supply chain. The current predominantly “large batch” and centralized manufacturing system designed for the “blockbuster” drug has driven a slow-paced, inventory heavy operating model that is increasingly regarded as inflexible and unsustainable. Indeed, new markets and the rapidly evolving technology landscape will drive more product variety, shorter product life-cycles, and smaller drug volumes, which will exacerbate an already unsustainable economic model. Future supply chains will be required to enhance affordability and availability for patients and healthcare providers alike despite the increased product complexity. In this more challenging supply scenario, we examine the potential for a more pull driven, near real-time demand-based supply chain, utilizing continuous processing where appropriate as a key element of a more “flow-through” operating model. In this discussion paper on future supply chain models underpinned by developments in the continuous manufacture of pharmaceuticals, we have set out; The significant opportunities to moving to a supply chain flow-through operating model, with substantial opportunities in inventory reduction, lead-time to patient, and radically different product assurance/stability regimes. Scenarios for decentralized production models producing a greater variety of products with enhanced volume flexibility. Production, supply, and value chain footprints that are radically different from today's monolithic and centralized batch manufacturing operations. Clinical trial and drug product development cost savings that support more rapid scale-up and market entry models with early involvement of SC designers within New Product Development. The major supply chain and industrial transformational challenges that need to be addressed. The paper recognizes that although current batch operational performance in pharma is far from optimal and not necessarily an appropriate end-state benchmark for batch technology, the adoption of continuous supply chain operating models underpinned by continuous production processing, as full or hybrid solutions in selected product supply chains, can support industry transformations to deliver right-first-time quality at substantially lower inventory profiles. © 2015 The Authors. Journal of Pharmaceutical Sciences published by Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 104:840–849, 2015 PMID:25631279

Facile Control of the Porous Structure of Larch-Derived Mesoporous Carbons via Self-Assembly for Supercapacitors

PubMed Central

Zhao, Xin; Li, Wei; Chen, Honglei; Wang, Shoujuan; Kong, Fangong; Liu, Shouxin

2017-01-01

Mesoporous carbons have been successfully synthesized via self-assembly using larch-based resins as precursors and triblock copolymers as soft templates. The porous structure of mesoporous carbons can be tailored by adjusting the ratio of hydrophilic/hydrophobic (EO/PO) units owing to interfacial curvature. Interestingly, the porous structures show a distinct change from vortex-like to worm-like pores, to stripe-like pores, and to ordered two-dimensional hexagonal pores as the ratio of hydrophilic/hydrophobic units increases, indicating the significant effect of EO/PO ratio on the porous structure. The mesoporous carbons as supercapacitor electrodes exhibit superior electrochemical capacitive performance and a high degree of reversibility after 2000 cycles for supercapacitors due to the well-defined mesoporosity of the carbon materials. Meanwhile, the superior carbon has a high specific capacitance of 107 F·g−1 in 6 M KOH at a current density of 10 A·g−1. PMID:29156641

Facile Control of the Porous Structure of Larch-Derived Mesoporous Carbons via Self-Assembly for Supercapacitors.

PubMed

Zhao, Xin; Li, Wei; Chen, Honglei; Wang, Shoujuan; Kong, Fangong; Liu, Shouxin

2017-11-20

Mesoporous carbons have been successfully synthesized via self-assembly using larch-based resins as precursors and triblock copolymers as soft templates. The porous structure of mesoporous carbons can be tailored by adjusting the ratio of hydrophilic/hydrophobic (EO/PO) units owing to interfacial curvature. Interestingly, the porous structures show a distinct change from vortex-like to worm-like pores, to stripe-like pores, and to ordered two-dimensional hexagonal pores as the ratio of hydrophilic/hydrophobic units increases, indicating the significant effect of EO/PO ratio on the porous structure. The mesoporous carbons as supercapacitor electrodes exhibit superior electrochemical capacitive performance and a high degree of reversibility after 2000 cycles for supercapacitors due to the well-defined mesoporosity of the carbon materials. Meanwhile, the superior carbon has a high specific capacitance of 107 F·g -1 in 6 M KOH at a current density of 10 A·g -1 .

Direct synthesis of Ti-containing SBA-16-type mesoporous material by the evaporation-induced self-assembly method and its catalytic performance for oxidative desulfurization.

PubMed

Shah, Asma Tufail; Li, Baoshan; Abdalla, Zaki Eldin Ali

2009-08-15

A novel Ti-containing SBA-16-type mesoporous material (with various Ti loadings of 5, 10, and 15 wt%) was synthesized by an evaporation-induced self-assembly method using F127 copolymer as template. The materials were characterized by XRD, FTIR, TG-DTA, N(2) adsorption, SEM, HRTEM, and XPS. The characterization results show that the material possesses high thermal stability, thick pore walls (10.43-10.68 nm), and high surface area (642.26-691.5 m(2)/g) with a mesoporous worm-like structure, and titanium was successfully incorporated into the silica matrix with a tetrahedral environment. The material showed high activity in the oxidative desulfurization of DBT and its activity was not reduced even after three times recycling; further reuse resulted in a gradual decrease in its activity.

Paleopathological evidence of the cranial remains from the Sima de los Huesos Middle Pleistocene site (Sierra de Atapuerca, Spain). Description and preliminary inferences.

PubMed

Pérez, P J; Gracía, A; Martínez, I; Arsuaga, J L

1997-01-01

The large Sima de los Huesos sample provides for the first time the opportunity of performing a paleopathological study of a Middle Pleistocene population. A high frequency of bilateral temporomandibular arthropathy has been observed. We found an ear hyperostosis in Cranium 4, that probably caused deafness that we consider to be of infectious origin. Three osteomata were found in the cranial collection. One severe trauma was evident on the left supraorbital torus of an immature individual. Many cranial vault erosions, mostly restricted to the external table, are found in the sample. Cranium 5 displays thirteen of these. Cranium 5 also shows an extensive maxillary osteitis associated with a dental apical abscess, as well as another dental apical abscess in its mandible. Most of the adult frontal bones show a worm-like pattern of vascular channelling in the orbital roof, also found in modern populations.

Bioinspired, cysteamine-catalyzed co-silicification of (1H, 1H, 2H, 2HPerfluorooctyl) triethoxysilane and tetraethyl orthosilicate: formation of superhydrophobic surfaces.

PubMed

Park, Ji Hun; Kim, Ji Yup; Cho, Woo Kyung; Choi, Insung S

2014-03-01

Bioinspired silicification attracts a great deal of interest because of its physiologically relevant, mild conditions for hydrolysis and condensation of silica precursors, which makes the bioinspired approach superior to the conventional sol–gel process, particularly when dealing with biological entities. However, the morphological control of silica structures with incorporation of functional groups in the bioinspired silicilication has been unexplored. In this work, we co-silicificated (1H, 1H, 2H, 2H-perfluorooctyl)triethoxysilane and tetraethyl orthosilicate to investigate the morphological evolution of fluorinated silica structures in the cetyltrimethylammonium bromide-mediated, cysteamine-catalyzed silicification. The generated micrometer-long wormlike and spherical silica structures display superhydrophobicity after film formation. Interestingly, the measurement of dynamic water contact angles shows that the morphological difference leads to a different wetting state, either the self-cleaning or the pinning state of the superhydrophobic surface.

Electrical current nanogeneration driven by spontaneous nanofluidic oscillations.

PubMed

Gimenez, R; Mercuri, M; Berli, C L A; Bellino, M G

2018-02-15

Exploiting natural phenomena is a central route for providing electricity to sustainably drive wearable electronics. Here we report a nano-scale water-driven energy generator that produces tiny electrical currents from spontaneous wetting-drying oscillations in mesoporous thin films. The system was fabricated with a wormlike mesoporous silica film, which was packed in between Cu and silicon contacts. The nanogenerator runs autonomously when a water droplet is laid over the film close to the Cu electrode, as water infiltration into the film under the electrode produces a direct-current. Wetting-drying cycles, which are spontaneously triggered by water evaporation, are perfectly correlated to the generated electrical current. The autonomous water displacement through the film yields a sustained energy conversion until the droplet reservoir vanishes. This novel water-driven nanogenerator opens new alternatives for versatile, mobile and cost-effective self-powering of nanosystems and nanodevices.

Synthesis and structure characterization of chromium oxide prepared by solid thermal decomposition reaction.

PubMed

Li, Li; Yan, Zi F; Lu, Gao Q; Zhu, Zhong H

2006-01-12

Mesoporous chromium oxide (Cr2O3) nanocrystals were first synthesized by the thermal decomposition reaction of Cr(NO3)3.9H2O using citric acid monohydrate (CA) as the mesoporous template agent. The texture and chemistry of chromium oxide nanocrystals were characterized by N2 adsorption-desorption isotherms, FTIR, X-ray diffraction (XRD), UV-vis, and thermoanalytical methods. It was shown that the hydrate water and CA are the crucial factors in influencing the formation of mesoporous Cr2O3 nanocrystals in the mixture system. The decomposition of CA results in the formation of a mesoporous structure with wormlike pores. The hydrate water of the mixture provides surface hydroxyls that act as binders, making the nanocrystals aggregate. The pore structures and phases of chromium oxide are affected by the ratio of precursor-to-CA, thermal temperature, and time.

Coopetitive Supply Chain Relationship Model: Application to the Smartphone Manufacturing Network.

PubMed

Kwok, Jeremy Jie Ming; Lee, Dong-Yup

2015-01-01

Previous researches for understanding supply chain relationship have mostly focused on its vertical collaboration between buyers and suppliers. However, there have been some instances of volatile and stable collaborative relationships amongst competitors such as Apple-Samsung product manufacturer-component supplier relationship and airline alliances, respectively, which is recognized as coopetition. Even though there have been several qualitative studies and a number of game theory models on coopetition, it is rare to find any attempts on quantitative characterization of such coopetitive dynamic behavior in supply chain relationship. Hence, in this work, we formulated a MINLP model mathematically representing coopetitive relationships in a cost efficient supply chain network. In particular, the coopetition factor was newly introduced to measure the degree of coopetition among supply chain players and determine the optimal level of coopetition to engage in. The utility and practicality of the model were strongly demonstrated using a case study of a hypothetical smartphone supply chain network under different scenarios, thus proposing their strategically viable optimal interactions. Therefore, this exploratory study can herald a new era of global coopetitive business.

Coopetitive Supply Chain Relationship Model: Application to the Smartphone Manufacturing Network

PubMed Central

Kwok, Jeremy Jie Ming; Lee, Dong-Yup

2015-01-01

Previous researches for understanding supply chain relationship have mostly focused on its vertical collaboration between buyers and suppliers. However, there have been some instances of volatile and stable collaborative relationships amongst competitors such as Apple-Samsung product manufacturer-component supplier relationship and airline alliances, respectively, which is recognized as coopetition. Even though there have been several qualitative studies and a number of game theory models on coopetition, it is rare to find any attempts on quantitative characterization of such coopetitive dynamic behavior in supply chain relationship. Hence, in this work, we formulated a MINLP model mathematically representing coopetitive relationships in a cost efficient supply chain network. In particular, the coopetition factor was newly introduced to measure the degree of coopetition among supply chain players and determine the optimal level of coopetition to engage in. The utility and practicality of the model were strongly demonstrated using a case study of a hypothetical smartphone supply chain network under different scenarios, thus proposing their strategically viable optimal interactions. Therefore, this exploratory study can herald a new era of global coopetitive business. PMID:26186227

Irreversible Local Markov Chains with Rapid Convergence towards Equilibrium.

PubMed

Kapfer, Sebastian C; Krauth, Werner

2017-12-15

We study the continuous one-dimensional hard-sphere model and present irreversible local Markov chains that mix on faster time scales than the reversible heat bath or Metropolis algorithms. The mixing time scales appear to fall into two distinct universality classes, both faster than for reversible local Markov chains. The event-chain algorithm, the infinitesimal limit of one of these Markov chains, belongs to the class presenting the fastest decay. For the lattice-gas limit of the hard-sphere model, reversible local Markov chains correspond to the symmetric simple exclusion process (SEP) with periodic boundary conditions. The two universality classes for irreversible Markov chains are realized by the totally asymmetric SEP (TASEP), and by a faster variant (lifted TASEP) that we propose here. We discuss how our irreversible hard-sphere Markov chains generalize to arbitrary repulsive pair interactions and carry over to higher dimensions through the concept of lifted Markov chains and the recently introduced factorized Metropolis acceptance rule.

Irreversible Local Markov Chains with Rapid Convergence towards Equilibrium

NASA Astrophysics Data System (ADS)

Kapfer, Sebastian C.; Krauth, Werner

2017-12-01

We study the continuous one-dimensional hard-sphere model and present irreversible local Markov chains that mix on faster time scales than the reversible heat bath or Metropolis algorithms. The mixing time scales appear to fall into two distinct universality classes, both faster than for reversible local Markov chains. The event-chain algorithm, the infinitesimal limit of one of these Markov chains, belongs to the class presenting the fastest decay. For the lattice-gas limit of the hard-sphere model, reversible local Markov chains correspond to the symmetric simple exclusion process (SEP) with periodic boundary conditions. The two universality classes for irreversible Markov chains are realized by the totally asymmetric SEP (TASEP), and by a faster variant (lifted TASEP) that we propose here. We discuss how our irreversible hard-sphere Markov chains generalize to arbitrary repulsive pair interactions and carry over to higher dimensions through the concept of lifted Markov chains and the recently introduced factorized Metropolis acceptance rule.

Production and characterization of murine models of classic and intermediate maple syrup urine disease

PubMed Central

Homanics, Gregg E; Skvorak, Kristen; Ferguson, Carolyn; Watkins, Simon; Paul, Harbhajan S

2006-01-01

Background Maple Syrup Urine Disease (MSUD) is an inborn error of metabolism caused by a deficiency of branched-chain keto acid dehydrogenase. MSUD has several clinical phenotypes depending on the degree of enzyme deficiency. Current treatments are not satisfactory and require new approaches to combat this disease. A major hurdle in developing new treatments has been the lack of a suitable animal model. Methods To create a murine model of classic MSUD, we used gene targeting and embryonic stem cell technologies to create a mouse line that lacked a functional E2 subunit gene of branched-chain keto acid dehydrogenase. To create a murine model of intermediate MSUD, we used transgenic technology to express a human E2 cDNA on the knockout background. Mice of both models were characterized at the molecular, biochemical, and whole animal levels. Results By disrupting the E2 subunit gene of branched-chain keto acid dehydrogenase, we created a gene knockout mouse model of classic MSUD. The homozygous knockout mice lacked branched-chain keto acid dehydrogenase activity, E2 immunoreactivity, and had a 3-fold increase in circulating branched-chain amino acids. These metabolic derangements resulted in neonatal lethality. Transgenic expression of a human E2 cDNA in the liver of the E2 knockout animals produced a model of intermediate MSUD. Branched-chain keto acid dehydrogenase activity was 5–6% of normal and was sufficient to allow survival, but was insufficient to normalize circulating branched-chain amino acids levels, which were intermediate between wildtype and the classic MSUD mouse model. Conclusion These mice represent important animal models that closely approximate the phenotype of humans with the classic and intermediate forms of MSUD. These animals provide useful models to further characterize the pathogenesis of MSUD, as well as models to test novel therapeutic strategies, such as gene and cellular therapies, to treat this devastating metabolic disease. PMID:16579849

Population pharmacokinetics of recombinant coagulation factor VIII-SingleChain in patients with severe hemophilia A.

PubMed

Zhang, Y; Roberts, J; Tortorici, M; Veldman, A; St Ledger, K; Feussner, A; Sidhu, J

2017-06-01

Essentials rVIII-SingleChain is a unique recombinant factor VIII (FVIII) molecule. A population pharmacokinetic model was based on FVIII activity of severe hemophilia A patients. The model was used to simulate factor VIII activity-time profiles for various dosing scenarios. The model supports prolonged dosing of rVIII-SingleChain with intervals of up to twice per week. Background Single-chain recombinant coagulation factor VIII (rVIII-SingleChain) is a unique recombinant coagulation factor VIII molecule. Objectives To: (i) characterize the population pharmacokinetics (PK) of rVIII-SingleChain in patients with severe hemophilia A; (ii) identify correlates of variability in rVIII-SingleChain PK; and (iii) simulate various dosing scenarios of rVIII-SingleChain. Patients/Methods A population PK model was developed, based on FVIII activity levels of 130 patients with severe hemophilia A (n = 91 for ≥ 12-65 years; n = 39 for < 12 years) who had participated in a single-dose PK investigation with rVIII-SingleChain 50 IU kg -1 . PK sampling was performed for up to 96 h. Results A two-compartment population PK model with first-order elimination adequately described FVIII activity. Body weight and predose level of von Willebrand factor were significant covariates on clearance, and body weight was a significant covariate on the central distribution volume. Simulations using the model with various dosing scenarios estimated that > 85% and > 93% of patients were predicted to maintain FVIII activity level above 1 IU dL -1 , at all times with three-times-weekly dosing (given on days 0, 2, and 4.5) at the lowest (20 IU kg -1 ) and highest (50 IU kg -1 ) doses, respectively. For twice weekly dosing (days 0 and 3.5) of 50 IU kg -1 rVIII-SingleChain, 62-80% of patients across all ages were predicted to maintain a FVIII activity level above 1 IU dL -1 at day 7. Conclusions The population PK model adequately characterized rVIII-SingleChain PK, and the model can be utilized to simulate FVIII activity-time profiles for various dosing scenarios. © 2017 The Authors. Journal of Thrombosis and Haemostasis published by Wiley Periodicals, Inc. on behalf of International Society on Thrombosis and Haemostasis.

SCRL-Model for Human Space Flight Operations Enterprise Supply Chain

NASA Technical Reports Server (NTRS)

Tucker, Brian

2010-01-01

Standard approach to evaluate and configure adaptable and sustainable program and mission supply chains at an enterprise level. End-to-end view. Total Lifecycle. Evaluate the readiness of the supply chain during the supply chain development phase.

Microstructural evolution of a model, shear-banding micellar solution during shear startup and cessation.

PubMed

López-Barrón, Carlos R; Gurnon, A Kate; Eberle, Aaron P R; Porcar, Lionel; Wagner, Norman J

2014-04-01

We present direct measurements of the evolution of the segmental-level microstructure of a stable shear-banding polymerlike micelle solution during flow startup and cessation in the plane of flow. These measurements provide a definitive, quantitative microstructural understanding of the stages observed during flow startup: an initial elastic response with limited alignment that yields with a large stress overshoot to a homogeneous flow with associated micellar alignment that persists for approximately three relaxation times. This transient is followed by a shear (kink) band formation with a flow-aligned low-viscosity band that exhibits shear-induced concentration fluctuations and coexists with a nearly isotropic band of homogenous, highly viscoelastic micellar solution. Stable, steady banding flow is achieved only after approximately two reptation times. Flow cessation from this shear-banded state is also found to be nontrivial, exhibiting an initial fast relaxation with only minor structural relaxation, followed by a slower relaxation of the aligned micellar fluid with the equilibrium fluid's characteristic relaxation time. These measurements resolve a controversy in the literature surrounding the mechanism of shear banding in entangled wormlike micelles and, by means of comparison to existing literature, provide further insights into the mechanisms driving shear-banding instabilities in related systems. The methods and instrumentation described should find broad use in exploring complex fluid rheology and testing microstructure-based constitutive equations.

Markov chains for testing redundant software

NASA Technical Reports Server (NTRS)

White, Allan L.; Sjogren, Jon A.

1988-01-01

A preliminary design for a validation experiment has been developed that addresses several problems unique to assuring the extremely high quality of multiple-version programs in process-control software. The procedure uses Markov chains to model the error states of the multiple version programs. The programs are observed during simulated process-control testing, and estimates are obtained for the transition probabilities between the states of the Markov chain. The experimental Markov chain model is then expanded into a reliability model that takes into account the inertia of the system being controlled. The reliability of the multiple version software is computed from this reliability model at a given confidence level using confidence intervals obtained for the transition probabilities during the experiment. An example demonstrating the method is provided.

Unique Aspects of the Structure and Dynamics of Elementary Iβ Cellulose Microfibrils Revealed by Computational Simulations1[OPEN

PubMed Central

Oehme, Daniel P.; Downton, Matthew T.; Doblin, Monika S.; Wagner, John; Gidley, Michael J.; Bacic, Antony

2015-01-01

The question of how many chains an elementary cellulose microfibril contains is critical to understanding the molecular mechanism(s) of cellulose biosynthesis and regulation. Given the hexagonal nature of the cellulose synthase rosette, it is assumed that the number of chains must be a multiple of six. We present molecular dynamics simulations on three different models of Iβ cellulose microfibrils, 18, 24, and 36 chains, to investigate their structure and dynamics in a hydrated environment. The 36-chain model stays in a conformational space that is very similar to the initial crystalline phase, while the 18- and 24-chain models sample a conformational space different from the crystalline structure yet similar to conformations observed in recent high-temperature molecular dynamics simulations. Major differences in the conformations sampled between the different models result from changes to the tilt of chains in different layers, specifically a second stage of tilt, increased rotation about the O2-C2 dihedral, and a greater sampling of non-TG exocyclic conformations, particularly the GG conformation in center layers and GT conformation in solvent-exposed exocyclic groups. With a reinterpretation of nuclear magnetic resonance data, specifically for contributions made to the C6 peak, data from the simulations suggest that the 18- and 24-chain structures are more viable models for an elementary cellulose microfibril, which also correlates with recent scattering and diffraction experimental data. These data inform biochemical and molecular studies that must explain how a six-particle cellulose synthase complex rosette synthesizes microfibrils likely comprised of either 18 or 24 chains. PMID:25786828

Modeling logistic performance in quantitative microbial risk assessment.

PubMed

Rijgersberg, Hajo; Tromp, Seth; Jacxsens, Liesbeth; Uyttendaele, Mieke

2010-01-01

In quantitative microbial risk assessment (QMRA), food safety in the food chain is modeled and simulated. In general, prevalences, concentrations, and numbers of microorganisms in media are investigated in the different steps from farm to fork. The underlying rates and conditions (such as storage times, temperatures, gas conditions, and their distributions) are determined. However, the logistic chain with its queues (storages, shelves) and mechanisms for ordering products is usually not taken into account. As a consequence, storage times-mutually dependent in successive steps in the chain-cannot be described adequately. This may have a great impact on the tails of risk distributions. Because food safety risks are generally very small, it is crucial to model the tails of (underlying) distributions as accurately as possible. Logistic performance can be modeled by describing the underlying planning and scheduling mechanisms in discrete-event modeling. This is common practice in operations research, specifically in supply chain management. In this article, we present the application of discrete-event modeling in the context of a QMRA for Listeria monocytogenes in fresh-cut iceberg lettuce. We show the potential value of discrete-event modeling in QMRA by calculating logistic interventions (modifications in the logistic chain) and determining their significance with respect to food safety.

Closed loop supply chain network design with fuzzy tactical decisions

NASA Astrophysics Data System (ADS)

Sherafati, Mahtab; Bashiri, Mahdi

2016-09-01

One of the most strategic and the most significant decisions in supply chain management is reconfiguration of the structure and design of the supply chain network. In this paper, a closed loop supply chain network design model is presented to select the best tactical and strategic decision levels simultaneously considering the appropriate transportation mode in activated links. The strategic decisions are made for a long term; thus, it is more satisfactory and more appropriate when the decision variables are considered uncertain and fuzzy, because it is more flexible and near to the real world. This paper is the first research which considers fuzzy decision variables in the supply chain network design model. Moreover, in this study a new fuzzy optimization approach is proposed to solve a supply chain network design problem with fuzzy tactical decision variables. Finally, the proposed approach and model are verified using several numerical examples. The comparison of the results with other existing approaches confirms efficiency of the proposed approach. Moreover the results confirms that by considering the vagueness of tactical decisions some properties of the supply chain network will be improved.

Rouse mode analysis of chain relaxation in homopolymer melts

DOE PAGES

Kalathi, Jagannathan T.; Kumar, Sanat K.; Rubinstein, Michael; ...

2014-09-15

We use molecular dynamics simulations of the Kremer–Grest (KG) bead–spring model of polymer chains of length between 10 and 500, and a closely related analogue that allows for chain crossing, to clearly delineate the effects of entanglements on the length-scale-dependent chain relaxation in polymer melts. We analyze the resulting trajectories using the Rouse modes of the chains and find that entanglements strongly affect these modes. The relaxation rates of the chains show two limiting effective monomeric frictions, with the local modes experiencing much lower effective friction than the longer modes. The monomeric relaxation rates of longer modes vary approximately inverselymore » with chain length due to kinetic confinement effects. The time-dependent relaxation of Rouse modes has a stretched exponential character with a minimum of stretching exponent in the vicinity of the entanglement chain length. None of these trends are found in models that allow for chain crossing. As a result, these facts, in combination, argue for the confined motion of chains for time scales between the entanglement time and their ultimate free diffusion.« less

Nonmetallic electronegativity equalization and point-dipole interaction model including exchange interactions for molecular dipole moments and polarizabilities.

PubMed

Smalø, Hans S; Astrand, Per-Olof; Jensen, Lasse

2009-07-28

The electronegativity equalization model (EEM) has been combined with a point-dipole interaction model to obtain a molecular mechanics model consisting of atomic charges, atomic dipole moments, and two-atom relay tensors to describe molecular dipole moments and molecular dipole-dipole polarizabilities. The EEM has been phrased as an atom-atom charge-transfer model allowing for a modification of the charge-transfer terms to avoid that the polarizability approaches infinity for two particles at infinite distance and for long chains. In the present work, these shortcomings have been resolved by adding an energy term for transporting charges through individual atoms. A Gaussian distribution is adopted for the atomic charge distributions, resulting in a damping of the electrostatic interactions at short distances. Assuming that an interatomic exchange term may be described as the overlap between two electronic charge distributions, the EEM has also been extended by a short-range exchange term. The result is a molecular mechanics model where the difference of charge transfer in insulating and metallic systems is modeled regarding the difference in bond length between different types of system. For example, the model is capable of modeling charge transfer in both alkanes and alkenes with alternating double bonds with the same set of carbon parameters only relying on the difference in bond length between carbon sigma- and pi-bonds. Analytical results have been obtained for the polarizability of a long linear chain. These results show that the model is capable of describing the polarizability scaling both linearly and nonlinearly with the size of the system. Similarly, a linear chain with an end atom with a high electronegativity has been analyzed analytically. The dipole moment of this model system can either be independent of the length or increase linearly with the length of the chain. In addition, the model has been parametrized for alkane and alkene chains with data from density functional theory calculations, where the polarizability behaves differently with the chain length. For the molecular dipole moment, the same two systems have been studied with an aldehyde end group. Both the molecular polarizability and the dipole moment are well described as a function of the chain length for both alkane and alkene chains demonstrating the power of the presented model.

Evolutionary Game Model Study of Construction Green Supply Chain Management under the Government Intervention

NASA Astrophysics Data System (ADS)

Xing, Yuanzhi; Deng, Xiaoyi

2017-11-01

The paper first has defined the concepts of green supply chain management and evolution game theory, and pointed out the characteristics of green supply chain management in construction. The main participants and key links of the construction green supply chain management are determined by constructing the organization framework. This paper established the evolutionary game model between construction enterprises and recycling enterprises for the green supply chain closed-loop structure. The waste recycling evolutionary stability equilibrium solution is obtained to explore the principle and effective scope of government policy intervention. This paper put forward the relevant countermeasures to the green supply chain management in construction recycling stage from the government point of view. The conclusion has reference value and guidance to the final product construction enterprises, recycling enterprises and the government during green supply chain.

Scale-Dependent Stiffness and Internal Tension of a Model Brush Polymer

NASA Astrophysics Data System (ADS)

Berezney, John P.; Marciel, Amanda B.; Schroeder, Charles M.; Saleh, Omar A.

2017-09-01

Bottle-brush polymers exhibit closely grafted side chains that interact by steric repulsion, thereby causing stiffening of the main polymer chain. We use single-molecule elasticity measurements of model brush polymers to quantify this effect. We find that stiffening is only significant on long length scales, with the main chain retaining flexibility on short scales. From the elasticity data, we extract an estimate of the internal tension generated by side-chain repulsion; this estimate is consistent with the predictions of blob-based scaling theories.

Biodiversity on island chains: Neutral model simulations

NASA Astrophysics Data System (ADS)

Warren, Patrick B.

2010-11-01

A neutral ecology model is simulated on an island chain, in which neighboring islands can exchange individuals but only the first island is able to receive immigrants from a metacommunity. It is found by several measures that α -diversity decreases along the chain. Subtle changes in taxon abundance distributions can be detected when islands in the chain are compared to diversity-matched single islands. The island chain is found to have unexpectedly rich dynamics. Significant β -diversity correlations are found between islands in the chain, which are absent between diversity-matched single islands. The results potentially apply to human microbial biodiversity and biogeography and suggest that measurements of interindividual and intraindividual β -diversity may give insights into microbial community assembly mechanisms.

Simplification of irreversible Markov chains by removal of states with fast leaving rates.

PubMed

Jia, Chen

2016-07-07

In the recent work of Ullah et al. (2012a), the authors developed an effective method to simplify reversible Markov chains by removal of states with low equilibrium occupancies. In this paper, we extend this result to irreversible Markov chains. We show that an irreversible chain can be simplified by removal of states with fast leaving rates. Moreover, we reveal that the irreversibility of the chain will always decrease after model simplification. This suggests that although model simplification can retain almost all the dynamic information of the chain, it will lose some thermodynamic information as a trade-off. Examples from biology are also given to illustrate the main results of this paper. Copyright © 2016 Elsevier Ltd. All rights reserved.

An Interval Type-2 Fuzzy Multiple Echelon Supply Chain Model

NASA Astrophysics Data System (ADS)

Miller, Simon; John, Robert

Planning resources for a supply chain is a major factor determining its success or failure. In this paper we build on previous work introducing an Interval Type-2 Fuzzy Logic model of a multiple echelon supply chain. It is believed that the additional degree of uncertainty provided by Interval Type-2 Fuzzy Logic will allow for better representation of the uncertainty and vagueness present in resource planning models. First, the subject of Supply Chain Management is introduced, then some background is given on related work using Type-1 Fuzzy Logic. A description of the Interval Type-2 Fuzzy model is given, and a test scenario detailed. A Genetic Algorithm uses the model to search for a near-optimal plan for the scenario. A discussion of the results follows, along with conclusions and details of intended further work.

78 FR 24368 - Airworthiness Directives; Bell Helicopter Textron, Inc. (Bell) Model Helicopters

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-25

... chain and cable control system with a push-pull control system. Since we issued that AD, we have... requires replacing the existing chain and cable control system with a push-pull control system. Both... Model 205A-1 to replace the tail rotor chain and cable control system with a push-pull control system...

Peppytides: Interactive Models of Polypeptide Chains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zuckermann, Ron; Chakraborty, Promita; Derisi, Joe

2014-01-21

Peppytides are scaled, 3D-printed models of polypeptide chains that can be folded into accurate protein structures. Designed and created by Berkeley Lab Researcher, Promita Chakraborty, and Berkeley Lab Senior Scientist, Dr. Ron Zuckermann, Peppytides are accurate physical models of polypeptide chains that anyone can interact with and fold intro various protein structures - proving to be a great educational tool, resulting in a deeper understanding of these fascinating structures and how they function. Build your own Peppytide model and learn about how nature's machines fold into their intricate architectures!

Peppytides: Interactive Models of Polypeptide Chains

ScienceCinema

Zuckermann, Ron; Chakraborty, Promita; Derisi, Joe

2018-06-08

Peppytides are scaled, 3D-printed models of polypeptide chains that can be folded into accurate protein structures. Designed and created by Berkeley Lab Researcher, Promita Chakraborty, and Berkeley Lab Senior Scientist, Dr. Ron Zuckermann, Peppytides are accurate physical models of polypeptide chains that anyone can interact with and fold intro various protein structures - proving to be a great educational tool, resulting in a deeper understanding of these fascinating structures and how they function. Build your own Peppytide model and learn about how nature's machines fold into their intricate architectures!

Survival condition for low-frequency quasi-one-dimensional breathers in a two-dimensional strongly anisotropic crystal

NASA Astrophysics Data System (ADS)

Savin, A. V.; Zubova, E. A.; Manevitch, L. I.

2005-06-01

We investigate a two-dimensional (2D) strongly anisotropic crystal (2D SAC) on substrate: 2D system of coupled linear chains of particles with strong intrachain and weak interchain interactions, each chain being subjected to the sine background potential. Nonlinear dynamics of one of these chains when the rest of them are fixed is reduced to the well known Frenkel-Kontorova (FK) model. Depending on strengh of the substrate, the 2D SAC models a variety of physical systems: polymer crystals with identical chains having light side groups, an array of inductively coupled long Josephson junctions, anisotropic crystals having light and heavy sublattices. Continuum limit of the FK model, the sine-Gordon (sG) equation, allows two types of soliton solutions: topological solitons and breathers. It is known that the quasi-one-dimensional topological solitons can propagate also in a chain of 2D system of coupled chains and even in a helix chain in a three-dimensional model of polymer crystal. In contrast to this, numerical simulation shows that the long-living breathers inherent to the FK model do not exist in the 2D SAC with weak background potential. The effect changes scenario of kink-antikink collision with small relative velocity: at weak background potential the collision always results only in intensive phonon radiation while kink-antikink recombination in the FK model results in long-living low-frequency sG breather creation. We found the survival condition for breathers in the 2D SAC on substrate depending on breather frequency and strength of the background potential. The survival condition bears no relation to resonances between breather frequency and frequencies of phonon band—contrary to the case of the FK model.

Peroxy radical detection by chemical amplification (PERCA)

NASA Technical Reports Server (NTRS)

Stedman, D. H.

1986-01-01

Important reactions of atmospheric free radicals are the chain oxidation of NO and CO. Thus: H2O + NO yields OH + NO2; OH + CO yields H + CO2; H + O2 + M yields HO2 + M. In most models, the need to know the free radical concentration could also be described as the need to know the rate of the above oxidation chain in the atmosphere. It is the total rate of this chain (also carried by RO2 and RO) which was measured using the PERCA. The PERCA is thus essentially a RO sub X meter. The PERCA works by adding excess CO (10%) and NO (5ppm) to a stream of air and measuring the NO2 produced after 3s of reaction time. Since other processes produce NO2, the chain reaction is modulated by switching the CO for N2. The chain length is limited by the reaction OH + NO yields HONO and is modeled to be somewhat over 1000. Measured chain lengths agree with the modeled numbers.

Orientation of chain molecules in ionotropic gels: a Brownian dynamics model

NASA Astrophysics Data System (ADS)

Woelki, Stefan; Kohler, Hans-Helmut

2003-09-01

As is known from birefringence measurements, polysaccharide molecules of ionotropic gels are preferentially orientated normal to the direction of gel growth. In this paper the orientation effect is investigated by means of an off-lattice Brownian dynamics model simulating the gel formation process. The model describes the integration of a single coarse grained phantom chain into the growing gel. The equations of motion of the chain are derived. The computer simulations show that, during the process of integration, the chain is contracting normal to the direction of gel growth. A scaling relation is obtained for the degree of contraction as a function of the length parameters of the chain, the velocity of the gel formation front and the rate constant of the crosslinking reaction. It is shown that the scaling relation, if applied to the example of ionotropic copper alginate gel, leads to reasonable predictions of the time course of the degree of contraction of the alginate chains.

Assessment of Protein Side-Chain Conformation Prediction Methods in Different Residue Environments

PubMed Central

Peterson, Lenna X.; Kang, Xuejiao; Kihara, Daisuke

2016-01-01

Computational prediction of side-chain conformation is an important component of protein structure prediction. Accurate side-chain prediction is crucial for practical applications of protein structure models that need atomic detailed resolution such as protein and ligand design. We evaluated the accuracy of eight side-chain prediction methods in reproducing the side-chain conformations of experimentally solved structures deposited to the Protein Data Bank. Prediction accuracy was evaluated for a total of four different structural environments (buried, surface, interface, and membrane-spanning) in three different protein types (monomeric, multimeric, and membrane). Overall, the highest accuracy was observed for buried residues in monomeric and multimeric proteins. Notably, side-chains at protein interfaces and membrane-spanning regions were better predicted than surface residues even though the methods did not all use multimeric and membrane proteins for training. Thus, we conclude that the current methods are as practically useful for modeling protein docking interfaces and membrane-spanning regions as for modeling monomers. PMID:24619909

SCRL-Model for Human Space Flight Operations Enterprise Supply Chain

NASA Technical Reports Server (NTRS)

Tucker, Brian; Paxton, Joseph

2010-01-01

This paper will present a Supply Chain Readiness Level (SCRL) model that can be used to evaluate and configure adaptable and sustainable program and mission supply chains at an enterprise level. It will also show that using SCRL in conjunction with Technology Readiness Levels (TRLs), Manufacturing Readiness Levels (MRLs) and National Aeronautics Space Administrations (NASA s) Project Lifecycle Process will provide a more complete means of developing and evaluating a robust sustainable supply chain that encompasses the entire product, system and mission lifecycle. In addition, it will be shown that by implementing the SCRL model, NASA can additionally define supplier requirements to enable effective supply chain management (SCM). Developing and evaluating overall supply chain readiness for any product, system and mission lifecycle is critical for mission success. Readiness levels are presently being used to evaluate the maturity of technology and manufacturing capability during development and deployment phases of products and systems. For example, TRLs are used to support the assessment of the maturity of a particular technology and compare maturity of different types of technologies. MRLs are designed to assess the maturity and risk of a given technology from a manufacturing perspective. In addition, when these measurement systems are used collectively they can offer a more comprehensive view of the maturity of the system. While some aspects of the supply chain and supply chain planning are considered in these familiar metric systems, certain characteristics of an effective supply chain, when evaluated in more detail, will provide an improved insight into the readiness and risk throughout the supply chain. Therefore, a system that concentrates particularly on supply chain attributes is required to better assess enterprise supply chain readiness.

An investigation into UV light exposure as an experimental model for artificial aging on tensile strength and force delivery of elastomeric chain.

PubMed

Wahab, Siti Waznah; Bister, Dirk; Sherriff, Martyn

2014-02-01

This study investigated the effect of ultraviolet type A light (UVA) exposure on the tensile properties of elastomeric chain. UVA light exposure was used as model for artificial aging, simulating prolonged storage of elastomeric chain. Tensile strength (n = 60) was measured after exposing Ormco, Forestadent and 3M chains to UVA light for 0, 2, 3, and 4 weeks. Force decay was measured (n = 60) using chain exposed for 5, 10, and 14 days. The chains were subsequently stretched at a constant distance and the resulting forces measured at 0, 1, 24 hours and 7, 14, 21, and 28 days. This test simulated a clinical scenario of pre-stretching and subsequent shortening of elastomeric chain. Tensile strength had statistically significant difference and was directly related to the duration of ultraviolet (UV) light exposure. Forestadent chain, which had the second highest value for the 'as received' product, showed the most consistent values over time with the lowest degradation. Ormco showed the lowest values for 'as received' as well as after UV exposure; 3M chain had the highest loss of tensile strength. Force decay was also significantly different. UV light exposure of 10 days or more appears to mark a 'watershed' between products: 3M had most survivors, Forestadent chain had some survivors, depending on the time the chain was stretched for. None of the Ormco product survived UV light exposure for more than 5 days. UVA light exposure may be used as a model for artificial aging as it reduces force delivery and tensile strength of exposed chains.

Effect of counterion binding efficiency on structure and dynamics of wormlike micelles.

PubMed

Oelschlaeger, C; Suwita, P; Willenbacher, N

2010-05-18

We have studied the effect of counterion binding efficiency on the linear viscoelastic properties of wormlike micelles formed from hexadecyltrimethylammonium bromide (CTAB) in the presence of different nonpenetrating inorganic salts: potassium bromide (KBr), sodium nitrate (NaNO(3)), and sodium chlorate (NaClO(3)). We have varied the salt/surfactant ratio R at fixed surfactant concentration of 350 mM. Results are compared to data for the system cetylpyridinium chloride (CPyCl) and the penetrating counterion sodium salicylate (NaSal) (Oelschlaeger, C.; Schopferer, M.; Scheffold, F.; Willenbacher, N. Langmuir 2009, 25, 716-723). Mechanical high-frequency rheology and diffusing wave spectroscopy (DWS) based tracer microrheology are used to determine the shear moduli G' and G'' in the frequency range from 0.1 Hz up to 1 MHz (Willenbacher, N.; Oelschlaeger, C.; Schopferer, M.; Fischer, P.; Cardinaux, F.; Scheffold, F. Phys. Rev. Lett. 2007, 99, 068302, 1-4). This enables us to determine the plateau modulus G(0), which is related to the cross-link density or mesh size of the entanglement network, the bending stiffness kappa (also expressed as persistence length l(p) = kappa/k(B)T) corresponding to the semiflexible nature of the micelles, and the scission energy E(sciss), which is related to their contour length. The viscosity maximum shifts to higher R values, and the variation of viscosity with R is less pronounced as the binding strength decreases. The plateau modulus increases with R at low ionic strength and is constant around the viscosity maximum; the increase in G(0) at high R, which is presumably due to branching, is weak compared to the system with penetrating counterion. The scission energy E(sciss) approximately = 20 k(B)T is independent of counterion binding efficiency irrespective of R and is slightly higher compared to the system CPyCl/NaSal, indicating that branching may be significant already at the viscosity maximum in this latter case. The micellar flexibility increases with increasing binding efficiency of counterions according to the Hofmeister series. The persistence length values for systems CTAB/KBr, CTAB/NaNO(3), and CTAB/NaClO(3) are 40, 34, and 29 nm, respectively, independent of R, and are significantly higher than in the case of CPyCl/NaSal.

Conditional solvation thermodynamics of isoleucine in model peptides and the limitations of the group-transfer model.

PubMed

Tomar, Dheeraj S; Weber, Valéry; Pettitt, B Montgomery; Asthagiri, D

2014-04-17

The hydration thermodynamics of the amino acid X relative to the reference G (glycine) or the hydration thermodynamics of a small-molecule analog of the side chain of X is often used to model the contribution of X to protein stability and solution thermodynamics. We consider the reasons for successes and limitations of this approach by calculating and comparing the conditional excess free energy, enthalpy, and entropy of hydration of the isoleucine side chain in zwitterionic isoleucine, in extended penta-peptides, and in helical deca-peptides. Butane in gauche conformation serves as a small-molecule analog for the isoleucine side chain. Parsing the hydrophobic and hydrophilic contributions to hydration for the side chain shows that both of these aspects of hydration are context-sensitive. Furthermore, analyzing the solute-solvent interaction contribution to the conditional excess enthalpy of the side chain shows that what is nominally considered a property of the side chain includes entirely nonobvious contributions of the background. The context-sensitivity of hydrophobic and hydrophilic hydration and the conflation of background contributions with energetics attributed to the side chain limit the ability of a single scaling factor, such as the fractional solvent exposure of the group in the protein, to map the component energetic contributions of the model-compound data to their value in the protein. But ignoring the origin of cancellations in the underlying components the group-transfer model may appear to provide a reasonable estimate of the free energy for a given error tolerance.

Selective and directional actuation of elastomer films using chained magnetic nanoparticles

NASA Astrophysics Data System (ADS)

Mishra, Sumeet R.; Dickey, Michael D.; Velev, Orlin D.; Tracy, Joseph B.

2016-01-01

We report selective and directional actuation of elastomer films utilizing magnetic anisotropy introduced by chains of Fe3O4 magnetic nanoparticles (MNPs). Under uniform magnetic fields or field gradients, dipolar interactions between the MNPs favor magnetization along the chain direction and cause selective lifting. This mechanism is described using a simple model.We report selective and directional actuation of elastomer films utilizing magnetic anisotropy introduced by chains of Fe3O4 magnetic nanoparticles (MNPs). Under uniform magnetic fields or field gradients, dipolar interactions between the MNPs favor magnetization along the chain direction and cause selective lifting. This mechanism is described using a simple model. Electronic supplementary information (ESI) available: Two videos for actuation while rotating the sample, experimental details of nanoparticle synthesis, polymer composite preparation, and alignment and bending studies, details of the theoretical model of actuation, and supplemental figures for understanding the behavior of rotating samples and results from modelling. See DOI: 10.1039/c5nr07410j

Directed Bak-Sneppen Model for Food Chains

NASA Astrophysics Data System (ADS)

Stauffer, D.; Jan, N.

A modification of the Bak-Sneppen model to include simple elements of Darwinian evolution is used to check the survival of prey and predators in long food chains. Mutations, selection, and starvation resulting from depleted prey are incorporated in this model.

Residue-Specific Side-Chain Polymorphisms via Particle Belief Propagation.

PubMed

Ghoraie, Laleh Soltan; Burkowski, Forbes; Li, Shuai Cheng; Zhu, Mu

2014-01-01

Protein side chains populate diverse conformational ensembles in crystals. Despite much evidence that there is widespread conformational polymorphism in protein side chains, most of the X-ray crystallography data are modeled by single conformations in the Protein Data Bank. The ability to extract or to predict these conformational polymorphisms is of crucial importance, as it facilitates deeper understanding of protein dynamics and functionality. In this paper, we describe a computational strategy capable of predicting side-chain polymorphisms. Our approach extends a particular class of algorithms for side-chain prediction by modeling the side-chain dihedral angles more appropriately as continuous rather than discrete variables. Employing a new inferential technique known as particle belief propagation, we predict residue-specific distributions that encode information about side-chain polymorphisms. Our predicted polymorphisms are in relatively close agreement with results from a state-of-the-art approach based on X-ray crystallography data, which characterizes the conformational polymorphisms of side chains using electron density information, and has successfully discovered previously unmodeled conformations.

Side-chain mobility in the folded state of Myoglobin

NASA Astrophysics Data System (ADS)

Lammert, Heiko; Onuchic, Jose

We study the accessibility of alternative side-chain rotamer configurations in the native state of Myoglobin, using an all-atom structure-based model. From long, unbiased simulation trajectories we determine occupancies of rotameric states and also estimate configurational and vibrational entropies. Direct sampling of the full native-state dynamics, enabled by the simple model, reveals facilitation of side-chain motions by backbone dynamics. Correlations between different dihedral angles are quantified and prove to be weak. We confirm global trends in the mobilities of side-chains, following burial and also the chemical character of residues. Surface residues loose little configurational entropy upon folding; side-chains contribute significantly to the entropy of the folded state. Mobilities of buried side-chains vary strongly with temperature. At ambient temperature, individual side-chains in the core of the protein gain substantial access to alternative rotamers, with occupancies that are likely observable experimentally. Finally, the dynamics of buried side-chains may be linked to the internal pockets, available to ligand gas molecules in Myoglobin.

Modeling and Implementation of Cattle/Beef Supply Chain Traceability Using a Distributed RFID-Based Framework in China.

PubMed

Liang, Wanjie; Cao, Jing; Fan, Yan; Zhu, Kefeng; Dai, Qiwei

2015-01-01

In recent years, traceability systems have been developed as effective tools for improving the transparency of supply chains, thereby guaranteeing the quality and safety of food products. In this study, we proposed a cattle/beef supply chain traceability model and a traceability system based on radio frequency identification (RFID) technology and the EPCglobal network. First of all, the transformations of traceability units were defined and analyzed throughout the cattle/beef chain. Secondly, we described the internal and external traceability information acquisition, transformation, and transmission processes throughout the beef supply chain in detail, and explained a methodology for modeling traceability information using the electronic product code information service (EPCIS) framework. Then, the traceability system was implemented based on Fosstrak and FreePastry software packages, and animal ear tag code and electronic product code (EPC) were employed to identify traceability units. Finally, a cattle/beef supply chain included breeding business, slaughter and processing business, distribution business and sales outlet was used as a case study to evaluate the beef supply chain traceability system. The results demonstrated that the major advantages of the traceability system are the effective sharing of information among business and the gapless traceability of the cattle/beef supply chain.

Modeling and Implementation of Cattle/Beef Supply Chain Traceability Using a Distributed RFID-Based Framework in China

PubMed Central

Liang, Wanjie; Cao, Jing; Fan, Yan; Zhu, Kefeng; Dai, Qiwei

2015-01-01

In recent years, traceability systems have been developed as effective tools for improving the transparency of supply chains, thereby guaranteeing the quality and safety of food products. In this study, we proposed a cattle/beef supply chain traceability model and a traceability system based on radio frequency identification (RFID) technology and the EPCglobal network. First of all, the transformations of traceability units were defined and analyzed throughout the cattle/beef chain. Secondly, we described the internal and external traceability information acquisition, transformation, and transmission processes throughout the beef supply chain in detail, and explained a methodology for modeling traceability information using the electronic product code information service (EPCIS) framework. Then, the traceability system was implemented based on Fosstrak and FreePastry software packages, and animal ear tag code and electronic product code (EPC) were employed to identify traceability units. Finally, a cattle/beef supply chain included breeding business, slaughter and processing business, distribution business and sales outlet was used as a case study to evaluate the beef supply chain traceability system. The results demonstrated that the major advantages of the traceability system are the effective sharing of information among business and the gapless traceability of the cattle/beef supply chain. PMID:26431340

Falling Chains as Variable-Mass Systems: Theoretical Model and Experimental Analysis

ERIC Educational Resources Information Center

de Sousa, Celia A.; Gordo, Paulo M.; Costa, Pedro

2012-01-01

In this paper, we revisit, theoretically and experimentally, the fall of a folded U-chain and of a pile-chain. The model calculation implies the division of the whole system into two subsystems of variable mass, allowing us to explore the role of tensional contact forces at the boundary of the subsystems. This justifies, for instance, that the…

Simulation modelling of central order processing system under resource sharing strategy in demand-driven garment supply chains

NASA Astrophysics Data System (ADS)

Ma, K.; Thomassey, S.; Zeng, X.

2017-10-01

In this paper we proposed a central order processing system under resource sharing strategy for demand-driven garment supply chains to increase supply chain performances. We examined this system by using simulation technology. Simulation results showed that significant improvement in various performance indicators was obtained in new collaborative model with proposed system.

Modelisation de l'historique d'operation de groupes turbine-alternateur

NASA Astrophysics Data System (ADS)

Szczota, Mickael

Because of their ageing fleet, the utility managers are increasingly in needs of tools that can help them to plan efficiently maintenance operations. Hydro-Quebec started a project that aim to foresee the degradation of their hydroelectric runner, and use that information to classify the generating unit. That classification will help to know which generating unit is more at risk to undergo a major failure. Cracks linked to the fatigue phenomenon are a predominant degradation mode and the loading sequences applied to the runner is a parameter impacting the crack growth. So, the aim of this memoir is to create a generator able to generate synthetic loading sequences that are statistically equivalent to the observed history. Those simulated sequences will be used as input in a life assessment model. At first, we describe how the generating units are operated by Hydro-Quebec and analyse the available data, the analysis shows that the data are non-stationnary. Then, we review modelisation and validation methods. In the following chapter a particular attention is given to a precise description of the validation and comparison procedure. Then, we present the comparison of three kind of model : Discrete Time Markov Chains, Discrete Time Semi-Markov Chains and the Moving Block Bootstrap. For the first two models, we describe how to take account for the non-stationnarity. Finally, we show that the Markov Chain is not adapted for our case, and that the Semi-Markov chains are better when they include the non-stationnarity. The final choice between Semi-Markov Chains and the Moving Block Bootstrap depends of the user. But, with a long term vision we recommend the use of Semi-Markov chains for their flexibility. Keywords: Stochastic models, Models validation, Reliability, Semi-Markov Chains, Markov Chains, Bootstrap

Unique aspects of the structure and dynamics of elementary Iβ cellulose microfibrils revealed by computational simulations.

PubMed

Oehme, Daniel P; Downton, Matthew T; Doblin, Monika S; Wagner, John; Gidley, Michael J; Bacic, Antony

2015-05-01

The question of how many chains an elementary cellulose microfibril contains is critical to understanding the molecular mechanism(s) of cellulose biosynthesis and regulation. Given the hexagonal nature of the cellulose synthase rosette, it is assumed that the number of chains must be a multiple of six. We present molecular dynamics simulations on three different models of Iβ cellulose microfibrils, 18, 24, and 36 chains, to investigate their structure and dynamics in a hydrated environment. The 36-chain model stays in a conformational space that is very similar to the initial crystalline phase, while the 18- and 24-chain models sample a conformational space different from the crystalline structure yet similar to conformations observed in recent high-temperature molecular dynamics simulations. Major differences in the conformations sampled between the different models result from changes to the tilt of chains in different layers, specifically a second stage of tilt, increased rotation about the O2-C2 dihedral, and a greater sampling of non-TG exocyclic conformations, particularly the GG conformation in center layers and GT conformation in solvent-exposed exocyclic groups. With a reinterpretation of nuclear magnetic resonance data, specifically for contributions made to the C6 peak, data from the simulations suggest that the 18- and 24-chain structures are more viable models for an elementary cellulose microfibril, which also correlates with recent scattering and diffraction experimental data. These data inform biochemical and molecular studies that must explain how a six-particle cellulose synthase complex rosette synthesizes microfibrils likely comprised of either 18 or 24 chains. © 2015 American Society of Plant Biologists. All Rights Reserved.

A Framework of Multi Objectives Negotiation for Dynamic Supply Chain Model

NASA Astrophysics Data System (ADS)

Chai, Jia Yee; Sakaguchi, Tatsuhiko; Shirase, Keiichi

Trends of globalization and advances in Information Technology (IT) have created opportunity in collaborative manufacturing across national borders. A dynamic supply chain utilizes these advances to enable more flexibility in business cooperation. This research proposes a concurrent decision making framework for a three echelons dynamic supply chain model. The dynamic supply chain is formed by autonomous negotiation among agents based on multi agents approach. Instead of generating negotiation aspects (such as amount, price and due date) arbitrary, this framework proposes to utilize the information available at operational level of an organization in order to generate realistic negotiation aspect. The effectiveness of the proposed model is demonstrated by various case studies.

Thermodynamic limit and boundary energy of the su(3) spin chain with non-diagonal boundary fields

NASA Astrophysics Data System (ADS)

Wen, Fakai; Yang, Tao; Yang, Zhanying; Cao, Junpeng; Hao, Kun; Yang, Wen-Li

2017-02-01

We investigate the thermodynamic limit of the su (n)-invariant spin chain models with unparallel boundary fields. It is found that the contribution of the inhomogeneous term in the associated T-Q relation to the ground state energy does vanish in the thermodynamic limit. This fact allows us to calculate the boundary energy of the system. Taking the su (2) (or the XXX) spin chain and the su (3) spin chain as concrete examples, we have studied the corresponding boundary energies of the models. The method used in this paper can be generalized to study the thermodynamic properties and boundary energy of other high rank models with non-diagonal boundary fields.

SAChES: Scalable Adaptive Chain-Ensemble Sampling.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swiler, Laura Painton; Ray, Jaideep; Ebeida, Mohamed Salah

We present the development of a parallel Markov Chain Monte Carlo (MCMC) method called SAChES, Scalable Adaptive Chain-Ensemble Sampling. This capability is targed to Bayesian calibration of com- putationally expensive simulation models. SAChES involves a hybrid of two methods: Differential Evo- lution Monte Carlo followed by Adaptive Metropolis. Both methods involve parallel chains. Differential evolution allows one to explore high-dimensional parameter spaces using loosely coupled (i.e., largely asynchronous) chains. Loose coupling allows the use of large chain ensembles, with far more chains than the number of parameters to explore. This reduces per-chain sampling burden, enables high-dimensional inversions and the usemore » of computationally expensive forward models. The large number of chains can also ameliorate the impact of silent-errors, which may affect only a few chains. The chain ensemble can also be sampled to provide an initial condition when an aberrant chain is re-spawned. Adaptive Metropolis takes the best points from the differential evolution and efficiently hones in on the poste- rior density. The multitude of chains in SAChES is leveraged to (1) enable efficient exploration of the parameter space; and (2) ensure robustness to silent errors which may be unavoidable in extreme-scale computational platforms of the future. This report outlines SAChES, describes four papers that are the result of the project, and discusses some additional results.« less

Designing Performance Measurement For Supply Chain's Actors And Regulator Using Scale Balanced Scorecard And Data Envelopment Analysis

NASA Astrophysics Data System (ADS)

Kusrini, Elisa; Subagyo; Aini Masruroh, Nur

2016-01-01

This research is a sequel of the author's earlier conducted researches in the fields of designing of integrated performance measurement between supply chain's actors and regulator. In the previous paper, the design of performance measurement is done by combining Balanced Scorecard - Supply Chain Operation Reference - Regulator Contribution model and Data Envelopment Analysis. This model referred as B-S-Rc-DEA model. The combination has the disadvantage that all the performance variables have the same weight. This paper investigates whether by giving weight to performance variables will produce more sensitive performance measurement in detecting performance improvement. Therefore, this paper discusses the development of the model B-S-Rc-DEA by giving weight to its performance'variables. This model referred as Scale B-S-Rc-DEA model. To illustrate the model of development, some samples from small medium enterprises of leather craft industry supply chain in province of Yogyakarta, Indonesia are used in this research. It is found that Scale B-S-Rc-DEA model is more sensitive to detecting performance improvement than B-S- Rc-DEA model.

Molecular weight kinetics and chain scission models for dextran polymers during ultrasonic degradation.

PubMed

Pu, Yuanyuan; Zou, Qingsong; Hou, Dianzhi; Zhang, Yiping; Chen, Shan

2017-01-20

Ultrasonic degradation of six dextran samples with different initial molecular weights (IMW) has been performed to investigate the degradation behavior and chain scission mechanism of dextrans. The weight-average molecular weight (Mw) and polydispersity index (D value) were monitored by High Performance Gel Permeation Chromatography (HPGPC). Results showed that Mw and D value decreased with increasing ultrasonic time, resulting in a more homologous dextran solution with lower molecular weight. A significant degradation occurred in dextrans with higher IMW, particularly at the initial stage of the ultrasonic treatment. The Malhotra model was found to well describe the molecular weight kinetics for all dextran samples. Experimental data was fitted into two chain scission models to study dextran chain scission mechanism and the model performance was compared. Results indicated that the midpoint scission model agreed well with experimental results, with a linear regression factor of R 2 >0.99. Copyright © 2016 Elsevier Ltd. All rights reserved.

Protein structure modeling for CASP10 by multiple layers of global optimization.

PubMed

Joo, Keehyoung; Lee, Juyong; Sim, Sangjin; Lee, Sun Young; Lee, Kiho; Heo, Seungryong; Lee, In-Ho; Lee, Sung Jong; Lee, Jooyoung

2014-02-01

In the template-based modeling (TBM) category of CASP10 experiment, we introduced a new protocol called protein modeling system (PMS) to generate accurate protein structures in terms of side-chains as well as backbone trace. In the new protocol, a global optimization algorithm, called conformational space annealing (CSA), is applied to the three layers of TBM procedure: multiple sequence-structure alignment, 3D chain building, and side-chain re-modeling. For 3D chain building, we developed a new energy function which includes new distance restraint terms of Lorentzian type (derived from multiple templates), and new energy terms that combine (physical) energy terms such as dynamic fragment assembly (DFA) energy, DFIRE statistical potential energy, hydrogen bonding term, etc. These physical energy terms are expected to guide the structure modeling especially for loop regions where no template structures are available. In addition, we developed a new quality assessment method based on random forest machine learning algorithm to screen templates, multiple alignments, and final models. For TBM targets of CASP10, we find that, due to the combination of three stages of CSA global optimizations and quality assessment, the modeling accuracy of PMS improves at each additional stage of the protocol. It is especially noteworthy that the side-chains of the final PMS models are far more accurate than the models in the intermediate steps. Copyright © 2013 Wiley Periodicals, Inc.

Event-chain algorithm for the Heisenberg model: Evidence for z≃1 dynamic scaling.

PubMed

Nishikawa, Yoshihiko; Michel, Manon; Krauth, Werner; Hukushima, Koji

2015-12-01

We apply the event-chain Monte Carlo algorithm to the three-dimensional ferromagnetic Heisenberg model. The algorithm is rejection-free and also realizes an irreversible Markov chain that satisfies global balance. The autocorrelation functions of the magnetic susceptibility and the energy indicate a dynamical critical exponent z≈1 at the critical temperature, while that of the magnetization does not measure the performance of the algorithm. We show that the event-chain Monte Carlo algorithm substantially reduces the dynamical critical exponent from the conventional value of z≃2.

Distribution Free Approach for Coordination of a Supply Chain with Consumer Return

NASA Astrophysics Data System (ADS)

Hu, Jinsong; Xu, Yuanji

Consumer return is considered in a coordination of a supply chain consisting of one manufacturer and one retailer. A distribution free approach is employed to deal with a centralized decision model and a decentralized model which are constructed under the situation with only knowing the demand function's mean and variance, respectively. A markdown money contract is designed to coordinate the supply chain, and it is also proved that the contract can make the supply chain perfectly coordinated. Several numerical examples are given at the end of this paper.

Single-chain behavior of poly(3-hexylthiophene)

NASA Astrophysics Data System (ADS)

Ivanov, Momchil; Gross, Jonathan; Janke, Wolfhard

2017-03-01

Poly(3-hexylthiophene) (P3HT) has been in the focus of recent studies due to its promising future use in organic photovoltaics, electronics and photonics. Recent publications investigate the melt behavior of P3HT, its interaction with other molecules, mainly various fullerene derivates, and isolated chains interacting with substrates. In this work we lay the focus on the single-chain properties of P3HT in vacuum. We compare structural properties obtained from simulations using two coarse-grained models and an atomistic model of the polymer for various chain lengths and temperatures.

Enhancement of Markov chain model by integrating exponential smoothing: A case study on Muslims marriage and divorce

NASA Astrophysics Data System (ADS)

Jamaluddin, Fadhilah; Rahim, Rahela Abdul

2015-12-01

Markov Chain has been introduced since the 1913 for the purpose of studying the flow of data for a consecutive number of years of the data and also forecasting. The important feature in Markov Chain is obtaining the accurate Transition Probability Matrix (TPM). However to obtain the suitable TPM is hard especially in involving long-term modeling due to unavailability of data. This paper aims to enhance the classical Markov Chain by introducing Exponential Smoothing technique in developing the appropriate TPM.

Invited commentary: Lost in estimation--searching for alternatives to markov chains to fit complex Bayesian models.

PubMed

Molitor, John

2012-03-01

Bayesian methods have seen an increase in popularity in a wide variety of scientific fields, including epidemiology. One of the main reasons for their widespread application is the power of the Markov chain Monte Carlo (MCMC) techniques generally used to fit these models. As a result, researchers often implicitly associate Bayesian models with MCMC estimation procedures. However, Bayesian models do not always require Markov-chain-based methods for parameter estimation. This is important, as MCMC estimation methods, while generally quite powerful, are complex and computationally expensive and suffer from convergence problems related to the manner in which they generate correlated samples used to estimate probability distributions for parameters of interest. In this issue of the Journal, Cole et al. (Am J Epidemiol. 2012;175(5):368-375) present an interesting paper that discusses non-Markov-chain-based approaches to fitting Bayesian models. These methods, though limited, can overcome some of the problems associated with MCMC techniques and promise to provide simpler approaches to fitting Bayesian models. Applied researchers will find these estimation approaches intuitively appealing and will gain a deeper understanding of Bayesian models through their use. However, readers should be aware that other non-Markov-chain-based methods are currently in active development and have been widely published in other fields.

Antibody side chain conformations are position-dependent.

PubMed

Leem, Jinwoo; Georges, Guy; Shi, Jiye; Deane, Charlotte M

2018-04-01

Side chain prediction is an integral component of computational antibody design and structure prediction. Current antibody modelling tools use backbone-dependent rotamer libraries with conformations taken from general proteins. Here we present our antibody-specific rotamer library, where rotamers are binned according to their immunogenetics (IMGT) position, rather than their local backbone geometry. We find that for some amino acid types at certain positions, only a restricted number of side chain conformations are ever observed. Using this information, we are able to reduce the breadth of the rotamer sampling space. Based on our rotamer library, we built a side chain predictor, position-dependent antibody rotamer swapper (PEARS). On a blind test set of 95 antibody model structures, PEARS had the highest average χ 1 and χ1+2 accuracy (78.7% and 64.8%) compared to three leading backbone-dependent side chain predictors. Our use of IMGT position, rather than backbone ϕ/ψ, meant that PEARS was more robust to errors in the backbone of the model structure. PEARS also achieved the lowest number of side chain-side chain clashes. PEARS is freely available as a web application at http://opig.stats.ox.ac.uk/webapps/pears. © 2018 Wiley Periodicals, Inc.

Antiretroviral procurement and supply chain management.

PubMed

Ripin, David J; Jamieson, David; Meyers, Amy; Warty, Umesh; Dain, Mary; Khamsi, Cyril

2014-01-01

Procurement, the country-level process of ordering antiretrovirals (ARVs), and supply chain management, the mechanism by which they are delivered to health-care facilities, are critical processes required to move ARVs from manufacturers to patients. To provide a glimpse into the ARV procurement and supply chain, the following pages provide an overview of the primary stakeholders, principal operating models, and policies and regulations involved in ARV procurement. Also presented are key challenges that need to be addressed to ensure that the supply chain is not a barrier to the goal of universal coverage. This article will cover the steps necessary to order and distribute ARVs, including different models of delivery, key stakeholders involved, strategic considerations that vary depending on context and policies affecting them. The single drug examples given illustrate the complications inherent in fragmented supply and demand-driven models of procurement and supply chain management, and suggest tools for navigating these hurdles that will ultimately result in more secure and reliable ARV provision. Understanding the dynamics of ARV supply chain is important for the global health community, both to ensure full and efficient treatment of persons living with HIV as well as to inform the supply chain decisions for other public health products.

Supply chain analysis of e-tailing versus retailing operation - a case study

NASA Astrophysics Data System (ADS)

Kumar, Sameer; Tiffany, Maryellen; Vaidya, Salil

2016-07-01

The swift growth of e-commerce or e-tailing as a consumer retail channel has made it a serious competitor to traditional retail channels and is changing consumers' purchasing behaviour. The purpose of this case study, based on Target and Amazon.com, is to analyse the attributes of traditional retailing, e-tailing, and hybrid supply chain models to form conclusions about the feasibility of an idealised supply chain model for the future. An integrated and generalised modelling framework is used that incorporates Six Sigma - define, measure, analyse, improve, control methodology leveraging various tools, including process flow maps, cause and effect diagram, performance efficiency metrics, failure mode and effects analysis (FMEA), and Monte Carlo simulation. Based on this analysis and research, the conclusion is that the idealised supply chain of the future may evolve into a hybrid supply chain, which includes both e-tail and retail channels. The main recommendations from this study include assessing the risks of migrating to such a hybrid supply chain and to leverage the recommended actions provided in the hybrid FMEA. To facilitate more effective and mature processes, this study can guide researchers in exhaustive empirical evaluations of hybrid supply chains, gather experiences and lessons learned for practitioners.

Polymerization as a Model Chain Reaction

ERIC Educational Resources Information Center

Morton, Maurice

1973-01-01

Describes the features of the free radical, anionic, and cationic mechanisms of chain addition polymerization. Indicates that the nature of chain reactions can be best taught through the study of macromolecules. (CC)

A strategic decision-making model considering the social costs of carbon dioxide emissions for sustainable supply chain management.

PubMed

Tseng, Shih-Chang; Hung, Shiu-Wan

2014-01-15

Incorporating sustainability into supply chain management has become a critical issue driven by pressures from governments, customers, and various stakeholder groups over the past decade. This study proposes a strategic decision-making model considering both the operational costs and social costs caused by the carbon dioxide emissions from operating such a supply chain network for sustainable supply chain management. This model was used to evaluate carbon dioxide emissions and operational costs under different scenarios in an apparel manufacturing supply chain network. The results showed that the higher the social cost rate of carbon dioxide emissions, the lower the amount of the emission of carbon dioxide. The results also suggested that a legislation that forces the enterprises to bear the social costs of carbon dioxide emissions resulting from their economic activities is an effective approach to reducing carbon dioxide emissions. Copyright © 2013 Elsevier Ltd. All rights reserved.

Negativity as the entanglement measure to probe the Kondo regime in the spin-chain Kondo model

NASA Astrophysics Data System (ADS)

Bayat, Abolfazl; Sodano, Pasquale; Bose, Sougato

2010-02-01

We study the entanglement of an impurity at one end of a spin chain with a block of spins using negativity as a true measure of entanglement to characterize the unique features of the gapless Kondo regime in the spin-chain Kondo model. For this spin chain in the Kondo regime we determine—with a true entanglement measure—the spatial extent of the Kondo screening cloud, we propose an ansatz for its ground state and demonstrate that the impurity spin is indeed maximally entangled with the cloud. To better evidence the peculiarities of the Kondo regime, we carry a parallel analysis of the entanglement properties of the Kondo spin-chain model in the gapped dimerized regime. Our study shows how a genuine entanglement measure stemming from quantum information theory can fully characterize also nonperturbative regimes accessible to certain condensed matter systems.

A quantile-based scenario analysis approach to biomass supply chain optimization under uncertainty

DOE PAGES

Zamar, David S.; Gopaluni, Bhushan; Sokhansanj, Shahab; ...

2016-11-21

Supply chain optimization for biomass-based power plants is an important research area due to greater emphasis on renewable power energy sources. Biomass supply chain design and operational planning models are often formulated and studied using deterministic mathematical models. While these models are beneficial for making decisions, their applicability to real world problems may be limited because they do not capture all the complexities in the supply chain, including uncertainties in the parameters. This study develops a statistically robust quantile-based approach for stochastic optimization under uncertainty, which builds upon scenario analysis. We apply and evaluate the performance of our approach tomore » address the problem of analyzing competing biomass supply chains subject to stochastic demand and supply. Finally, the proposed approach was found to outperform alternative methods in terms of computational efficiency and ability to meet the stochastic problem requirements.« less

A quantile-based scenario analysis approach to biomass supply chain optimization under uncertainty

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zamar, David S.; Gopaluni, Bhushan; Sokhansanj, Shahab

Supply chain optimization for biomass-based power plants is an important research area due to greater emphasis on renewable power energy sources. Biomass supply chain design and operational planning models are often formulated and studied using deterministic mathematical models. While these models are beneficial for making decisions, their applicability to real world problems may be limited because they do not capture all the complexities in the supply chain, including uncertainties in the parameters. This study develops a statistically robust quantile-based approach for stochastic optimization under uncertainty, which builds upon scenario analysis. We apply and evaluate the performance of our approach tomore » address the problem of analyzing competing biomass supply chains subject to stochastic demand and supply. Finally, the proposed approach was found to outperform alternative methods in terms of computational efficiency and ability to meet the stochastic problem requirements.« less

A stochastic inventory management model for a dual sourcing supply chain with disruptions

NASA Astrophysics Data System (ADS)

Iakovou, Eleftherios; Vlachos, Dimitrios; Xanthopoulos, Anastasios

2010-03-01

As companies continue to globalise their operations and outsource significant portion of their value chain activities, they often end up relying heavily on order replenishments from distant suppliers. The explosion in long-distance sourcing is exposing supply chains and shareholder value at ever increasing operational and disruption risks. It is well established, both in academia and in real-world business environments, that resource flexibility is an effective method for hedging against supply chain disruption risks. In this contextual framework, we propose a single period stochastic inventory decision-making model that could be employed for capturing the trade-off between inventory policies and disruption risks for an unreliable dual sourcing supply network for both the capacitated and uncapacitated cases. Through the developed model, we obtain some important managerial insights and evaluate the merit of contingency strategies in managing uncertain supply chains.

A simplified parsimonious higher order multivariate Markov chain model

NASA Astrophysics Data System (ADS)

Wang, Chao; Yang, Chuan-sheng

2017-09-01

In this paper, a simplified parsimonious higher-order multivariate Markov chain model (SPHOMMCM) is presented. Moreover, parameter estimation method of TPHOMMCM is give. Numerical experiments shows the effectiveness of TPHOMMCM.

An ellipsoid-chain model for conjugated polymer solutions

NASA Astrophysics Data System (ADS)

Lee, Cheng K.; Hua, Chi C.; Chen, Show A.

2012-02-01

We propose an ellipsoid-chain model which may be routinely parameterized to capture large-scale properties of semiflexible, amphiphilic conjugated polymers in various solvent media. The model naturally utilizes the defect locations as pivotal centers connecting adjacent ellipsoids (each currently representing ten monomer units), and a variant umbrella-sampling scheme is employed to construct the potentials of mean force (PMF) for specific solvent media using atomistic dynamics data and simplex optimization. The performances, both efficacy and efficiency, of the model are thoroughly evaluated by comparing the simulation results on long, single-chain (i.e., 300-mer) structures with those from two existing, finer-grained models for a standard conjugated polymer (i.e., poly(2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylenevinylene) or MEH-PPV) in two distinct solvents (i.e., chloroform or toluene) as well as a hybrid, binary-solvent medium (i.e., chloroform/toluene = 1:1 in number density). The coarse-grained Monte Carlo (CGMC) simulation of the ellipsoid-chain model is shown to be the most efficient—about 300 times faster than the coarse-grained molecular dynamics (CGMD) simulation of the finest CG model that employs explicit solvents—in capturing elementary single-chain structures for both single-solvent media, and is a few times faster than the coarse-grained Langevin dynamics (CGLD) simulation of another implicit-solvent polymer model with a slightly greater coarse-graining level than in the CGMD simulation. For the binary-solvent system considered, however, both of the two implicit-solvent schemes (i.e., CGMC and CGLD) fail to capture the effects of conspicuous concentration fluctuations near the polymer-solvent interface, arising from a pronounced coupling between the solvent molecules and different parts of the polymer. Essential physical implications are elaborated on the success as well as the failure of the two implicit-solvent CG schemes under varying solvent conditions. Within the ellipsoid-chain model, the impact of synthesized defects on local segmental ordering as well as bulk chain conformation is also scrutinized, and essential consequences in practical applications discussed. In future perspectives, we remark on strategy that takes advantage of the coordination among various CG models and simulation schemes to warrant computational efficiency and accuracy, with the anticipated capability of simulating larger-scale, many-chain aggregate systems.

Accessing the dynamics of end-grafted flexible polymer chains by atomic force-electrochemical microscopy. Theoretical modeling of the approach curves by the elastic bounded diffusion model and Monte Carlo simulations. Evidence for compression-induced lateral chain escape.

PubMed

Abbou, Jeremy; Anne, Agnès; Demaille, Christophe

2006-11-16

The dynamics of a molecular layer of linear poly(ethylene glycol) (PEG) chains of molecular weight 3400, bearing at one end a ferrocene (Fc) label and thiol end-grafted at a low surface coverage onto a gold substrate, is probed using combined atomic force-electrochemical microscopy (AFM-SECM), at the scale of approximately 100 molecules. Force and current approach curves are simultaneously recorded as a force-sensing microelectrode (tip) is inserted within the approximately 10 nm thick, redox labeled, PEG chain layer. Whereas the force approach curve gives access to the structure of the compressed PEG layer, the tip-current, resulting from tip-to-substrate redox cycling of the Fc head of the chain, is controlled by chain dynamics. The elastic bounded diffusion model, which considers the motion of the Fc head as diffusion in a conformational field, complemented by Monte Carlo (MC) simulations, from which the chain conformation can be derived for any degree of confinement, allows the theoretical tip-current approach curve to be calculated. The experimental current approach curve can then be very satisfyingly reproduced by theory, down to a tip-substrate separation of approximately 2 nm, using only one adjustable parameter characterizing the chain dynamics: the effective diffusion coefficient of the chain head. At closer tip-substrate separations, an unpredicted peak is observed in the experimental current approach curve, which is shown to find its origin in a compression-induced escape of the chain from within the narrowing tip-substrate gap. MC simulations provide quantitative support for lateral chain elongation as the escape mechanism.

Protein side chain conformation predictions with an MMGBSA energy function.

PubMed

Gaillard, Thomas; Panel, Nicolas; Simonson, Thomas

2016-06-01

The prediction of protein side chain conformations from backbone coordinates is an important task in structural biology, with applications in structure prediction and protein design. It is a difficult problem due to its combinatorial nature. We study the performance of an "MMGBSA" energy function, implemented in our protein design program Proteus, which combines molecular mechanics terms, a Generalized Born and Surface Area (GBSA) solvent model, with approximations that make the model pairwise additive. Proteus is not a competitor to specialized side chain prediction programs due to its cost, but it allows protein design applications, where side chain prediction is an important step and MMGBSA an effective energy model. We predict the side chain conformations for 18 proteins. The side chains are first predicted individually, with the rest of the protein in its crystallographic conformation. Next, all side chains are predicted together. The contributions of individual energy terms are evaluated and various parameterizations are compared. We find that the GB and SA terms, with an appropriate choice of the dielectric constant and surface energy coefficients, are beneficial for single side chain predictions. For the prediction of all side chains, however, errors due to the pairwise additive approximation overcome the improvement brought by these terms. We also show the crucial contribution of side chain minimization to alleviate the rigid rotamer approximation. Even without GB and SA terms, we obtain accuracies comparable to SCWRL4, a specialized side chain prediction program. In particular, we obtain a better RMSD than SCWRL4 for core residues (at a higher cost), despite our simpler rotamer library. Proteins 2016; 84:803-819. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Characterization of Hydrophobic Interactions of Polymers with Water and Phospholipid Membranes Using Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Drenscko, Mihaela

Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid membrane. To begin with, we characterize the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained molecular simulation. We next explore the scaling behavior of the collapsed globular shape at the minimum energy configuration, characterized by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behavior of the Solvent Accessible Surface Area (SASA) as a function of chain length, finding a similar exponent for both all-atomistic and coarse-grained simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths. Next, in order to investigate the molecular interactions between single hydrophobic polymer chains and lipids in biological membranes and at lipid membrane/solvent interface, we perform a series of molecular dynamics simulations of small membranes using all atomistic and coarse-grained methods. The molecular interaction between common polymer chains used in biomedical applications and the cell membrane is unknown. This interaction may affect the biocompatibility of the polymer chains. Molecular dynamics simulations offer an emerging tool to characterize the interaction between common degradable polymer chains used in biomedical applications, such as polycaprolactone, and model cell membranes. We systematically characterize with long-time all-atomistic molecular dynamics simulations the interaction between single polycaprolactone chains of varying chain lengths with a model phospholipid membrane. We find that the length of polymer chain greatly affects the nature of interaction with the membrane, as well as the membrane properties. Furthermore, we next utilize advanced sampling techniques in molecular dynamics to characterize the two-dimensional free energy surface for the interaction of varying polymer chain lengths (short, intermediate, and long) with model cell membranes. We find that the free energy minimum shifts from the membrane-water interface to the hydrophobic core of the phospholipid membrane as a function of chain length. These results can be used to design polymer chain lengths and chemistries to optimize their interaction with cell membranes at the molecular level.

A Chain-Retrieval Model for Voluntary Task Switching

ERIC Educational Resources Information Center

Vandierendonck, Andre; Demanet, Jelle; Liefooghe, Baptist; Verbruggen, Frederick

2012-01-01

To account for the findings obtained in voluntary task switching, this article describes and tests the chain-retrieval model. This model postulates that voluntary task selection involves retrieval of task information from long-term memory, which is then used to guide task selection and task execution. The model assumes that the retrieved…

Building Higher-Order Markov Chain Models with EXCEL

ERIC Educational Resources Information Center

Ching, Wai-Ki; Fung, Eric S.; Ng, Michael K.

2004-01-01

Categorical data sequences occur in many applications such as forecasting, data mining and bioinformatics. In this note, we present higher-order Markov chain models for modelling categorical data sequences with an efficient algorithm for solving the model parameters. The algorithm can be implemented easily in a Microsoft EXCEL worksheet. We give a…

Exact solution of the relativistic quantum Toda chain

NASA Astrophysics Data System (ADS)

Zhang, Xin; Cao, Junpeng; Yang, Wen-Li; Shi, Kangjie; Wang, Yupeng

2017-03-01

The relativistic quantum Toda chain model is studied with the generalized algebraic Bethe Ansatz method. By employing a set of local gauge transformations, proper local vacuum states can be obtained for this model. The exact spectrum and eigenstates of the model are thus constructed simultaneously.

All-atom ensemble modeling to analyze small angle X-ray scattering of glycosylated proteins

PubMed Central

Guttman, Miklos; Weinkam, Patrick; Sali, Andrej; Lee, Kelly K.

2013-01-01

Summary The flexible and heterogeneous nature of carbohydrate chains often renders glycoproteins refractory to traditional structure determination methods. Small Angle X-ray scattering (SAXS) can be a useful tool for obtaining structural information of these systems. All-atom modeling of glycoproteins with flexible glycan chains was applied to interpret the solution SAXS data for a set of glycoproteins. For simpler systems (single glycan, with a well defined protein structure), all-atom modeling generates models in excellent agreement with the scattering pattern, and reveals the approximate spatial occupancy of the glycan chain in solution. For more complex systems (several glycan chains, or unknown protein substructure), the approach can still provide insightful models, though the orientations of glycans become poorly determined. Ab initio shape reconstructions appear to capture the global morphology of glycoproteins, but in most cases offer little information about glycan spatial occupancy. The all-atom modeling methodology is available as a webserver at http://modbase.compbio.ucsf.edu/allosmod-foxs. PMID:23473666

Cloud Computing Value Chains: Understanding Businesses and Value Creation in the Cloud

NASA Astrophysics Data System (ADS)

Mohammed, Ashraf Bany; Altmann, Jörn; Hwang, Junseok

Based on the promising developments in Cloud Computing technologies in recent years, commercial computing resource services (e.g. Amazon EC2) or software-as-a-service offerings (e.g. Salesforce. com) came into existence. However, the relatively weak business exploitation, participation, and adoption of other Cloud Computing services remain the main challenges. The vague value structures seem to be hindering business adoption and the creation of sustainable business models around its technology. Using an extensive analyze of existing Cloud business models, Cloud services, stakeholder relations, market configurations and value structures, this Chapter develops a reference model for value chains in the Cloud. Although this model is theoretically based on porter's value chain theory, the proposed Cloud value chain model is upgraded to fit the diversity of business service scenarios in the Cloud computing markets. Using this model, different service scenarios are explained. Our findings suggest new services, business opportunities, and policy practices for realizing more adoption and value creation paths in the Cloud.

Development of structure in natural silk spinning and poly(vinyl alcohol) hydrogel formation

NASA Astrophysics Data System (ADS)

Willcox, Patricia Jeanene

This research involves the characterization of structure and structure formation in aqueous systems. Particularly, these studies investigate the effect of various processing variables on the structure formation that occurs upon conversion from aqueous solution to fiber or hydrogel. The two processes studied include natural silk fiber spinning and physical gelation of poly(vinyl alcohol), PVOH, in water. The techniques employed combine cryogenic technology for sample preparation and direct observation by transmission electron microscopy with electron diffraction, atomic force microscopy, optical rheometry, X-ray scattering and optical microscopy. In order to explore the full range of structure formation in natural silk spinning, studies are conducted in vivo and in vitro. In vivo structural investigations are accomplished through the cryogenic quenching and subsequent microtoming of live silk-spinning animals, Nephila clavipes (spider) and Bombyx mori (silkworm). Observations made using transmission electron microscopy, electron diffraction and atomic force microscopy indicate a cholesteric liquid crystalline mesophase of aqueous silk fibroin in both species. The mechanism of structure formation in solution is studied in vitro using optical rheometry on aqueous solutions made from regenerated Bombyx mori cocoon silk. Concentrated solutions exhibit birefringence under flow, with a wormlike conformation of the silk molecules in concentrated salt solution. Changes in salt concentration and pH of the aqueous silk solutions result in differing degrees of alignment and aggregation. These results suggest that structural control in the natural silk spinning process is accomplished by chemical manipulation of the electrostatic interactions and hydrogen bonding between chains. Application of cryogenic methods in transmission electron microscopy also provides a unique look at hydration-dependent structures in gels of poly(vinyl alcohol) produced by freeze-thaw processing. Morphologies ranging from circular pores to fibrillar networks are observed in gels formed from aqueous PVOH solutions subjected to cycles of freezing and thawing. These morphologies can be directly associated with the progressive nature of the mechanism of gelation as it proceeds from liquid-liquid phase separation to crystallization with increased cycling. A comparison of the structures produced by cycling and by aging suggests that there is a similarity in structural changes, but a superposition of the effects of cycling and aging is not possible.

A tridiagonal parsimonious higher order multivariate Markov chain model

NASA Astrophysics Data System (ADS)

Wang, Chao; Yang, Chuan-sheng

2017-09-01

In this paper, we present a tridiagonal parsimonious higher-order multivariate Markov chain model (TPHOMMCM). Moreover, estimation method of the parameters in TPHOMMCM is give. Numerical experiments illustrate the effectiveness of TPHOMMCM.

Characterizing Oregon's supply chains.

DOT National Transportation Integrated Search

2013-03-01

In many regions throughout the world, freight models are used to aid infrastructure investment and : policy decisions. Since freight is such an integral part of efficient supply chains, more realistic : transportation models can be of greater assista...

A decision model for cost effective design of biomass based green energy supply chains.

PubMed

Yılmaz Balaman, Şebnem; Selim, Hasan

2015-09-01

The core driver of this study is to deal with the design of anaerobic digestion based biomass to energy supply chains in a cost effective manner. In this concern, a decision model is developed. The model is based on fuzzy multi objective decision making in order to simultaneously optimize multiple economic objectives and tackle the inherent uncertainties in the parameters and decision makers' aspiration levels for the goals. The viability of the decision model is explored with computational experiments on a real-world biomass to energy supply chain and further analyses are performed to observe the effects of different conditions. To this aim, scenario analyses are conducted to investigate the effects of energy crop utilization and operational costs on supply chain structure and performance measures. Copyright © 2015 Elsevier Ltd. All rights reserved.

Modeling qRT-PCR dynamics with application to cancer biomarker quantification.

PubMed

Chervoneva, Inna; Freydin, Boris; Hyslop, Terry; Waldman, Scott A

2017-01-01

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is widely used for molecular diagnostics and evaluating prognosis in cancer. The utility of mRNA expression biomarkers relies heavily on the accuracy and precision of quantification, which is still challenging for low abundance transcripts. The critical step for quantification is accurate estimation of efficiency needed for computing a relative qRT-PCR expression. We propose a new approach to estimating qRT-PCR efficiency based on modeling dynamics of polymerase chain reaction amplification. In contrast, only models for fluorescence intensity as a function of polymerase chain reaction cycle have been used so far for quantification. The dynamics of qRT-PCR efficiency is modeled using an ordinary differential equation model, and the fitted ordinary differential equation model is used to obtain effective polymerase chain reaction efficiency estimates needed for efficiency-adjusted quantification. The proposed new qRT-PCR efficiency estimates were used to quantify GUCY2C (Guanylate Cyclase 2C) mRNA expression in the blood of colorectal cancer patients. Time to recurrence and GUCY2C expression ratios were analyzed in a joint model for survival and longitudinal outcomes. The joint model with GUCY2C quantified using the proposed polymerase chain reaction efficiency estimates provided clinically meaningful results for association between time to recurrence and longitudinal trends in GUCY2C expression.

A Coarse Grained Model for Methylcellulose: Spontaneous Ring Formation at Elevated Temperature

NASA Astrophysics Data System (ADS)

Huang, Wenjun; Larson, Ronald

Methylcellulose (MC) is widely used as food additives and pharma applications, where its thermo-reversible gelation behavior plays an important role. To date the gelation mechanism is not well understood, and therefore attracts great research interest. In this study, we adopted coarse-grained (CG) molecular dynamics simulations to model the MC chains, including the homopolymers and random copolymers that models commercial METHOCEL A, in an implicit water environment, where each MC monomer modeled with a single bead. The simulations are carried using a LAMMPS program. We parameterized our CG model using the radial distribution functions from atomistic simulations of short MC oligomers, extrapolating the results to long chains. We used dissociation free energy to validate our CG model against the atomistic model. The CG model captured the effects of monomer substitution type and temperature from the atomistic simulations. We applied this CG model to simulate single chains up to 1000 monomers long and obtained persistence lengths that are close to those determined from experiment. We observed the chain collapse transition for random copolymer at 600 monomers long at 50C. The chain collapsed into a stable ring structure with outer diameter around 14nm, which appears to be a precursor to the fibril structure observed in the methylcellulose gel observed by Lodge et al. in the recent studies. Our CG model can be extended to other MC derivatives for studying the interaction between these polymers and small molecules, such as hydrophobic drugs.

Research of Trust Chain of Operating System

NASA Astrophysics Data System (ADS)

Li, Hongjiao; Tian, Xiuxia

Trust chain is one of the key technologies in designing secure operating system based on TC technology. Constructions of trust chain and trust models are analyzed. Future works in these directions are discussed.

Joint modelling rationale for chained equations

PubMed Central

2014-01-01

Background Chained equations imputation is widely used in medical research. It uses a set of conditional models, so is more flexible than joint modelling imputation for the imputation of different types of variables (e.g. binary, ordinal or unordered categorical). However, chained equations imputation does not correspond to drawing from a joint distribution when the conditional models are incompatible. Concurrently with our work, other authors have shown the equivalence of the two imputation methods in finite samples. Methods Taking a different approach, we prove, in finite samples, sufficient conditions for chained equations and joint modelling to yield imputations from the same predictive distribution. Further, we apply this proof in four specific cases and conduct a simulation study which explores the consequences when the conditional models are compatible but the conditions otherwise are not satisfied. Results We provide an additional “non-informative margins” condition which, together with compatibility, is sufficient. We show that the non-informative margins condition is not satisfied, despite compatible conditional models, in a situation as simple as two continuous variables and one binary variable. Our simulation study demonstrates that as a consequence of this violation order effects can occur; that is, systematic differences depending upon the ordering of the variables in the chained equations algorithm. However, the order effects appear to be small, especially when associations between variables are weak. Conclusions Since chained equations is typically used in medical research for datasets with different types of variables, researchers must be aware that order effects are likely to be ubiquitous, but our results suggest they may be small enough to be negligible. PMID:24559129

Decentralized supply chain network design: monopoly, duopoly and oligopoly competitions under uncertainty

NASA Astrophysics Data System (ADS)

Seyedhosseini, Seyed Mohammad; Fahimi, Kaveh; Makui, Ahmad

2017-12-01

This paper presents the competitive supply chain network design problem in which n decentralized supply chains simultaneously enter the market with no existing rival chain, shape their networks and set wholesale and retail prices in competitive mode. The customer demand is elastic and price dependent, customer utility function is based on the Hoteling model and the chains produce identical or highly substitutable products. We construct a solution algorithm based on bi-level programming and possibility theory. In the proposed bi-level model, the inner part sets the prices based on simultaneous extra- and Stackleberg intra- chains competitions, and the outer part shapes the networks in cooperative competitions. Finally, we use a real-word study to discuss the effect of the different structures of the competitors on the equilibrium solution. Moreover, sensitivity analyses are conducted and managerial insights are offered.

Conditional Solvation Thermodynamics of Isoleucine in Model Peptides and the Limitations of the Group-Transfer Model

PubMed Central

2015-01-01

The hydration thermodynamics of the amino acid X relative to the reference G (glycine) or the hydration thermodynamics of a small-molecule analog of the side chain of X is often used to model the contribution of X to protein stability and solution thermodynamics. We consider the reasons for successes and limitations of this approach by calculating and comparing the conditional excess free energy, enthalpy, and entropy of hydration of the isoleucine side chain in zwitterionic isoleucine, in extended penta-peptides, and in helical deca-peptides. Butane in gauche conformation serves as a small-molecule analog for the isoleucine side chain. Parsing the hydrophobic and hydrophilic contributions to hydration for the side chain shows that both of these aspects of hydration are context-sensitive. Furthermore, analyzing the solute–solvent interaction contribution to the conditional excess enthalpy of the side chain shows that what is nominally considered a property of the side chain includes entirely nonobvious contributions of the background. The context-sensitivity of hydrophobic and hydrophilic hydration and the conflation of background contributions with energetics attributed to the side chain limit the ability of a single scaling factor, such as the fractional solvent exposure of the group in the protein, to map the component energetic contributions of the model-compound data to their value in the protein. But ignoring the origin of cancellations in the underlying components the group-transfer model may appear to provide a reasonable estimate of the free energy for a given error tolerance. PMID:24650057

Application of a transmission model to estimate performance objectives for Salmonella in the broiler supply chain.

PubMed

van der Fels-Klerx, H J; Tromp, S; Rijgersberg, H; van Asselt, E D

2008-11-30

The aim of the present study was to demonstrate how Performance Objectives (POs) for Salmonella at various points in the broiler supply chain can be estimated, starting from pre-set levels of the PO in finished products. The estimations were performed using an analytical transmission model, based on prevalence data collected throughout the chain in The Netherlands. In the baseline (current) situation, the end PO was set at 2.5% of the finished products (at end of processing) being contaminated with Salmonella. Scenario analyses were performed by reducing this baseline end PO to 1.5% and 0.5%. The results showed the end PO could be reduced by spreading the POs over the various stages of the broiler supply chain. Sensitivity analyses were performed by changing the values of the model parameters. Results indicated that, in general, decreasing Salmonella contamination between points in the chain is more effective in reducing the baseline PO than increasing the reduction of the pathogen, implying contamination should be prevented rather than treated. Application of both approaches at the same time showed to be most effective in reducing the end PO, especially at the abattoir and during processing. The modelling approach of this study proved to be useful to estimate the implications for preceding stages of the chain by setting a PO at the end of the chain as well as to evaluate the effectiveness of potential interventions in reducing the end PO. The model estimations may support policy-makers in their decision-making process with regard to microbiological food safety.

Future Supply Chains Enabled by Continuous Processing-Opportunities Challenges May 20-21 2014 Continuous Manufacturing Symposium.

PubMed

Srai, Jagjit Singh; Badman, Clive; Krumme, Markus; Futran, Mauricio; Johnston, Craig

2015-03-01

This paper examines the opportunities and challenges facing the pharmaceutical industry in moving to a primarily "continuous processing"-based supply chain. The current predominantly "large batch" and centralized manufacturing system designed for the "blockbuster" drug has driven a slow-paced, inventory heavy operating model that is increasingly regarded as inflexible and unsustainable. Indeed, new markets and the rapidly evolving technology landscape will drive more product variety, shorter product life-cycles, and smaller drug volumes, which will exacerbate an already unsustainable economic model. Future supply chains will be required to enhance affordability and availability for patients and healthcare providers alike despite the increased product complexity. In this more challenging supply scenario, we examine the potential for a more pull driven, near real-time demand-based supply chain, utilizing continuous processing where appropriate as a key element of a more "flow-through" operating model. In this discussion paper on future supply chain models underpinned by developments in the continuous manufacture of pharmaceuticals, we have set out; The paper recognizes that although current batch operational performance in pharma is far from optimal and not necessarily an appropriate end-state benchmark for batch technology, the adoption of continuous supply chain operating models underpinned by continuous production processing, as full or hybrid solutions in selected product supply chains, can support industry transformations to deliver right-first-time quality at substantially lower inventory profiles. © 2015 The Authors. Journal of Pharmaceutical Sciences published by Wiley Periodicals, Inc. and the American Pharmacists Association. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nekrasov, Nikita; ITEP, Moscow; Shatashvili, Samson

Supersymmetric vacua of two dimensional N = 4 gauge theories with matter, softly broken by the twisted masses down to N = 2, are shown to be in one-to-one correspondence with the eigenstates of integrable spin chain Hamiltonians. Examples include: the Heisenberg SU(2)XXX spin chain which is mapped to the two dimensional U(N) theory with fundamental hypermultiplets, the XXZ spin chain which is mapped to the analogous three dimensional super-Yang-Mills theory compactified on a circle, the XYZ spin chain and eight-vertex model which are related to the four dimensional theory compactified on T{sup 2}. A consequence of our correspondence ismore » the isomorphism of the quantum cohomology ring of various quiver varieties, such as cotangent bundles to (partial) flag varieties and the ring of quantum integrals of motion of various spin chains. The correspondence extends to any spin group, representations, boundary conditions, and inhomogeneity, it includes Sinh-Gordon and non-linear Schroedinger models as well as the dynamical spin chains like Hubbard model. Compactifications of four dimensional N = 2 theories on a two-sphere lead to the instanton-corrected Bethe equations.« less

The Determination of Production and Distribution Policy in Push-Pull Production Chain with Supply Hub as the Junction Point

NASA Astrophysics Data System (ADS)

Sinaga, A. T.; Wangsaputra, R.

2018-03-01

The development of technology causes the needs of products and services become increasingly complex, diverse, and fluctuating. This causes the level of inter-company dependencies within a production chains increased. To be able to compete, efficiency improvements need to be done collaboratively in the production chain network. One of the efforts to increase efficiency is to harmonize production and distribution activities in the production chain network. This paper describes the harmonization of production and distribution activities by applying the use of push-pull system and supply hub in the production chain between two companies. The research methodology begins with conducting empirical and literature studies, formulating research questions, developing mathematical models, conducting trials and analyses, and taking conclusions. The relationship between the two companies is described in the MINLP mathematical model with the total cost of production chain as the objective function. Decisions generated by the mathematical models are the size of production lot, size of delivery lot, number of kanban, frequency of delivery, and the number of understock and overstock lot.

Bayesian analysis of non-homogeneous Markov chains: application to mental health data.

PubMed

Sung, Minje; Soyer, Refik; Nhan, Nguyen

2007-07-10

In this paper we present a formal treatment of non-homogeneous Markov chains by introducing a hierarchical Bayesian framework. Our work is motivated by the analysis of correlated categorical data which arise in assessment of psychiatric treatment programs. In our development, we introduce a Markovian structure to describe the non-homogeneity of transition patterns. In doing so, we introduce a logistic regression set-up for Markov chains and incorporate covariates in our model. We present a Bayesian model using Markov chain Monte Carlo methods and develop inference procedures to address issues encountered in the analyses of data from psychiatric treatment programs. Our model and inference procedures are implemented to some real data from a psychiatric treatment study. Copyright 2006 John Wiley & Sons, Ltd.

Entanglement Theories: Packing vs. Percolation

NASA Astrophysics Data System (ADS)

Wool, Richard

2007-03-01

There are two emergent theories of polymer entanglements, the Packing Model (Fetters, Lohse, Graessley, Milner, Whitten, ˜'98) and the Percolation Model (Wool ˜'93). The Packing model suggests that the entanglement molecular weight Me is determined by Me = K p^3, where the packing length parameter p = V/R^2 in which V is the volume of the chain (V=M/ρNa), R is the end-to end vector of the chain, and K 357 ρNa, is an empirical constant. The Percolation model states that an entanglement network develops when the number of chains per unit area σ, intersecting any load bearing plane, is equal to 3 times the number of chain segments (1/a cross-section), such that when 3aσ =1 at the percolation threshold, Me 31 MjC∞, in which Mj is the step molecular weight and C∞ is the characteristic ratio. There are no fitting parameters in the Percolation model. The Packing model predicts that Me decreases rapidly with chain stiffness, as Me˜1/C∞^3, while the Percolation model predicts that Me increases with C∞, as Me˜C∞. The Percolation model was found to be the correct model based on computer simulations (M. Bulacu et al) and a re-analysis of the Packing model experimental data. The Packing model can be derived from the Percolation model, but not visa versa, and reveals a surprising accidental relation between C∞ and Mj in the front factor K. This result significantly impacts the interpretation of the dynamics of rheology and fracture of entangled polymers.

Room temperature ionic liquids: A simple model. Effect of chain length and size of intermolecular potential on critical temperature.

PubMed

Chapela, Gustavo A; Guzmán, Orlando; Díaz-Herrera, Enrique; del Río, Fernando

2015-04-21

A model of a room temperature ionic liquid can be represented as an ion attached to an aliphatic chain mixed with a counter ion. The simple model used in this work is based on a short rigid tangent square well chain with an ion, represented by a hard sphere interacting with a Yukawa potential at the head of the chain, mixed with a counter ion represented as well by a hard sphere interacting with a Yukawa potential of the opposite sign. The length of the chain and the depth of the intermolecular forces are investigated in order to understand which of these factors are responsible for the lowering of the critical temperature. It is the large difference between the ionic and the dispersion potentials which explains this lowering of the critical temperature. Calculation of liquid-vapor equilibrium orthobaric curves is used to estimate the critical points of the model. Vapor pressures are used to obtain an estimate of the triple point of the different models in order to calculate the span of temperatures where they remain a liquid. Surface tensions and interfacial thicknesses are also reported.

Markov chain model for demersal fish catch analysis in Indonesia

NASA Astrophysics Data System (ADS)

Firdaniza; Gusriani, N.

2018-03-01

As an archipelagic country, Indonesia has considerable potential fishery resources. One of the fish resources that has high economic value is demersal fish. Demersal fish is a fish with a habitat in the muddy seabed. Demersal fish scattered throughout the Indonesian seas. Demersal fish production in each Indonesia’s Fisheries Management Area (FMA) varies each year. In this paper we have discussed the Markov chain model for demersal fish yield analysis throughout all Indonesia’s Fisheries Management Area. Data of demersal fish catch in every FMA in 2005-2014 was obtained from Directorate of Capture Fisheries. From this data a transition probability matrix is determined by the number of transitions from the catch that lie below the median or above the median. The Markov chain model of demersal fish catch data was an ergodic Markov chain model, so that the limiting probability of the Markov chain model can be determined. The predictive value of demersal fishing yields was obtained by calculating the combination of limiting probability with average catch results below the median and above the median. The results showed that for 2018 and long-term demersal fishing results in most of FMA were below the median value.

Development of coordination system model on single-supplier multi-buyer for multi-item supply chain with probabilistic demand

NASA Astrophysics Data System (ADS)

Olivia, G.; Santoso, A.; Prayogo, D. N.

2017-11-01

Nowadays, the level of competition between supply chains is getting tighter and a good coordination system between supply chains members is very crucial in solving the issue. This paper focused on a model development of coordination system between single supplier and buyers in a supply chain as a solution. Proposed optimization model was designed to determine the optimal number of deliveries from a supplier to buyers in order to minimize the total cost over a planning horizon. Components of the total supply chain cost consist of transportation costs, handling costs of supplier and buyers and also stock out costs. In the proposed optimization model, the supplier can supply various types of items to retailers whose item demand patterns are probabilistic. Sensitivity analysis of the proposed model was conducted to test the effect of changes in transport costs, handling costs and production capacities of the supplier. The results of the sensitivity analysis showed a significant influence on the changes in the transportation cost, handling costs and production capacity to the decisions of the optimal numbers of product delivery for each item to the buyers.

Critical role of FcR gamma-chain, LAT, PLCgamma2 and thrombin in arteriolar thrombus formation upon mild, laser-induced endothelial injury in vivo.

PubMed

Kalia, Neena; Auger, Jocelyn M; Atkinson, Ben; Watson, Steve P

2008-05-01

The role of collagen receptor complex GPVI-FcR gamma-chain, PLCgamma2 and LAT in laser-induced thrombosis is unclear. Controversy surrounds whether collagen is exposed in this model or whether thrombosis is dependent on thrombin. This study hypothesized that collagen exposure plays a critical role in thrombus formation in this model, which was tested by investigating contributions of FcR gamma-chain, LAT, PLCgamma2 and thrombin. Thrombi were monitored using intravital microscopy in anesthetized wild-type and FcR gamma-chain, LAT and PLCgamma2 knockout mice. Hirudin (thrombin inhibitor) was administered to wild-type and FcR gamma-chain knockout mice. Significantly reduced thrombus formation was observed in FcR gamma-chain and PLCgamma2 knockouts with a greater decrease observed in LAT knockouts. Dramatic reduction was observed in wild-types treated with hirudin, with abolished thrombus formation only observed in FcR gamma-chain knockouts treated with hirudin. GPVI-FcR gamma-chain, LAT and PLCgamma2 are essential for thrombus generation and stability in this laser-induced model of injury. More importantly, a greater role for LAT was identified, which may reflect a role for it downstream of a second matrix protein receptor. However, inhibition of platelet activation by matrix proteins and thrombin generation are both required to maximally prevent thrombus formation.

Evaluating approaches to find exon chains based on long reads.

PubMed

Kuosmanen, Anna; Norri, Tuukka; Mäkinen, Veli

2018-05-01

Transcript prediction can be modeled as a graph problem where exons are modeled as nodes and reads spanning two or more exons are modeled as exon chains. Pacific Biosciences third-generation sequencing technology produces significantly longer reads than earlier second-generation sequencing technologies, which gives valuable information about longer exon chains in a graph. However, with the high error rates of third-generation sequencing, aligning long reads correctly around the splice sites is a challenging task. Incorrect alignments lead to spurious nodes and arcs in the graph, which in turn lead to incorrect transcript predictions. We survey several approaches to find the exon chains corresponding to long reads in a splicing graph, and experimentally study the performance of these methods using simulated data to allow for sensitivity/precision analysis. Our experiments show that short reads from second-generation sequencing can be used to significantly improve exon chain correctness either by error-correcting the long reads before splicing graph creation, or by using them to create a splicing graph on which the long-read alignments are then projected. We also study the memory and time consumption of various modules, and show that accurate exon chains lead to significantly increased transcript prediction accuracy. The simulated data and in-house scripts used for this article are available at http://www.cs.helsinki.fi/group/gsa/exon-chains/exon-chains-bib.tar.bz2.

Dissolution of covalent adaptable network polymers in organic solvent

NASA Astrophysics Data System (ADS)

Yu, Kai; Yang, Hua; Dao, Binh H.; Shi, Qian; Yakacki, Christopher M.

2017-12-01

It was recently reported that thermosetting polymers can be fully dissolved in a proper organic solvent utilizing a bond-exchange reaction (BER), where small molecules diffuse into the polymer, break the long polymer chains into short segments, and eventually dissolve the network when sufficient solvent is provided. The solvent-assisted dissolution approach was applied to fully recycle thermosets and their fiber composites. This paper presents the first multi-scale modeling framework to predict the dissolution kinetics and mechanics of thermosets in organic solvent. The model connects the micro-scale network dynamics with macro-scale material properties: in the micro-scale, a model is developed based on the kinetics of BERs to describe the cleavage rate of polymer chains and evolution of chain segment length during the dissolution. The micro-scale model is then fed into a continuum-level model with considerations of the transportation of solvent molecules and chain segments in the system. The model shows good prediction on conversion rate of functional groups, degradation of network mechanical properties, and dissolution rate of thermosets during the dissolution. It identifies the underlying kinetic factors governing the dissolution process, and reveals the influence of different material and processing variables on the dissolution process, such as time, temperature, catalyst concentration, and chain length between cross-links.

Source term evaluation model for high-level radioactive waste repository with decay chain build-up.

PubMed

Chopra, Manish; Sunny, Faby; Oza, R B

2016-09-18

A source term model based on two-component leach flux concept is developed for a high-level radioactive waste repository. The long-lived radionuclides associated with high-level waste may give rise to the build-up of activity because of radioactive decay chains. The ingrowths of progeny are incorporated in the model using Bateman decay chain build-up equations. The model is applied to different radionuclides present in the high-level radioactive waste, which form a part of decay chains (4n to 4n + 3 series), and the activity of the parent and daughter radionuclides leaching out of the waste matrix is estimated. Two cases are considered: one when only parent is present initially in the waste and another where daughters are also initially present in the waste matrix. The incorporation of in situ production of daughter radionuclides in the source is important to carry out realistic estimates. It is shown that the inclusion of decay chain build-up is essential to avoid underestimation of the radiological impact assessment of the repository. The model can be a useful tool for evaluating the source term of the radionuclide transport models used for the radiological impact assessment of high-level radioactive waste repositories.

Materials Flow through Industry Supply Chain Modeling Tool | Advanced

Science.gov Websites

efficiency. It also performs supply chain scale analyses to quantify the impacts and benefits of next , read Evaluating opportunities to improve material and energy impacts in commodity supply chains

Application of a food chain model to polychlorinated biphenyl contamination of the lobster and winter flounder food chains in New Bedford Harbor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Connolly, J.P.

As part of a Remedial Investigation/Feasibility Study for the New Bedford Harbor Superfund site a model of polychlorinated biphenyls (PCBs) in the lobster and winter flounder food chains was developed. This model successfully reproduces tri-, tetra-, penta-, and hexachlorobiphenyl concentrations observed at all levels of the food chain and across the 2 order of magnitude concentration gradient in the system. The model indicated that PCB concentrations in the flounder and, to a lesser extent, in the lobster are derived from the sediment. Dietary uptake exceeds uptake across the gill for all four homologues and becomes the dominant route at themore » higher chlorinated homologues. The assimilation efficiency of ingested PCB apparently declines from relatively high values for tri-chlorobiphenyl to relatively low values for hexachlorobiphenyl. Differences in observed lobster and flounder PCB concentrations appear to be due to differences in the importance of the benthic component of the food chains of these animals and differences in whole body lipid content.« less

3D finite element modelling of force transmission and particle fracture of sand

DOE Office of Scientific and Technical Information (OSTI.GOV)

Imseeh, Wadi H.; Alshibli, Khalid A.

Global compressive loading of granular media causes rearrangements of particles into a denser configuration. Under 1D compression, researchers observed that particles initially translate and rotate which lead to more contacts between particles and the development of force chains to resist applied loads. Particles within force chains resist most of the applied loads while neighbor particles provide lateral support to prevent particles within force chains from buckling. Several experimental and numerical models have been proposed in the literature to characterize force chains within granular materials. This paper presents a 3D finite element (FE) model that simulates 1D compression experiment on F-75more » Ottawa sand. The FE mesh of particles closely matched 3D physical shape of sand particles that were acquired using 3D synchrotron micro-computed tomography (SMT) technique. The paper presents a quantitative assessment of the model, in which evolution of force chains, fracture modes, and stress-strain relationships showed an excellent agreement with experimental measurements reported by Cil et al. Alshibli (2017).« less

The Advancement Value Chain: An Exploratory Model

ERIC Educational Resources Information Center

Leonard, Edward F., III

2005-01-01

Since the introduction of the value chain concept in 1985, several varying, yet virtually similar, value chains have been developed for the business enterprise. Shifting to higher education, can a value chain be found that links together the various activities of advancement so that an institution's leaders can actually look at the philanthropic…

Reasons for Staying: A Test of the Chain of Response Model among Community-College Students. AIR 2001 Annual Forum Paper.

ERIC Educational Resources Information Center

Salomonson, Kristen; Moss, Brian G.; Hill, H. Leon

This paper uses the Chain of Response Model (CRM) to help explain retention in the community college population. In the CRM, the student's decision to remain at an educational institution is not an isolated act, but rather the result of a complex chain of responses based on her/his cognitive evaluation of the present situation. The authors applied…

Asymptotic study of pulsating evolution of overdriven and CJ detonation with a chain-branching kinetics model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Short, Mark; Chliquete, Carlos

2011-01-20

The pulsating dynamics of gaseous detonations with a model two-step chain-branching kinetic mechanism are studied both numerically and asymptotically. The model studied here was also used in [4], [3] and [2] and mimics the attributes of some chain-branching reaction mechanisms. Specifically, the model comprises a chain-initiationlbranching zone with an Arrhenius temperature-sensitive rate behind the detonation shock where fuel is converted into chain-radical with no heat release. This is followed by a chain-termination zone having a temperature insensitive rate where the exothermic heat of reaction is released. The lengths of these two zones depend on the relative rates of each stage.more » It was determined in [4] and [3] via asymptotic and numerical analysis that the ratio of the length of the chain-branching zone to that of the chain-initation zone relative to the size of the von Neumann state scaled activation energy in the chain initiation/branching zone has a primary influence of the stability of one-dimensional pulsating instability behavior for this model. In [2], the notion of a specific stability parameter related to this ratio was proposed that determines the boundary between stable and unstable waves. In [4], a slow-time varying asymptotic study was conducted of pulsating instability of Chapman-Jouguet (CJ) detonations with the above two-step rate model, assuming a large activation energy for the chain-initiation zone and a chain-termination zone longer than the chain-initiation zone. Deviations D{sub n}{sup (1)} ({tau}) of the detonation velocity from Chapman-Jouguet were of the order of the non-dimensional activation energy. Solutions were sought for a pulsation timescale of the order of the non-dimensional activation energy times the particle transit time through the induction zone. On this time-scale, the evolution of the chain-initation zone is quasi-steady. In [4], a time-dependent non-linear evolution equation for D{sub n}{sup (1)} ({tau}) was then constructed via a perturbation procedure for cases where the ratio of the length of the chain-termination zone to chain-initiation zone was less than the non-dimensional activation energy. To leading order, the steady CJ detonation was found to be unstable; higher-order corrections lead to the construction of a stability limit between stable and unsteady pulsating solutions. One conclusion from this study is that for a stability limit to occur at leading order, the period of pulsation of the detonation must occur on the time scale of particle passage through the longer chain-termination zone, while the length of the chain-termination zone must be of order of the non-dimensional activation energy longer than the chain-initiation zone. The relevance of these suggested scalings was verified via numerical solutions of the full Euler system in [3], and formed the basis of the stability parameter criteria suggested in [2]. In the following, we formulate an asymptotic study based on these new suggested scales, studying the implications for describing pulsating behavior in gaseous chain-branching detonations. Specifically, we find that the chain-induction zone structure is the same as that studied in [4]. However, the study of unsteady evolution in the chain-termination region is now governed by a set of asymptotically derived nonlinear POEs. Equations for the linear stablity behavior of this set of POE's is obtained, while the nonlinear POEs are solved numerically using a shock-attached, shock-fitting method developed by Henrick et aJ. [1]. The results thus far show that the stability threshold calculated using the new ratio of the chain-termination zone length to that of the chain-initiation zone yields a marked improvement over [2]. Additionally, solutions will be compared with predictions obtained from the solution of the full Euler system. Finally, the evolution equation previously derived in [4] has been generalized to consider both arbitrary reaction orders and any degree of overdrive.« less

An Overview of Markov Chain Methods for the Study of Stage-Sequential Developmental Processes

ERIC Educational Resources Information Center

Kapland, David

2008-01-01

This article presents an overview of quantitative methodologies for the study of stage-sequential development based on extensions of Markov chain modeling. Four methods are presented that exemplify the flexibility of this approach: the manifest Markov model, the latent Markov model, latent transition analysis, and the mixture latent Markov model.…

Toward tailoring Majorana bound states in artificially constructed magnetic atom chains on elemental superconductors

PubMed Central

Thorwart, Michael

2018-01-01

Realizing Majorana bound states (MBS) in condensed matter systems is a key challenge on the way toward topological quantum computing. As a promising platform, one-dimensional magnetic chains on conventional superconductors were theoretically predicted to host MBS at the chain ends. We demonstrate a novel approach to design of model-type atomic-scale systems for studying MBS using single-atom manipulation techniques. Our artificially constructed atomic Fe chains on a Re surface exhibit spin spiral states and a remarkable enhancement of the local density of states at zero energy being strongly localized at the chain ends. Moreover, the zero-energy modes at the chain ends are shown to emerge and become stabilized with increasing chain length. Tight-binding model calculations based on parameters obtained from ab initio calculations corroborate that the system resides in the topological phase. Our work opens new pathways to design MBS in atomic-scale hybrid structures as a basis for fault-tolerant topological quantum computing. PMID:29756034

Toward tailoring Majorana bound states in artificially constructed magnetic atom chains on elemental superconductors.

PubMed

Kim, Howon; Palacio-Morales, Alexandra; Posske, Thore; Rózsa, Levente; Palotás, Krisztián; Szunyogh, László; Thorwart, Michael; Wiesendanger, Roland

2018-05-01

Realizing Majorana bound states (MBS) in condensed matter systems is a key challenge on the way toward topological quantum computing. As a promising platform, one-dimensional magnetic chains on conventional superconductors were theoretically predicted to host MBS at the chain ends. We demonstrate a novel approach to design of model-type atomic-scale systems for studying MBS using single-atom manipulation techniques. Our artificially constructed atomic Fe chains on a Re surface exhibit spin spiral states and a remarkable enhancement of the local density of states at zero energy being strongly localized at the chain ends. Moreover, the zero-energy modes at the chain ends are shown to emerge and become stabilized with increasing chain length. Tight-binding model calculations based on parameters obtained from ab initio calculations corroborate that the system resides in the topological phase. Our work opens new pathways to design MBS in atomic-scale hybrid structures as a basis for fault-tolerant topological quantum computing.

Growth Behavior, Geometrical Shape, and Second CMC of Micelles Formed by Cationic Gemini Esterquat Surfactants.

PubMed

Bergström, L Magnus; Tehrani-Bagha, Alireza; Nagy, Gergely

2015-04-28

Micelles formed by novel gemini esterquat surfactants have been investigated with small-angle neutron scattering (SANS). The growth behavior of the micelles is found to differ conspicuously depending on the length of the gemini surfactant spacer group. The gemini surfactant with a long spacer form rather small triaxial ellipsoidal tablet-shaped micelles that grow weakly with surfactant concentration in the entire range of measured concentrations. Geminis with a short spacer, on the other hand, form weakly growing oblates or tablets at low concentrations that start to grow much more strongly into polydisperse rodlike or wormlike micelles at higher concentrations. The latter behavior is consistent with the presence of a second CMC that marks the transition from the weakly to the strongly growing regime. It is found that the growth behavior in terms of aggregation number as a function of surfactant concentration always appear concave in weakly growing regimes, while switching to convex behavior in strongly growing regimes. As a result, we are able to determine the second CMC of the geminis with short spacer by means of suggesting a rather precise definition of it, located at the point of inflection of the growth curve that corresponds to the transition from concave to convex growth behavior. Our SANS results are rationalized by comparison with the recently developed general micelle model. In particular, this theory is able to explain and reproduce the characteristic appearances of the experimental growth curves, including the presence of a second CMC and the convex strongly growing regime beyond. By means of optimizing the agreement between predictions from the general micelle model and results from SANS experiments, we are able to determine the three bending elasticity constants spontaneous curvature, bending rigidity, and saddle-splay constant for each surfactant.

Modified allocation capacitated planning model in blood supply chain management

NASA Astrophysics Data System (ADS)

Mansur, A.; Vanany, I.; Arvitrida, N. I.

2018-04-01

Blood supply chain management (BSCM) is a complex process management that involves many cooperating stakeholders. BSCM involves four echelon processes, which are blood collection or procurement, production, inventory, and distribution. This research develops an optimization model of blood distribution planning. The efficiency of decentralization and centralization policies in a blood distribution chain are compared, by optimizing the amount of blood delivered from a blood center to a blood bank. This model is developed based on allocation problem of capacitated planning model. At the first stage, the capacity and the cost of transportation are considered to create an initial capacitated planning model. Then, the inventory holding and shortage costs are added to the model. These additional parameters of inventory costs lead the model to be more realistic and accurate.

Characterizing the tradeoffs and costs associated with transportation congestion in supply chains.

DOT National Transportation Integrated Search

2010-01-21

We consider distribution and location-planning models for supply chains that explicitly : account for traffic congestion effects. The majority of facility location and transportation : planning models in the operations research literature consider fa...

Integrated forward and reverse supply chain: A tire case study.

PubMed

Pedram, Ali; Yusoff, Nukman Bin; Udoncy, Olugu Ezutah; Mahat, Abu Bakar; Pedram, Payam; Babalola, Ayo

2017-02-01

This paper attempts to integrate both a forward and reverse supply chain to design a closed-loop supply chain network (CLSC). The problem in the design of a CLSC network is uncertainty in demand, return products and the quality of return products. Scenario analyses are generated to overcome this uncertainty. In contrast to the existing supply chain network design models, a new application of a CLSC network was studied in this paper to reduce waste. A multi-product, multi-tier mixed integer linear model is developed for a CLSC network design. The main objective is to maximize profit and provide waste management decision support in order to minimize pollution. The result shows applicability of the model in the tire industry. The model determines the number and the locations of facilities and the material flows between these facilities. Copyright © 2016 Elsevier Ltd. All rights reserved.

Chemical supply chain modeling for analysis of homeland security events

DOE PAGES

Ehlen, Mark A.; Sun, Amy C.; Pepple, Mark A.; ...

2013-09-06

The potential impacts of man-made and natural disasters on chemical plants, complexes, and supply chains are of great importance to homeland security. To be able to estimate these impacts, we developed an agent-based chemical supply chain model that includes: chemical plants with enterprise operations such as purchasing, production scheduling, and inventories; merchant chemical markets, and multi-modal chemical shipments. Large-scale simulations of chemical-plant activities and supply chain interactions, running on desktop computers, are used to estimate the scope and duration of disruptive-event impacts, and overall system resilience, based on the extent to which individual chemical plants can adjust their internal operationsmore » (e.g., production mixes and levels) versus their external interactions (market sales and purchases, and transportation routes and modes). As a result, to illustrate how the model estimates the impacts of a hurricane disruption, a simple example model centered on 1,4-butanediol is presented.« less

Predicting the stability of nanodevices

NASA Astrophysics Data System (ADS)

Lin, Z. Z.; Yu, W. F.; Wang, Y.; Ning, X. J.

2011-05-01

A simple model based on the statistics of single atoms is developed to predict the stability or lifetime of nanodevices without empirical parameters. Under certain conditions, the model produces the Arrhenius law and the Meyer-Neldel compensation rule. Compared with the classical molecular-dynamics simulations for predicting the stability of monatomic carbon chain at high temperature, the model is proved to be much more accurate than the transition state theory. Based on the ab initio calculation of the static potential, the model can give out a corrected lifetime of monatomic carbon and gold chains at higher temperature, and predict that the monatomic chains are very stable at room temperature.

Molecular dynamics modeling of PPTA crystallite mechanical properties in the presence of defects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mercer, Brian; Zywicz, Edward; Papadopoulos, Panayiotis

Here, the mechanical properties of PPTA crystallites, the fundamental building blocks of aramid polymer fibers such as Kevlar® and Twaron®, are studied here using molecular dynamics simulations. The ReaxFF interatomic potential is employed to study crystallite failure via covalent and hydrogen bond rupture in constant strain-rate tensile loading simulations. Emphasis is placed on analyzing how chain-end defects in the crystallite influence its mechanical response and fracture strength. Chain-end defects are found to affect the behavior of nearby chains in a region of the PPTA crystallite that is small relative to the typical crystallite size in manufactured aramid fibers. The centralmore » Csingle bondN bond along the backbone chain is identified as the weakest in the PPTA polymer chain backbone in dynamic strain-to-failure simulations of the crystallite. It is found that clustering of chain-ends leads to reduced crystallite strength and crystallite failure via hydrogen bond rupture and chain sliding, whereas randomly scattered defects impact the strength less and failure is by covalent bond rupture and chain scission. The axial crystallite modulus increases with increasing chain length and is independent of chain-end defect locations. On the basis of these findings, a theoretical model is proposed to predict the axial modulus as a function of chain length.« less

Molecular dynamics modeling of PPTA crystallite mechanical properties in the presence of defects

DOE PAGES

Mercer, Brian; Zywicz, Edward; Papadopoulos, Panayiotis

2017-03-11

Here, the mechanical properties of PPTA crystallites, the fundamental building blocks of aramid polymer fibers such as Kevlar® and Twaron®, are studied here using molecular dynamics simulations. The ReaxFF interatomic potential is employed to study crystallite failure via covalent and hydrogen bond rupture in constant strain-rate tensile loading simulations. Emphasis is placed on analyzing how chain-end defects in the crystallite influence its mechanical response and fracture strength. Chain-end defects are found to affect the behavior of nearby chains in a region of the PPTA crystallite that is small relative to the typical crystallite size in manufactured aramid fibers. The centralmore » Csingle bondN bond along the backbone chain is identified as the weakest in the PPTA polymer chain backbone in dynamic strain-to-failure simulations of the crystallite. It is found that clustering of chain-ends leads to reduced crystallite strength and crystallite failure via hydrogen bond rupture and chain sliding, whereas randomly scattered defects impact the strength less and failure is by covalent bond rupture and chain scission. The axial crystallite modulus increases with increasing chain length and is independent of chain-end defect locations. On the basis of these findings, a theoretical model is proposed to predict the axial modulus as a function of chain length.« less

Buckling of paramagnetic chains in soft gels

NASA Astrophysics Data System (ADS)

Huang, Shilin; Pessot, Giorgio; Cremer, Peet; Weeber, Rudolf; Holm, Christian; Nowak, Johannes; Odenbach, Stefan; Menzel, Andreas M.; Auernhammer, Günter K.

We study the magneto-elastic coupling behavior of paramagnetic chains in soft polymer gels exposed to external magnetic fields. To this end, a laser scanning confocal microscope is used to observe the morphology of the paramagnetic chains together with the deformation field of the surrounding gel network. The paramagnetic chains in soft polymer gels show rich morphological shape changes under oblique magnetic fields, in particular a pronounced buckling deformation. The details of the resulting morphological shapes depend on the length of the chain, the strength of the external magnetic field, and the modulus of the gel. Based on the observation that the magnetic chains are strongly coupled to the surrounding polymer network, a simplified model is developed to describe their buckling behavior. A coarse-grained molecular dynamics simulation model featuring an increased matrix stiffness on the surfaces of the particles leads to morphologies in agreement with the experimentally observed buckling effects.

R-matrix-valued Lax pairs and long-range spin chains

NASA Astrophysics Data System (ADS)

Sechin, I.; Zotov, A.

2018-06-01

In this paper we discuss R-matrix-valued Lax pairs for slN Calogero-Moser model and their relation to integrable quantum long-range spin chains of the Haldane-Shastry-Inozemtsev type. First, we construct the R-matrix-valued Lax pairs for the third flow of the classical Calogero-Moser model. Then we notice that the scalar parts (in the auxiliary space) of the M-matrices corresponding to the second and third flows have form of special spin exchange operators. The freezing trick restricts them to quantum Hamiltonians of long-range spin chains. We show that for a special choice of the R-matrix these Hamiltonians reproduce those for the Inozemtsev chain. In the general case related to the Baxter's elliptic R-matrix we obtain a natural anisotropic extension of the Inozemtsev chain. Commutativity of the Hamiltonians is verified numerically. Trigonometric limits lead to the Haldane-Shastry chains and their anisotropic generalizations.

Theory and simulation of the dynamics, deformation, and breakup of a chain of superparamagnetic beads under a rotating magnetic field

NASA Astrophysics Data System (ADS)

Vázquez-Quesada, A.; Franke, T.; Ellero, M.

2017-03-01

In this work, an analytical model for the behavior of superparamagnetic chains under the effect of a rotating magnetic field is presented. It is postulated that the relevant mechanisms for describing the shape and breakup of the chains into smaller fragments are the induced dipole-dipole magnetic force on the external beads, their translational and rotational drag forces, and the tangential lubrication between particles. Under this assumption, the characteristic S-shape of the chain can be qualitatively understood. Furthermore, based on a straight chain approximation, a novel analytical expression for the critical frequency for the chain breakup is obtained. In order to validate the model, the analytical expressions are compared with full three-dimensional smoothed particle hydrodynamics simulations of magnetic beads showing excellent agreement. Comparison with previous theoretical results and experimental data is also reported.

Design and analysis of the Gemini chain system in dual clutch transmission of automobile

NASA Astrophysics Data System (ADS)

Cheng, Yabing; Guo, Haitao; Fu, Zhenming; Wan, Nen; Li, Lei; Wang, Yang

2015-01-01

Chain drive system is widely used in the conditions of high-speed, overload, variable speed and load. Many studies are focused on the meshing theory and wear characteristics of chain drive system, but system design, analysis, and noise characteristics of the chain drive system are weak. System design and noise characteristic are studied for a new type Gemini chain of dual-clutch automatic transmission. Based on the meshing theory of silent chain, the design parameters of the Gemini chain system are calculated and the mathematical models and dynamic analysis models of the Gemini chain system are established. Dynamic characteristics of the Gemini chain system is simulated and the contact force of plate and pin, plate and sprockets, the chain tension forces, the transmission error and the stress of plates and pins are analyzed. According to the simulation results of the Gemini chain system, the noise experiment about system is carried out. The noise values are tested at different speed and load and spectral characteristics are analyzed. The results of simulation and experimental show that the contact forces of plate and pin, plate and sprockets are smaller than the allowable stress values, the chain tension force is less than ultimate tension and transmission error is limited in 1.2%. The noise values can meet the requirements of industrial design, and it is proved that the design and analysis method of the Gemini chain system is scientific and feasible. The design and test system is built from analysis to test of Gemini chain system. This research presented will provide a corresponding theoretical guidance for the design and dynamic characteristics and noise characteristics of chain drive system.

Modeling relief demands in an emergency supply chain system under large-scale disasters based on a queuing network.

PubMed

He, Xinhua; Hu, Wenfa

2014-01-01

This paper presents a multiple-rescue model for an emergency supply chain system under uncertainties in large-scale affected area of disasters. The proposed methodology takes into consideration that the rescue demands caused by a large-scale disaster are scattered in several locations; the servers are arranged in multiple echelons (resource depots, distribution centers, and rescue center sites) located in different places but are coordinated within one emergency supply chain system; depending on the types of rescue demands, one or more distinct servers dispatch emergency resources in different vehicle routes, and emergency rescue services queue in multiple rescue-demand locations. This emergency system is modeled as a minimal queuing response time model of location and allocation. A solution to this complex mathematical problem is developed based on genetic algorithm. Finally, a case study of an emergency supply chain system operating in Shanghai is discussed. The results demonstrate the robustness and applicability of the proposed model.

Modeling Relief Demands in an Emergency Supply Chain System under Large-Scale Disasters Based on a Queuing Network

PubMed Central

He, Xinhua

2014-01-01

This paper presents a multiple-rescue model for an emergency supply chain system under uncertainties in large-scale affected area of disasters. The proposed methodology takes into consideration that the rescue demands caused by a large-scale disaster are scattered in several locations; the servers are arranged in multiple echelons (resource depots, distribution centers, and rescue center sites) located in different places but are coordinated within one emergency supply chain system; depending on the types of rescue demands, one or more distinct servers dispatch emergency resources in different vehicle routes, and emergency rescue services queue in multiple rescue-demand locations. This emergency system is modeled as a minimal queuing response time model of location and allocation. A solution to this complex mathematical problem is developed based on genetic algorithm. Finally, a case study of an emergency supply chain system operating in Shanghai is discussed. The results demonstrate the robustness and applicability of the proposed model. PMID:24688367

Model Development of Cold Chains for Fresh Fruits and Vegetables Distribution: A Case Study in Bali Province

NASA Astrophysics Data System (ADS)

Waisnawa, I. N. G. S.; Santosa, I. D. M. C.; Sunu, I. P. W.; Wirajati, IGAB

2018-01-01

In developing countries such as Indonesia, as much as 40% of total vegetables and fruits production becomes waste because of lack refrigeration. This condition also contributes a food crisis problem besides other factor such as, climate change and number of population. Cold chain system that will be modelled in this study is for vegetables and fruits and refrigeration system as the main devices. In future, this system will play an important role for the food crisis solution where fresh food can be distributed very well with significant low waste. The fresh food also can be kept with good quality and hygienist (bacteria contaminated). Cold Chain model will be designed using refrigeration components including, pre cooling chiller, cold room, and truck refrigeration. This study will be conducted by survey and observation di around Bali Province focus on vegetables and fruits production center. Interviews and questionnaire will be also done to get some information about the conventional distribution obstacles and problem. Distribution mapping will be developed and created. The data base of the storage characteristic of the fruits and vegetable also collected through experiment and secondary data. Depend on the mapping and data base can be developed a cold chain model that has the best performance application. The model will be can directly apply in Bali to get eligible cold chain in Bali. The cold chain model will be compared with the conventional distribution system using ALCC/LCC method and also others factor and will be weighted to get better results.

Traveling-wave solutions in continuous chains of unidirectionally coupled oscillators

NASA Astrophysics Data System (ADS)

Glyzin, S. D.; Kolesov, A. Yu; Rozov, N. Kh

2017-12-01

Proposed is a mathematical model of a continuous annular chain of unidirectionally coupled generators given by certain nonlinear advection-type hyperbolic boundary value problem. Such problems are constructed by a limit transition from annular chains of unidirectionally coupled ordinary differential equations with an unbounded increase in the number of links. It is shown that any preassigned finite number of stable periodic motions of the traveling-wave type can coexist in the model.

Optimizing decentralized production-distribution planning problem in a multi-period supply chain network under uncertainty

NASA Astrophysics Data System (ADS)

Nourifar, Raheleh; Mahdavi, Iraj; Mahdavi-Amiri, Nezam; Paydar, Mohammad Mahdi

2017-09-01

Decentralized supply chain management is found to be significantly relevant in today's competitive markets. Production and distribution planning is posed as an important optimization problem in supply chain networks. Here, we propose a multi-period decentralized supply chain network model with uncertainty. The imprecision related to uncertain parameters like demand and price of the final product is appropriated with stochastic and fuzzy numbers. We provide mathematical formulation of the problem as a bi-level mixed integer linear programming model. Due to problem's convolution, a structure to solve is developed that incorporates a novel heuristic algorithm based on Kth-best algorithm, fuzzy approach and chance constraint approach. Ultimately, a numerical example is constructed and worked through to demonstrate applicability of the optimization model. A sensitivity analysis is also made.

Predicting the chemical stability of monatomic chains

NASA Astrophysics Data System (ADS)

Lin, Zheng-Zhe; Chen, Xi

2013-02-01

A simple model for evaluating the thermal atomic transfer rates in nanosystems (Lin Z.-Z. et al., EPL, 94 (2011) 40002) was developed to predict the chemical reaction rates of nanosystems with small gas molecules. The accuracy of the model was verified by MD simulations for molecular adsorption and desorption on a monatomic chain. By the prediction, a monatomic carbon chain should survive for 1.2 × 102 years in the ambient of 1 atm O2 at room temperature, and it is very invulnerable to N2, H2O, NO2, CO and CO2, while a monatomic gold chain quickly ruptures in vacuum. It is worth noting that since the model can be easily applied via common ab initio calculations, it could be widely used in the prediction of chemical stability of nanosystems.

Critical appraisal of assumptions in chains of model calculations used to project local climate impacts for adaptation decision support—the case of Baakse Beek

NASA Astrophysics Data System (ADS)

van der Sluijs, Jeroen P.; Arjan Wardekker, J.

2015-04-01

In order to enable anticipation and proactive adaptation, local decision makers increasingly seek detailed foresight about regional and local impacts of climate change. To this end, the Netherlands Models and Data-Centre implemented a pilot chain of sequentially linked models to project local climate impacts on hydrology, agriculture and nature under different national climate scenarios for a small region in the east of the Netherlands named Baakse Beek. The chain of models sequentially linked in that pilot includes a (future) weather generator and models of respectively subsurface hydrogeology, ground water stocks and flows, soil chemistry, vegetation development, crop yield and nature quality. These models typically have mismatching time step sizes and grid cell sizes. The linking of these models unavoidably involves the making of model assumptions that can hardly be validated, such as those needed to bridge the mismatches in spatial and temporal scales. Here we present and apply a method for the systematic critical appraisal of model assumptions that seeks to identify and characterize the weakest assumptions in a model chain. The critical appraisal of assumptions presented in this paper has been carried out ex-post. For the case of the climate impact model chain for Baakse Beek, the three most problematic assumptions were found to be: land use and land management kept constant over time; model linking of (daily) ground water model output to the (yearly) vegetation model around the root zone; and aggregation of daily output of the soil hydrology model into yearly input of a so called ‘mineralization reduction factor’ (calculated from annual average soil pH and daily soil hydrology) in the soil chemistry model. Overall, the method for critical appraisal of model assumptions presented and tested in this paper yields a rich qualitative insight in model uncertainty and model quality. It promotes reflectivity and learning in the modelling community, and leads to well informed recommendations for model improvement.

Educational Aspirations: Markov and Poisson Models. Rural Industrial Development Project Working Paper Number 14, August 1971.

ERIC Educational Resources Information Center

Kayser, Brian D.

The fit of educational aspirations of Illinois rural high school youths to 3 related one-parameter mathematical models was investigated. The models used were the continuous-time Markov chain model, the discrete-time Markov chain, and the Poisson distribution. The sample of 635 students responded to questionnaires from 1966 to 1969 as part of an…

Housing Value Projection Model Related to Educational Planning: The Feasibility of a New Methodology. Final Report.

ERIC Educational Resources Information Center

Helbock, Richard W.; Marker, Gordon

This study concerns the feasibility of a Markov chain model for projecting housing values and racial mixes. Such projections could be used in planning the layout of school districts to achieve desired levels of socioeconomic heterogeneity. Based upon the concepts and assumptions underlying a Markov chain model, it is concluded that such a model is…

Sustainable Supplier Performance Evaluation and Selection with Neofuzzy TOPSIS Method

PubMed Central

Chaharsooghi, S. K.; Ashrafi, Mehdi

2014-01-01

Supplier selection plays an important role in the supply chain management and traditional criteria such as price, quality, and flexibility are considered for supplier performance evaluation in researches. In recent years sustainability has received more attention in the supply chain management literature with triple bottom line (TBL) describing the sustainability in supply chain management with social, environmental, and economic initiatives. This paper explores sustainability in supply chain management and examines the problem of identifying a new model for supplier selection based on extended model of TBL approach in supply chain by presenting fuzzy multicriteria method. Linguistic values of experts' subjective preferences are expressed with fuzzy numbers and Neofuzzy TOPSIS is proposed for finding the best solution of supplier selection problem. Numerical results show that the proposed model is efficient for integrating sustainability in supplier selection problem. The importance of using complimentary aspects of sustainability and Neofuzzy TOPSIS concept in sustainable supplier selection process is shown with sensitivity analysis. PMID:27379267

Optimization of Location-Routing Problem for Cold Chain Logistics Considering Carbon Footprint.

PubMed

Wang, Songyi; Tao, Fengming; Shi, Yuhe

2018-01-06

In order to solve the optimization problem of logistics distribution system for fresh food, this paper provides a low-carbon and environmental protection point of view, based on the characteristics of perishable products, and combines with the overall optimization idea of cold chain logistics distribution network, where the green and low-carbon location-routing problem (LRP) model in cold chain logistics is developed with the minimum total costs as the objective function, which includes carbon emission costs. A hybrid genetic algorithm with heuristic rules is designed to solve the model, and an example is used to verify the effectiveness of the algorithm. Furthermore, the simulation results obtained by a practical numerical example show the applicability of the model while provide green and environmentally friendly location-distribution schemes for the cold chain logistics enterprise. Finally, carbon tax policies are introduced to analyze the impact of carbon tax on the total costs and carbon emissions, which proves that carbon tax policy can effectively reduce carbon dioxide emissions in cold chain logistics network.

Sustainable Supplier Performance Evaluation and Selection with Neofuzzy TOPSIS Method.

PubMed

Chaharsooghi, S K; Ashrafi, Mehdi

2014-01-01

Supplier selection plays an important role in the supply chain management and traditional criteria such as price, quality, and flexibility are considered for supplier performance evaluation in researches. In recent years sustainability has received more attention in the supply chain management literature with triple bottom line (TBL) describing the sustainability in supply chain management with social, environmental, and economic initiatives. This paper explores sustainability in supply chain management and examines the problem of identifying a new model for supplier selection based on extended model of TBL approach in supply chain by presenting fuzzy multicriteria method. Linguistic values of experts' subjective preferences are expressed with fuzzy numbers and Neofuzzy TOPSIS is proposed for finding the best solution of supplier selection problem. Numerical results show that the proposed model is efficient for integrating sustainability in supplier selection problem. The importance of using complimentary aspects of sustainability and Neofuzzy TOPSIS concept in sustainable supplier selection process is shown with sensitivity analysis.

An approach for formalising the supply chain operations

NASA Astrophysics Data System (ADS)

Zdravković, Milan; Panetto, Hervé; Trajanović, Miroslav; Aubry, Alexis

2011-11-01

Reference models play an important role in the knowledge management of the various complex collaboration domains (such as supply chain networks). However, they often show a lack of semantic precision and, they are sometimes incomplete. In this article, we present an approach to overcome semantic inconsistencies and incompleteness of the Supply Chain Operations Reference (SCOR) model and hence improve its usefulness and expand the application domain. First, we describe a literal web ontology language (OWL) specification of SCOR concepts (and related tools) built with the intention to preserve the original approach in the classification of process reference model entities, and hence enable the effectiveness of usage in original contexts. Next, we demonstrate the system for its exploitation, in specific - tools for SCOR framework browsing and rapid supply chain process configuration. Then, we describe the SCOR-Full ontology, its relations with relevant domain ontology and show how it can be exploited for improvement of SCOR ontological framework competence. Finally, we elaborate the potential impact of the presented approach, to interoperability of systems in supply chain networks.

Coarse-grained, foldable, physical model of the polypeptide chain.

PubMed

Chakraborty, Promita; Zuckermann, Ronald N

2013-08-13

Although nonflexible, scaled molecular models like Pauling-Corey's and its descendants have made significant contributions in structural biology research and pedagogy, recent technical advances in 3D printing and electronics make it possible to go one step further in designing physical models of biomacromolecules: to make them conformationally dynamic. We report here the design, construction, and validation of a flexible, scaled, physical model of the polypeptide chain, which accurately reproduces the bond rotational degrees of freedom in the peptide backbone. The coarse-grained backbone model consists of repeating amide and α-carbon units, connected by mechanical bonds (corresponding to ϕ and ψ) that include realistic barriers to rotation that closely approximate those found at the molecular scale. Longer-range hydrogen-bonding interactions are also incorporated, allowing the chain to readily fold into stable secondary structures. The model is easily constructed with readily obtainable parts and promises to be a tremendous educational aid to the intuitive understanding of chain folding as the basis for macromolecular structure. Furthermore, this physical model can serve as the basis for linking tangible biomacromolecular models directly to the vast array of existing computational tools to provide an enhanced and interactive human-computer interface.

Human disease mortality kinetics are explored through a chain model embodying principles of extreme value theory and competing risks.

PubMed

Juckett, D A; Rosenberg, B

1992-04-21

The distributions for human disease-specific mortality exhibit two striking characteristics: survivorship curves that intersect near the longevity limit; and, the clustering of best-fitting Weibull shape parameter values into groups centered on integers. Correspondingly, we have hypothesized that the distribution intersections result from either competitive processes or population partitioning and the integral clustering in the shape parameter results from the occurrence of a small number of rare, rate-limiting events in disease progression. In this report we initiate a theoretical examination of these questions by exploring serial chain model dynamics and parameteric competing risks theory. The links in our chain models are composed of more than one bond, where the number of bonds in a link are denoted the link size and are the number of events necessary to break the link and, hence, the chain. We explored chains with all links of the same size or with segments of the chain composed of different size links (competition). Simulations showed that chain breakage dynamics depended on the weakest-link principle and followed kinetics of extreme-values which were very similar to human mortality kinetics. In particular, failure distributions for simple chains were Weibull-type extreme-value distributions with shape parameter values that were identifiable with the integral link size in the limit of infinite chain length. Furthermore, for chains composed of several segments of differing link size, the survival distributions for the various segments converged at a point in the S(t) tails indistinguishable from human data. This was also predicted by parameteric competing risks theory using Weibull underlying distributions. In both the competitive chain simulations and the parametric competing risks theory, however, the shape values for the intersecting distributions deviated from the integer values typical of human data. We conclude that rare events can be the source of integral shapes in human mortality, that convergence is a salient feature of multiple endpoints, but that pure competition may not be the best explanation for the exact type of convergence observable in human mortality. Finally, while the chain models were not motivated by any specific biological structures, interesting biological correlates to them may be useful in gerontological research.

Modelling Faculty Replacement Strategies Using a Time-Dependent Finite Markov-Chain Process.

ERIC Educational Resources Information Center

Hackett, E. Raymond; Magg, Alexander A.; Carrigan, Sarah D.

1999-01-01

Describes the use of a time-dependent Markov-chain model to develop faculty-replacement strategies within a college at a research university. The study suggests that a stochastic modelling approach can provide valuable insight when planning for personnel needs in the immediate (five-to-ten year) future. (MSE)

A discrete scattering series representation for lattice embedded models of chain cyclization

NASA Astrophysics Data System (ADS)

Fraser, Simon J.; Winnik, Mitchell A.

1980-01-01

In this paper we develop a lattice based model of chain cyclization in the presence of a set of occupied sites V in the lattice. We show that within the approximation of a Markovian chain propagator the effect of V on the partition function for the system can be written as a time-ordered exponential series in which V behaves like a scattering potential and chainlength is the timelike parameter. The discrete and finite nature of this model allows us to obtain rigorous upper and lower bounds to the series limit. We adapt these formulas to calculation of the partition functions and cyclization probabilities of terminally and globally cyclizing chains. Two classes of cyclization are considered: in the first model the target set H may be visited repeatedly (the Markovian model); in the second case vertices in H may be visited at most once(the non-Markovian or taboo model). This formulation depends on two fundamental combinatorial structures, namely the inclusion-exclusion principle and the set of subsets of a set. We have tried to interpret these abstract structures with physical analogies throughout the paper.

An affine microsphere approach to modeling strain-induced crystallization in rubbery polymers

NASA Astrophysics Data System (ADS)

Nateghi, A.; Dal, H.; Keip, M.-A.; Miehe, C.

2018-01-01

Upon stretching a natural rubber sample, polymer chains orient themselves in the direction of the applied load and form crystalline regions. When the sample is retracted, the original amorphous state of the network is restored. Due to crystallization, properties of rubber change considerably. The reinforcing effect of the crystallites stiffens the rubber and increases the crack growth resistance. It is of great importance to understand the mechanism leading to strain-induced crystallization. However, limited theoretical work has been done on the investigation of the associated kinetics. A key characteristic observed in the stress-strain diagram of crystallizing rubber is the hysteresis, which is entirely attributed to strain-induced crystallization. In this work, we propose a micromechanically motivated material model for strain-induced crystallization in rubbers. Our point of departure is constructing a micromechanical model for a single crystallizing polymer chain. Subsequently, a thermodynamically consistent evolution law describing the kinetics of crystallization on the chain level is proposed. This chain model is then incorporated into the affine microsphere model. Finally, the model is numerically implemented and its performance is compared to experimental data.

Fuzzy Markov random fields versus chains for multispectral image segmentation.

PubMed

Salzenstein, Fabien; Collet, Christophe

2006-11-01

This paper deals with a comparison of recent statistical models based on fuzzy Markov random fields and chains for multispectral image segmentation. The fuzzy scheme takes into account discrete and continuous classes which model the imprecision of the hidden data. In this framework, we assume the dependence between bands and we express the general model for the covariance matrix. A fuzzy Markov chain model is developed in an unsupervised way. This method is compared with the fuzzy Markovian field model previously proposed by one of the authors. The segmentation task is processed with Bayesian tools, such as the well-known MPM (Mode of Posterior Marginals) criterion. Our goal is to compare the robustness and rapidity for both methods (fuzzy Markov fields versus fuzzy Markov chains). Indeed, such fuzzy-based procedures seem to be a good answer, e.g., for astronomical observations when the patterns present diffuse structures. Moreover, these approaches allow us to process missing data in one or several spectral bands which correspond to specific situations in astronomy. To validate both models, we perform and compare the segmentation on synthetic images and raw multispectral astronomical data.

Multi-scale modeling of diffusion-controlled reactions in polymers: renormalisation of reactivity parameters.

PubMed

Everaers, Ralf; Rosa, Angelo

2012-01-07

The quantitative description of polymeric systems requires hierarchical modeling schemes, which bridge the gap between the atomic scale, relevant to chemical or biomolecular reactions, and the macromolecular scale, where the longest relaxation modes occur. Here, we use the formalism for diffusion-controlled reactions in polymers developed by Wilemski, Fixman, and Doi to discuss the renormalisation of the reactivity parameters in polymer models with varying spatial resolution. In particular, we show that the adjustments are independent of chain length. As a consequence, it is possible to match reactions times between descriptions with different resolution for relatively short reference chains and to use the coarse-grained model to make quantitative predictions for longer chains. We illustrate our results by a detailed discussion of the classical problem of chain cyclization in the Rouse model, which offers the simplest example of a multi-scale descriptions, if we consider differently discretized Rouse models for the same physical system. Moreover, we are able to explore different combinations of compact and non-compact diffusion in the local and large-scale dynamics by varying the embedding dimension.

The distribution of conformational disorder in the high-temperature phases of the crystalline n-alkanes

NASA Astrophysics Data System (ADS)

Maroncelli, M.; Strauss, H. L.; Snyder, R. G.

1985-03-01

The distributions of conformational defects that exist in the high-temperature phase II (also referred to as the hexagonal or rotator phase) of the crystalline n-alkanes C21 and C29 have been measured by an infrared CD2-substitution technique and have been accounted for in terms of a lattice model that provides freedom for longitudinal displacement of the chains. The defects consist almost entirely of gtg' kinks distributed nonuniformly along the chain. The uneven distribution is indicated in the variation in the concentration of gauche bonds measured at various sites along the chain. The highest concentration is at the chain ends, and the concentrations at interior sites decrease exponentially in going toward the middle. To explain the distribution we used a modification of a lattice model that had been successfully applied to the lipid bilayer. Comparison of observed distributions with those computed from the model indicates that the factors that determine the shape of the distribution are quite different in the n-alkane and bilayer cases. For the bilayer, the dominant factor is the variation in the lateral density of chains; for the n-alkane, the dominant factor is associated with longitudinal displacement of the chains.

Markov Chain Model with Catastrophe to Determine Mean Time to Default of Credit Risky Assets

NASA Astrophysics Data System (ADS)

Dharmaraja, Selvamuthu; Pasricha, Puneet; Tardelli, Paola

2017-11-01

This article deals with the problem of probabilistic prediction of the time distance to default for a firm. To model the credit risk, the dynamics of an asset is described as a function of a homogeneous discrete time Markov chain subject to a catastrophe, the default. The behaviour of the Markov chain is investigated and the mean time to the default is expressed in a closed form. The methodology to estimate the parameters is given. Numerical results are provided to illustrate the applicability of the proposed model on real data and their analysis is discussed.

On extinction time of a generalized endemic chain-binomial model.

PubMed

Aydogmus, Ozgur

2016-09-01

We considered a chain-binomial epidemic model not conferring immunity after infection. Mean field dynamics of the model has been analyzed and conditions for the existence of a stable endemic equilibrium are determined. The behavior of the chain-binomial process is probabilistically linked to the mean field equation. As a result of this link, we were able to show that the mean extinction time of the epidemic increases at least exponentially as the population size grows. We also present simulation results for the process to validate our analytical findings. Copyright © 2016 Elsevier Inc. All rights reserved.

Rupturing the hemi-fission intermediate in membrane fission under tension: Reaction coordinates, kinetic pathways, and free-energy barriers

NASA Astrophysics Data System (ADS)

Zhang, Guojie; Müller, Marcus

2017-08-01

Membrane fission is a fundamental process in cells, involved inter alia in endocytosis, intracellular trafficking, and virus infection. Its underlying molecular mechanism, however, is only incompletely understood. Recently, experiments and computer simulation studies have revealed that dynamin-mediated membrane fission is a two-step process that proceeds via a metastable hemi-fission intermediate (or wormlike micelle) formed by dynamin's constriction. Importantly, this hemi-fission intermediate is remarkably metastable, i.e., its subsequent rupture that completes the fission process does not occur spontaneously but requires additional, external effects, e.g., dynamin's (unknown) conformational changes or membrane tension. Using simulations of a coarse-grained, implicit-solvent model of lipid membranes, we investigate the molecular mechanism of rupturing the hemi-fission intermediate, such as its pathway, the concomitant transition states, and barriers, as well as the role of membrane tension. The membrane tension is controlled by the chemical potential of the lipids, and the free-energy landscape as a function of two reaction coordinates is obtained by grand canonical Wang-Landau sampling. Our results show that, in the course of rupturing, the hemi-fission intermediate undergoes a "thinning → local pinching → rupture/fission" pathway, with a bottle-neck-shaped cylindrical micelle as a transition state. Although an increase of membrane tension facilitates the fission process by reducing the corresponding free-energy barrier, for biologically relevant tensions, the free-energy barriers still significantly exceed the thermal energy scale kBT.

Rupturing the hemi-fission intermediate in membrane fission under tension: Reaction coordinates, kinetic pathways, and free-energy barriers.

PubMed

Zhang, Guojie; Müller, Marcus

2017-08-14

Membrane fission is a fundamental process in cells, involved inter alia in endocytosis, intracellular trafficking, and virus infection. Its underlying molecular mechanism, however, is only incompletely understood. Recently, experiments and computer simulation studies have revealed that dynamin-mediated membrane fission is a two-step process that proceeds via a metastable hemi-fission intermediate (or wormlike micelle) formed by dynamin's constriction. Importantly, this hemi-fission intermediate is remarkably metastable, i.e., its subsequent rupture that completes the fission process does not occur spontaneously but requires additional, external effects, e.g., dynamin's (unknown) conformational changes or membrane tension. Using simulations of a coarse-grained, implicit-solvent model of lipid membranes, we investigate the molecular mechanism of rupturing the hemi-fission intermediate, such as its pathway, the concomitant transition states, and barriers, as well as the role of membrane tension. The membrane tension is controlled by the chemical potential of the lipids, and the free-energy landscape as a function of two reaction coordinates is obtained by grand canonical Wang-Landau sampling. Our results show that, in the course of rupturing, the hemi-fission intermediate undergoes a "thinning → local pinching → rupture/fission" pathway, with a bottle-neck-shaped cylindrical micelle as a transition state. Although an increase of membrane tension facilitates the fission process by reducing the corresponding free-energy barrier, for biologically relevant tensions, the free-energy barriers still significantly exceed the thermal energy scale k B T.

Z n clock models and chains of so(n)2 non-Abelian anyons: symmetries, integrable points and low energy properties

NASA Astrophysics Data System (ADS)

Finch, Peter E.; Flohr, Michael; Frahm, Holger

2018-02-01

We study two families of quantum models which have been used previously to investigate the effect of topological symmetries in one-dimensional correlated matter. Various striking similarities are observed between certain {Z}n quantum clock models, spin chains generalizing the Ising model, and chains of non-Abelian anyons constructed from the so(n)2 fusion category for odd n, both subject to periodic boundary conditions. In spite of the differences between these two types of quantum chains, e.g. their Hilbert spaces being spanned by tensor products of local spin states or fusion paths of anyons, the symmetries of the lattice models are shown to be closely related. Furthermore, under a suitable mapping between the parameters describing the interaction between spins and anyons the respective Hamiltonians share part of their energy spectrum (although their degeneracies may differ). This spin-anyon correspondence can be extended by fine-tuning of the coupling constants leading to exactly solvable models. We show that the algebraic structures underlying the integrability of the clock models and the anyon chain are the same. For n  =  3,5,7 we perform an extensive finite size study—both numerical and based on the exact solution—of these models to map out their ground state phase diagram and to identify the effective field theories describing their low energy behaviour. We observe that the continuum limit at the integrable points can be described by rational conformal field theories with extended symmetry algebras which can be related to the discrete ones of the lattice models.

Study of a tri-trophic prey-dependent food chain model of interacting populations.

PubMed

Haque, Mainul; Ali, Nijamuddin; Chakravarty, Santabrata

2013-11-01

The current paper accounts for the influence of intra-specific competition among predators in a prey dependent tri-trophic food chain model of interacting populations. We offer a detailed mathematical analysis of the proposed food chain model to illustrate some of the significant results that has arisen from the interplay of deterministic ecological phenomena and processes. Biologically feasible equilibria of the system are observed and the behaviours of the system around each of them are described. In particular, persistence, stability (local and global) and bifurcation (saddle-node, transcritical, Hopf-Andronov) analysis of this model are obtained. Relevant results from previous well known food chain models are compared with the current findings. Global stability analysis is also carried out by constructing appropriate Lyapunov functions. Numerical simulations show that the present system is capable enough to produce chaotic dynamics when the rate of self-interaction is very low. On the other hand such chaotic behaviour disappears for a certain value of the rate of self interaction. In addition, numerical simulations with experimented parameters values confirm the analytical results and shows that intra-specific competitions bears a potential role in controlling the chaotic dynamics of the system; and thus the role of self interactions in food chain model is illustrated first time. Finally, a discussion of the ecological applications of the analytical and numerical findings concludes the paper. Copyright © 2013 Elsevier Inc. All rights reserved.

A semiflexible alternating copolymer chain adsorption on a flat and a fluctuating surface.

PubMed

Mishra, Pramod Kumar

2010-04-21

A lattice model of a directed self-avoiding walk is used to investigate adsorption properties of a semiflexible alternating copolymer chain on an impenetrable flat and fluctuating surface in two (square, hexagonal and rectangular lattice) and three dimensions (cubic lattice). In the cubic lattice case the surface is two-dimensional impenetrable flat and in two dimensions the surface is a fluctuating impenetrable line (hexagonal lattice) and also flat impenetrable line (square and rectangular lattice). Walks of the copolymer chains are directed perpendicular to the plane of the surface and at a suitable value of monomer surface attraction, the copolymer chain gets adsorbed on the surface. To calculate the exact value of the monomer surface attraction, the directed walk model has been solved analytically using the generating function method to discuss results when one type of monomer of the copolymer chain has attractive, repulsive or no interaction with the surface. Results obtained in the flat surface case show that, for a stiffer copolymer chain, adsorption transition occurs at a smaller value of monomer surface attraction than a flexible copolymer chain while in the case of a fluctuating surface, the adsorption transition point is independent of bending energy of the copolymer chain. These features are similar to that of a semiflexible homopolymer chain adsorption.

Developing a suitable model for supplier selection based on supply chain risks: an empirical study from Iranian pharmaceutical companies.

PubMed

Mehralian, Gholamhossein; Rajabzadeh Gatari, Ali; Morakabati, Mohadese; Vatanpour, Hossein

2012-01-01

The supply chain represents the critical link between the development of new product and the market in pharmaceutical industry. Over the years, improvements made in supply chain operations have focused largely on ways to reduce cost and gain efficiencies in scale. In addition, powerful regulatory and market forces have provided new incentives for pharmaceutical firms to basically rethink the way they produce and distribute products, and also to re-imagine the role of the supply chain in driving strategic growth, brand differentiation and economic value in the health continuum. The purpose of this paper is to formulate basic factors involved in risk analysis of pharmaceutical industry, and also determine the effective factors involved in suppliers selection and their priorities. This paper is based on the results of literature review, experts' opinion acquisition, statistical analysis and also using MADM models on data gathered from distributed questionnaires. The model consists of the following steps and components: first factors involved in to supply chain risks are determined. Based on them a framework is considered. According the result of statistical analysis and MADM models the risk factors are formulated. The paper determines the main components and influenceial factors involving in the supply chain risks. Results showed that delivery risk can make an important contribution to mitigate the risk of pharmaceutical industry.

Developing a Suitable Model for Supplier Selection Based on Supply Chain Risks: An Empirical Study from Iranian Pharmaceutical Companies

PubMed Central

Mehralian, Gholamhossein; Rajabzadeh Gatari, Ali; Morakabati, Mohadese; Vatanpour, Hossein

2012-01-01

The supply chain represents the critical link between the development of new product and the market in pharmaceutical industry. Over the years, improvements made in supply chain operations have focused largely on ways to reduce cost and gain efficiencies in scale. In addition, powerful regulatory and market forces have provided new incentives for pharmaceutical firms to basically rethink the way they produce and distribute products, and also to re-imagine the role of the supply chain in driving strategic growth, brand differentiation and economic value in the health continuum. The purpose of this paper is to formulate basic factors involved in risk analysis of pharmaceutical industry, and also determine the effective factors involved in suppliers selection and their priorities. This paper is based on the results of literature review, experts’ opinion acquisition, statistical analysis and also using MADM models on data gathered from distributed questionnaires. The model consists of the following steps and components: first factors involved in to supply chain risks are determined. Based on them a framework is considered. According the result of statistical analysis and MADM models the risk factors are formulated. The paper determines the main components and influenceial factors involving in the supply chain risks. Results showed that delivery risk can make an important contribution to mitigate the risk of pharmaceutical industry. PMID:24250442

Equivalence of chain conformations in the surface region of a polymer melt and a single Gaussian chain under critical conditions.

PubMed

Skvortsov, A M; Leermakers, F A M; Fleer, G J

2013-08-07

In the melt polymer conformations are nearly ideal according to Flory's ideality hypothesis. Silberberg generalized this statement for chains in the interfacial region. We check the Silberberg argument by analyzing the conformations of a probe chain end-grafted at a solid surface in a sea of floating free chains of concentration φ by the self-consistent field (SCF) method. Apart from the grafting, probe chain and floating chains are identical. Most of the results were obtained for a standard SCF model with freely jointed chains on a six-choice lattice, where immediate step reversals are allowed. A few data were generated for a five-choice lattice, where such step reversals are forbidden. These coarse-grained models describe the equilibrium properties of flexible atactic polymer chains at the scale of the segment length. The concentration was varied over the whole range from φ = 0 (single grafted chain) to φ = 1 (probe chain in the melt). The number of contacts with the surface, average height of the free end and its dispersion, average loop and train length, tail size distribution, end-point and overall segment distributions were calculated for a grafted probe chain as a function of φ, for several chain lengths and substrate∕polymer interactions, which were varied from strong repulsion to strong adsorption. The computations show that the conformations of the probe chain in the melt do not depend on substrate∕polymer interactions and are very similar to the conformations of a single end-grafted chain under critical conditions, and can thus be described analytically. When the substrate∕polymer interaction is fixed at the value corresponding to critical conditions, all equilibrium properties of a probe chain are independent of φ, over the whole range from a dilute solution to the melt. We believe that the conformations of all flexible chains in the surface region of the melt are close to those of an appropriate single chain in critical conditions, provided that one end of the single chain is fixed at the same point as a chain in the melt.

Performance analysis of Supply Chain Management with Supply Chain Operation reference model

NASA Astrophysics Data System (ADS)

Hasibuan, Abdurrozzaq; Arfah, Mahrani; Parinduri, Luthfi; Hernawati, Tri; Suliawati; Harahap, Bonar; Rahmah Sibuea, Siti; Krianto Sulaiman, Oris; purwadi, Adi

2018-04-01

This research was conducted at PT. Shamrock Manufacturing Corpora, the company is required to think creatively to implement competition strategy by producing goods/services that are more qualified, cheaper. Therefore, it is necessary to measure the performance of Supply Chain Management in order to improve the competitiveness. Therefore, the company is required to optimize its production output to meet the export quality standard. This research begins with the creation of initial dimensions based on Supply Chain Management process, ie Plan, Source, Make, Delivery, and Return with hierarchy based on Supply Chain Reference Operation that is Reliability, Responsiveness, Agility, Cost, and Asset. Key Performance Indicator identification becomes a benchmark in performance measurement whereas Snorm De Boer normalization serves to equalize Key Performance Indicator value. Analiytical Hierarchy Process is done to assist in determining priority criteria. Measurement of Supply Chain Management performance at PT. Shamrock Manufacturing Corpora produces SC. Responsiveness (0.649) has higher weight (priority) than other alternatives. The result of performance analysis using Supply Chain Reference Operation model of Supply Chain Management performance at PT. Shamrock Manufacturing Corpora looks good because its monitoring system between 50-100 is good.

Development of an Assessment Model for Sustainable Supply Chain Management in Batik Industry

NASA Astrophysics Data System (ADS)

Mubiena, G. F.; Ma’ruf, A.

2018-03-01

This research proposes a dynamic assessment model for sustainable supply chain management in batik industry. The proposed model identifies the dynamic relationship between economic aspect, environment aspect and social aspect. The economic aspect refers to the supply chain operation reference model. The environment aspect uses carbon emissions and liquid waste as the attribute assessment, while the social aspect focus on employee’s welfare. Lean manufacturing concept was implemented as an alternative approach to sustainability. The simulation result shows that the average of sustainability score for 5 years increased from 65,3% to 70%. Future experiments will be conducted on design improvements to reach the company target on sustainability score.

An Integer Programming Model for Multi-Echelon Supply Chain Decision Problem Considering Inventories

NASA Astrophysics Data System (ADS)

Harahap, Amin; Mawengkang, Herman; Siswadi; Effendi, Syahril

2018-01-01

In this paper we address a problem that is of significance to the industry, namely the optimal decision of a multi-echelon supply chain and the associated inventory systems. By using the guaranteed service approach to model the multi-echelon inventory system, we develop a mixed integer; programming model to simultaneously optimize the transportation, inventory and network structure of a multi-echelon supply chain. To solve the model we develop a direct search approach using a strategy of releasing nonbasic variables from their bounds, combined with the “active constraint” method. This strategy is used to force the appropriate non-integer basic variables to move to their neighbourhood integer points.

Quality tracing in meat supply chains

PubMed Central

Mack, Miriam; Dittmer, Patrick; Veigt, Marius; Kus, Mehmet; Nehmiz, Ulfert; Kreyenschmidt, Judith

2014-01-01

The aim of this study was the development of a quality tracing model for vacuum-packed lamb that is applicable in different meat supply chains. Based on the development of relevant sensory parameters, the predictive model was developed by combining a linear primary model and the Arrhenius model as the secondary model. Then a process analysis was conducted to define general requirements for the implementation of the temperature-based model into a meat supply chain. The required hardware and software for continuous temperature monitoring were developed in order to use the model under practical conditions. Further on a decision support tool was elaborated in order to use the model as an effective tool in combination with the temperature monitoring equipment for the improvement of quality and storage management within the meat logistics network. Over the long term, this overall procedure will support the reduction of food waste and will improve the resources efficiency of food production. PMID:24797136

Quality tracing in meat supply chains.

PubMed

Mack, Miriam; Dittmer, Patrick; Veigt, Marius; Kus, Mehmet; Nehmiz, Ulfert; Kreyenschmidt, Judith

2014-06-13

The aim of this study was the development of a quality tracing model for vacuum-packed lamb that is applicable in different meat supply chains. Based on the development of relevant sensory parameters, the predictive model was developed by combining a linear primary model and the Arrhenius model as the secondary model. Then a process analysis was conducted to define general requirements for the implementation of the temperature-based model into a meat supply chain. The required hardware and software for continuous temperature monitoring were developed in order to use the model under practical conditions. Further on a decision support tool was elaborated in order to use the model as an effective tool in combination with the temperature monitoring equipment for the improvement of quality and storage management within the meat logistics network. Over the long term, this overall procedure will support the reduction of food waste and will improve the resources efficiency of food production.

Food-chain contamination evaluations in ecological risk assessments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Linder, G.

Food-chain models have become increasingly important within the ecological risk assessment process. This is the case particularly when acute effects are not readily apparent, or the contaminants of concern are not readily detoxified, have a high likelihood for partitioning into lipids, or have specific target organs or tissues that may increase their significance in evaluating their potential adverse effects. An overview of food-chain models -- conceptual, theoretical, and empirical -- will be considered through a series of papers that will focus on their application within the ecological risk assessment process. Whether a food-chain evaluation is being developed to address relativelymore » simple questions related to chronic effects of toxicants on target populations, or whether a more complex food-web model is being developed to address questions related to multiple-trophic level transfers of toxicants, the elements within the food chain contamination evaluation can be generalized to address the mechanisms of toxicant accumulation in individual organisms. This can then be incorporated into more elaborate models that consider these organismal-level processes within the context of a species life-history or community-level responses that may be associated with long-term exposures.« less

Study on the photo-induced oxygen reordering in YBa2Cu3O6+x

NASA Astrophysics Data System (ADS)

Milić, M. M.; Lazarov, N. Dj.; Cucić, D. A.

2012-05-01

Effect of the long term illumination of the YBa2Cu3O6+x with visible light or ultraviolet irradiation on its superconducting properties was studied in the frame of a simple theoretical model, which assumes that photodoping triggers rearrangement of oxygen monomers in the chain layers thus causing the enhancement of the average chain length, lav. Since, according to the model of charge transfer mechanism, long CuO chains are better electronic hole donors than the short ones, increase of the average chain length induces additional holes transfer from chain layers to the superconducting CuO2 planes which in turn leads to the increase of the superconducting transition temperature Tc. By the use of the expression for the chain length probability distribution and numerically calculated values for the average chain length in the non-excited system, we were able to estimate the doping p (number of holes per one Cu atom in the superconducting CuO2 planes) and Tc enhancement due to photo-induced oxygen reordering. The theoretical results are compared with available experimental data.

A Bullet-Block Experiment that Explains the Chain Fountain

NASA Astrophysics Data System (ADS)

Pantaleone, J.; Smith, R.

2018-05-01

It is common in science for two phenomena to appear to be very different, but in fact follow from the same basic principles. Here we consider such a case, the connection between the chain fountain and a bullet-block collision experiment. When an upward moving bullet strikes a wooden block resting on a horizontal table, the block will rise to a higher height when the bullet strikes near the end of the block. This is because the quickly rotating block experiences an additional upward "reaction" force from its contact with the table. Such a reaction force also explains the chain fountain. When a chain falls from a pile in a container to the floor below, the chain rises up above the container. This rise occurs because the quickly rotating links in the container push off of the surface beneath them. We derive a model that accurately describes our measurements in the bullet-block experiment, and then use this same model to calculate an approximate expression for the distance the chain rises above the container. More extensive discussions of the chain fountain are available elsewhere.

Implementation of system dynamic simulation method to optimize profit in supply chain network of vegetable product

NASA Astrophysics Data System (ADS)

Tama, I. P.; Akbar, Z.; Eunike, A.

2018-04-01

Vegetables are categorized as a perishable product, which is a product with short lifespan thus requires proper handling and planning to reduce losses caused by the short lifespan. In order to reduce the losses, coordination among the players in the supply chain is required. On the other hand, the decision in the supply chain of vegetables and other farming products in the traditional market of developing country is independent among the players. This research is conducted by using System Dynamic Simulation method to develop model and scenario by coordinating the supply quantity amongst players in the supply chain. The scenarios are developed based on newsboy inventory model. This study aims to compare scenarios combining tiers involved in coordination program. The result shows that coordination in supply chain increases total supply chain profit, although there will always be players who experienced decrements in profit. The scenario of coordination among the farmer, the distributor, and the wholesaler resulted in the highest increase in total supply chain profit compared to other coordination scenarios, with an increased value of 10.49%.

Cloud point phenomena for POE-type nonionic surfactants in a model room temperature ionic liquid.

PubMed

Inoue, Tohru; Misono, Takeshi

2008-10-15

The cloud point phenomenon has been investigated for the solutions of polyoxyethylene (POE)-type nonionic surfactants (C(12)E(5), C(12)E(6), C(12)E(7), C(10)E(6), and C(14)E(6)) in 1-butyl-3-methylimidazolium tetrafluoroborate (bmimBF(4)), a typical room temperature ionic liquid (RTIL). The cloud point, T(c), increases with the elongation of the POE chain, while decreases with the increase in the hydrocarbon chain length. This demonstrates that the solvophilicity/solvophobicity of the surfactants in RTIL comes from POE chain/hydrocarbon chain. When compared with an aqueous system, the chain length dependence of T(c) is larger for the RTIL system regarding both POE and hydrocarbon chains; in particular, hydrocarbon chain length affects T(c) much more strongly in the RTIL system than in equivalent aqueous systems. In a similar fashion to the much-studied aqueous systems, the micellar growth is also observed in this RTIL solvent as the temperature approaches T(c). The cloud point curves have been analyzed using a Flory-Huggins-type model based on phase separation in polymer solutions.

Electric vehicle (EV) storage supply chain risk and the energy market: A micro and macroeconomic risk management approach

NASA Astrophysics Data System (ADS)

Aguilar, Susanna D.

As a cost effective storage technology for renewable energy sources, Electric Vehicles can be integrated into energy grids. Integration must be optimized to ascertain that renewable energy is available through storage when demand exists so that cost of electricity is minimized. Optimization models can address economic risks associated with the EV supply chain- particularly the volatility in availability and cost of critical materials used in the manufacturing of EV motors and batteries. Supply chain risk can reflect itself in a shortage of storage, which can increase the price of electricity. We propose a micro-and macroeconomic framework for managing supply chain risk through utilization of a cost optimization model in combination with risk management strategies at the microeconomic and macroeconomic level. The study demonstrates how risk from the EVs vehicle critical material supply chain affects manufacturers, smart grid performance, and energy markets qualitatively and quantitatively. Our results illustrate how risk in the EV supply chain affects EV availability and the cost of ancillary services, and how EV critical material supply chain risk can be mitigated through managerial strategies and policy.

A decision support system for transportation infrastructure and supply chain system planning.

DOT National Transportation Integrated Search

2013-07-01

This project makes the results (models and methodology) of the research and development efforts on freight movement modeling (FMM) and supply chain design carried out by faculty at OSU and OU available to transportation and logistics professionals. A...

Flexible Epoxy Resin Formed Upon Blending with a Triblock Copolymer through Reaction-Induced Microphase Separation

PubMed Central

Chu, Wei-Cheng; Lin, Wei-Sheng; Kuo, Shiao-Wei

2016-01-01

In this study, we used diglycidyl ether bisphenol A (DGEBA) as a matrix, the ABA block copolymer poly(ethylene oxide–b–propylene oxide–b–ethylene oxide) (Pluronic F127) as an additive, and diphenyl diaminosulfone (DDS) as a curing agent to prepare flexible epoxy resins through reaction-induced microphase separation (RIMPS). Fourier transform infrared spectroscopy confirmed the existence of hydrogen bonding between the poly(ethylene oxide) segment of F127 and the OH groups of the DGEBA resin. Small-angle X-ray scattering, atomic force microscopy, and transmission electron microscopy all revealed evidence for the microphase separation of F127 within the epoxy resin. Glass transition temperature (Tg) phenomena and mechanical properties (modulus) were determined through differential scanning calorimetry and dynamic mechanical analysis, respectively, of samples at various blend compositions. The modulus data provided evidence for the formation of wormlike micelle structures, through a RIMPS mechanism, in the flexible epoxy resin upon blending with the F127 triblock copolymer. PMID:28773571

Common features in the unfolding and misfolding of PDZ domains and beyond: the modulatory effect of domain swapping and extra-elements.

PubMed

Murciano-Calles, Javier; Güell-Bosch, Jofre; Villegas, Sandra; Martinez, Jose C

2016-01-12

PDZ domains are protein-protein interaction modules sharing the same structural arrangement. To discern whether they display common features in their unfolding/misfolding behaviour we have analyzed in this work the unfolding thermodynamics, together with the misfolding kinetics, of the PDZ fold using three archetypical examples: the second and third PDZ domains of the PSD95 protein and the Erbin PDZ domain. Results showed that all domains passed through a common intermediate, which populated upon unfolding, and that this in turn drove the misfolding towards worm-like fibrillar structures. Thus, the unfolding/misfolding behaviour appears to be shared within these domains. We have also analyzed how this landscape can be modified upon the inclusion of extra-elements, as it is in the nNOS PDZ domain, or the organization of swapped species, as happens in the second PDZ domain of the ZO2 protein. Although the intermediates still formed upon thermal unfolding, the misfolding was prevented to varying degrees.