Exact mapping between system-reservoir quantum models and semi-infinite discrete chains using orthogonal polynomials

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

Chin, Alex W.; Rivas, Angel; Huelga, Susana F.

2010-09-15

By using the properties of orthogonal polynomials, we present an exact unitary transformation that maps the Hamiltonian of a quantum system coupled linearly to a continuum of bosonic or fermionic modes to a Hamiltonian that describes a one-dimensional chain with only nearest-neighbor interactions. This analytical transformation predicts a simple set of relations between the parameters of the chain and the recurrence coefficients of the orthogonal polynomials used in the transformation and allows the chain parameters to be computed using numerically stable algorithms that have been developed to compute recurrence coefficients. We then prove some general properties of this chain systemmore » for a wide range of spectral functions and give examples drawn from physical systems where exact analytic expressions for the chain properties can be obtained. Crucially, the short-range interactions of the effective chain system permit these open-quantum systems to be efficiently simulated by the density matrix renormalization group methods.« less

Rational design and dynamics of self-propelled colloidal bead chains: from rotators to flagella.

PubMed

Vutukuri, Hanumantha Rao; Bet, Bram; van Roij, René; Dijkstra, Marjolein; Huck, Wilhelm T S

2017-12-01

The quest for designing new self-propelled colloids is fuelled by the demand for simple experimental models to study the collective behaviour of their more complex natural counterparts. Most synthetic self-propelled particles move by converting the input energy into translational motion. In this work we address the question if simple self-propelled spheres can assemble into more complex structures that exhibit rotational motion, possibly coupled with translational motion as in flagella. We exploit a combination of induced dipolar interactions and a bonding step to create permanent linear bead chains, composed of self-propelled Janus spheres, with a well-controlled internal structure. Next, we study how flexibility between individual swimmers in a chain can affect its swimming behaviour. Permanent rigid chains showed only active rotational or spinning motion, whereas longer semi-flexible chains showed both translational and rotational motion resembling flagella like-motion, in the presence of the fuel. Moreover, we are able to reproduce our experimental results using numerical calculations with a minimal model, which includes full hydrodynamic interactions with the fluid. Our method is general and opens a new way to design novel self-propelled colloids with complex swimming behaviours, using different complex starting building blocks in combination with the flexibility between them.

Light Scattering Study of Mixed Micelles Made from Elastin-Like Polypeptide Linear Chains and Trimers

NASA Astrophysics Data System (ADS)

Terrano, Daniel; Tsuper, Ilona; Maraschky, Adam; Holland, Nolan; Streletzky, Kiril

Temperature sensitive nanoparticles were generated from a construct (H20F) of three chains of elastin-like polypeptides (ELP) linked to a negatively charged foldon domain. This ELP system was mixed at different ratios with linear chains of ELP (H40L) which lacks the foldon domain. The mixed system is soluble at room temperature and at a transition temperature (Tt) will form swollen micelles with the hydrophobic linear chains hidden inside. This system was studied using depolarized dynamic light scattering (DDLS) and static light scattering (SLS) to determine the size, shape, and internal structure of the mixed micelles. The mixed micelle in equal parts of H20F and H40L show a constant apparent hydrodynamic radius of 40-45 nm at the concentration window from 25:25 to 60:60 uM (1:1 ratio). At a fixed 50 uM concentration of the H20F, varying H40L concentration from 5 to 80 uM resulted in a linear growth in the hydrodynamic radius from about 11 to about 62 nm, along with a 1000-fold increase in VH signal. A possible simple model explaining the growth of the swollen micelles is considered. Lastly, the VH signal can indicate elongation in the geometry of the particle or could possibly be a result from anisotropic properties from the core of the micelle. SLS was used to study the molecular weight, and the radius of gyration of the micelle to help identify the structure and morphology of mixed micelles and the tangible cause of the VH signal.

Sustainable Engineering and Improved Recycling of PET for High-Value Applications: Transforming Linear PET to Lightly Branched PET with a Novel, Scalable Process

NASA Astrophysics Data System (ADS)

Pierre, Cynthia; Torkelson, John

2009-03-01

A major challenge for the most effective recycling of poly(ethylene terephthalate) concerns the fact that initial melt processing of PET into a product leads to substantial degradation of molecular weight. Thus, recycled PET has insufficient melt viscosity for reuse in high-value applications such as melt-blowing of PET bottles. Academic and industrial research has tried to remedy this situation by synthesis and use of ``chain extenders'' that can lead to branched PET (with higher melt viscosity than the linear recycled PET) via condensation reactions with functional groups on the PET. Here we show that simple processing of PET via solid-state shear pulverization (SSSP) leads to enhanced PET melt viscosity without need for chemical additives. We hypothesize that this branching results from low levels of chain scission accompanying SSSP, leading to formation of polymeric radicals that participate in chain transfer and combination reactions with other PET chains and thereby to in situ branch formation. The pulverized PET exhibits vastly enhanced crystallization kinetics, eliminating the need to employ cold crystallization to achieve maximum PET crystallinity. Results of SSSP processing of PET will be compared to results obtained with poly(butylene terephthalate).

Unlocking Chain Exchange in Highly Amphiphilic Block Polymer Micellar Systems: Influence of Agitation.

PubMed

Murphy, Ryan P; Kelley, Elizabeth G; Rogers, Simon A; Sullivan, Millicent O; Epps, Thomas H

2014-11-18

Chain exchange between block polymer micelles in highly selective solvents, such as water, is well-known to be arrested under quiescent conditions, yet this work demonstrates that simple agitation methods can induce rapid chain exchange in these solvents. Aqueous solutions containing either pure poly(butadiene- b -ethylene oxide) or pure poly(butadiene- b -ethylene oxide- d 4 ) micelles were combined and then subjected to agitation by vortex mixing, concentric cylinder Couette flow, or nitrogen gas sparging. Subsequently, the extent of chain exchange between micelles was quantified using small angle neutron scattering. Rapid vortex mixing induced chain exchange within minutes, as evidenced by a monotonic decrease in scattered intensity, whereas Couette flow and sparging did not lead to measurable chain exchange over the examined time scale of hours. The linear kinetics with respect to agitation time suggested a surface-limited exchange process at the air-water interface. These findings demonstrate the strong influence of processing conditions on block polymer solution assemblies.

Honest Importance Sampling with Multiple Markov Chains

PubMed Central

Tan, Aixin; Doss, Hani; Hobert, James P.

2017-01-01

Importance sampling is a classical Monte Carlo technique in which a random sample from one probability density, π1, is used to estimate an expectation with respect to another, π. The importance sampling estimator is strongly consistent and, as long as two simple moment conditions are satisfied, it obeys a central limit theorem (CLT). Moreover, there is a simple consistent estimator for the asymptotic variance in the CLT, which makes for routine computation of standard errors. Importance sampling can also be used in the Markov chain Monte Carlo (MCMC) context. Indeed, if the random sample from π1 is replaced by a Harris ergodic Markov chain with invariant density π1, then the resulting estimator remains strongly consistent. There is a price to be paid however, as the computation of standard errors becomes more complicated. First, the two simple moment conditions that guarantee a CLT in the iid case are not enough in the MCMC context. Second, even when a CLT does hold, the asymptotic variance has a complex form and is difficult to estimate consistently. In this paper, we explain how to use regenerative simulation to overcome these problems. Actually, we consider a more general set up, where we assume that Markov chain samples from several probability densities, π1, …, πk, are available. We construct multiple-chain importance sampling estimators for which we obtain a CLT based on regeneration. We show that if the Markov chains converge to their respective target distributions at a geometric rate, then under moment conditions similar to those required in the iid case, the MCMC-based importance sampling estimator obeys a CLT. Furthermore, because the CLT is based on a regenerative process, there is a simple consistent estimator of the asymptotic variance. We illustrate the method with two applications in Bayesian sensitivity analysis. The first concerns one-way random effects models under different priors. The second involves Bayesian variable selection in linear regression, and for this application, importance sampling based on multiple chains enables an empirical Bayes approach to variable selection. PMID:28701855

Honest Importance Sampling with Multiple Markov Chains.

PubMed

Tan, Aixin; Doss, Hani; Hobert, James P

2015-01-01

Importance sampling is a classical Monte Carlo technique in which a random sample from one probability density, π 1 , is used to estimate an expectation with respect to another, π . The importance sampling estimator is strongly consistent and, as long as two simple moment conditions are satisfied, it obeys a central limit theorem (CLT). Moreover, there is a simple consistent estimator for the asymptotic variance in the CLT, which makes for routine computation of standard errors. Importance sampling can also be used in the Markov chain Monte Carlo (MCMC) context. Indeed, if the random sample from π 1 is replaced by a Harris ergodic Markov chain with invariant density π 1 , then the resulting estimator remains strongly consistent. There is a price to be paid however, as the computation of standard errors becomes more complicated. First, the two simple moment conditions that guarantee a CLT in the iid case are not enough in the MCMC context. Second, even when a CLT does hold, the asymptotic variance has a complex form and is difficult to estimate consistently. In this paper, we explain how to use regenerative simulation to overcome these problems. Actually, we consider a more general set up, where we assume that Markov chain samples from several probability densities, π 1 , …, π k , are available. We construct multiple-chain importance sampling estimators for which we obtain a CLT based on regeneration. We show that if the Markov chains converge to their respective target distributions at a geometric rate, then under moment conditions similar to those required in the iid case, the MCMC-based importance sampling estimator obeys a CLT. Furthermore, because the CLT is based on a regenerative process, there is a simple consistent estimator of the asymptotic variance. We illustrate the method with two applications in Bayesian sensitivity analysis. The first concerns one-way random effects models under different priors. The second involves Bayesian variable selection in linear regression, and for this application, importance sampling based on multiple chains enables an empirical Bayes approach to variable selection.

The fidelity of paleomagnetic records carried by magnetosome chains

NASA Astrophysics Data System (ADS)

Paterson, Greig; Wang, Yinzhao; Pan, Yongxin

2013-04-01

Magnetotactic bacteria (MTB) and their fossilized magnetosomes are being increasingly identified in geological records from a broad range of environments and are believed to be a dominant carrier of magnetic remanence in sediments. Despite their prevalence, little is known about how well chains of biomineralized magnetic particles record the geomagnetic field. Using cultured Magnetospirillum magneticum strain AMB-1, we have conducted simple 2D (i.e., zero inclination) experiments to simulate NRM acquisition in order to assess the efficiency with which magnetosome chains align along magnetic field lines and the implications that this has for paleomagnetic records. Our results indicate that the NRM acquired by deposited MTB is near linear with the applied field, but that deviations from linearity up to 10% are discernible at high fields (120 μT). This slight non-linearity is propagated through into the calculation of both ARM and IRM normalized relative paleointensity (RPI) variations. RPI records, carried by magnetofossils, which vary by more than a factor of 5-6, are likely to misestimate the extreme values by ~10-15 % due to non-linear effects. This degree of non-linearity, however, is comparable or smaller than measured from redeposition experiments using detrital material, which suggests that over the range of typical geomagnetic field strengths explored here, MTB appear to be good recorders of the paleomagnetic field. The RPI discrepancies between nearby geological records, which have been inferred to be the result of abundant biogenic magnetic minerals, are likely to be related to the mixing of biogenic and detrital magnetic components, or through chemical processes that may subsequently affect the NRM carried by fossil magnetosomes.

Competing Thermodynamic and Dynamic Factors Select Molecular Assemblies on a Gold Surface

NASA Astrophysics Data System (ADS)

Haxton, Thomas K.; Zhou, Hui; Tamblyn, Isaac; Eom, Daejin; Hu, Zonghai; Neaton, Jeffrey B.; Heinz, Tony F.; Whitelam, Stephen

2013-12-01

Controlling the self-assembly of surface-adsorbed molecules into nanostructures requires understanding physical mechanisms that act across multiple length and time scales. By combining scanning tunneling microscopy with hierarchical ab initio and statistical mechanical modeling of 1,4-substituted benzenediamine (BDA) molecules adsorbed on a gold (111) surface, we demonstrate that apparently simple nanostructures are selected by a subtle competition of thermodynamics and dynamics. Of the collection of possible BDA nanostructures mechanically stabilized by hydrogen bonding, the interplay of intermolecular forces, surface modulation, and assembly dynamics select at low temperature a particular subset: low free energy oriented linear chains of monomers and high free energy branched chains.

Did the ever dead outnumber the living and when? A birth-and-death approach

NASA Astrophysics Data System (ADS)

Avan, Jean; Grosjean, Nicolas; Huillet, Thierry

2015-02-01

This paper is an attempt to formalize analytically the question raised in 'World Population Explained: Do Dead People Outnumber Living, Or Vice Versa?' Huffington Post, Howard (2012). We start developing simple deterministic Malthusian growth models of the problem (with birth and death rates either constant or time-dependent) before running into both linear birth and death Markov chain models and age-structured models.

A recurrent neural network for solving bilevel linear programming problem.

PubMed

He, Xing; Li, Chuandong; Huang, Tingwen; Li, Chaojie; Huang, Junjian

2014-04-01

In this brief, based on the method of penalty functions, a recurrent neural network (NN) modeled by means of a differential inclusion is proposed for solving the bilevel linear programming problem (BLPP). Compared with the existing NNs for BLPP, the model has the least number of state variables and simple structure. Using nonsmooth analysis, the theory of differential inclusions, and Lyapunov-like method, the equilibrium point sequence of the proposed NNs can approximately converge to an optimal solution of BLPP under certain conditions. Finally, the numerical simulations of a supply chain distribution model have shown excellent performance of the proposed recurrent NNs.

Nonlinear conduction via solitons in a topological mechanical insulator.

PubMed

Chen, Bryan Gin-ge; Upadhyaya, Nitin; Vitelli, Vincenzo

2014-09-09

Networks of rigid bars connected by joints, termed linkages, provide a minimal framework to design robotic arms and mechanical metamaterials built of folding components. Here, we investigate a chain-like linkage that, according to linear elasticity, behaves like a topological mechanical insulator whose zero-energy modes are localized at the edge. Simple experiments we performed using prototypes of the chain vividly illustrate how the soft motion, initially localized at the edge, can in fact propagate unobstructed all of the way to the opposite end. Using real prototypes, simulations, and analytical models, we demonstrate that the chain is a mechanical conductor, whose carriers are nonlinear solitary waves, not captured within linear elasticity. Indeed, the linkage prototype can be regarded as the simplest example of a topological metamaterial whose protected mechanical excitations are solitons, moving domain walls between distinct topological mechanical phases. More practically, we have built a topologically protected mechanism that can perform basic tasks such as transporting a mechanical state from one location to another. Our work paves the way toward adopting the principle of topological robustness in the design of robots assembled from activated linkages as well as in the fabrication of complex molecular nanostructures.

Non-Linear Dynamics of Saturn’s Rings

NASA Astrophysics Data System (ADS)

Esposito, Larry W.

2015-11-01

Non-linear processes can explain why Saturn’s rings are so active and dynamic. Ring systems differ from simple linear systems in two significant ways: 1. They are systems of granular material: where particle-to-particle collisions dominate; thus a kinetic, not a fluid description needed. We find that stresses are strikingly inhomogeneous and fluctuations are large compared to equilibrium. 2. They are strongly forced by resonances: which drive a non-linear response, pushing the system across thresholds that lead to persistent states.Some of this non-linearity is captured in a simple Predator-Prey Model: Periodic forcing from the moon causes streamline crowding; This damps the relative velocity, and allows aggregates to grow. About a quarter phase later, the aggregates stir the system to higher relative velocity and the limit cycle repeats each orbit.Summary of Halo Results: A predator-prey model for ring dynamics produces transient structures like ‘straw’ that can explain the halo structure and spectroscopy: This requires energetic collisions (v ≈ 10m/sec, with throw distances about 200km, implying objects of scale R ≈ 20km).Transform to Duffing Eqn : With the coordinate transformation, z = M2/3, the Predator-Prey equations can be combined to form a single second-order differential equation with harmonic resonance forcing.Ring dynamics and history implications: Moon-triggered clumping at perturbed regions in Saturn’s rings creates both high velocity dispersion and large aggregates at these distances, explaining both small and large particles observed there. We calculate the stationary size distribution using a cell-to-cell mapping procedure that converts the phase-plane trajectories to a Markov chain. Approximating the Markov chain as an asymmetric random walk with reflecting boundaries allows us to determine the power law index from results of numerical simulations in the tidal environment surrounding Saturn. Aggregates can explain many dynamic aspects of the rings and can renew rings by shielding and recycling the material within them, depending on how long the mass is sequestered. We can ask: Are Saturn’s rings a chaotic non-linear driven system?

Scaling behavior of ground-state energy cluster expansion for linear polyenes

NASA Astrophysics Data System (ADS)

Griffin, L. L.; Wu, Jian; Klein, D. J.; Schmalz, T. G.; Bytautas, L.

Ground-state energies for linear-chain polyenes are additively expanded in a sequence of terms for chemically relevant conjugated substructures of increasing size. The asymptotic behavior of the large-substructure limit (i.e., high-polymer limit) is investigated as a means of characterizing the rapidity of convergence and consequent utility of this energy cluster expansion. Consideration is directed to computations via: simple Hückel theory, a refined Hückel scheme with geometry optimization, restricted Hartree-Fock self-consistent field (RHF-SCF) solutions of fixed bond-length Parisier-Parr-Pople (PPP)/Hubbard models, and ab initio SCF approaches with and without geometry optimization. The cluster expansion in what might be described as the more "refined" approaches appears to lead to qualitatively more rapid convergence: exponentially fast as opposed to an inverse power at the simple Hückel or SCF-Hubbard levels. The substructural energy cluster expansion then seems to merit special attention. Its possible utility in making accurate extrapolations from finite systems to extended polymers is noted.

Topological and metric properties of linear and circular DNA chains in nano-slits and nano-channels

NASA Astrophysics Data System (ADS)

Orlandini, Enzo; Micheletti, Cristian

2014-03-01

Motivated by recent advancements in single DNA molecule experiments, based on nanofluidic devices, we investigate numerically the metric and topological properties of a modelof open and circular DNA chains confined inside nano-slits and nano-channles. The results reveal an interesting characterization of the metric crossover behaviour in terms of the abundance, type and length of occuring knots. In particular we find that the knotting probability is nonmonotonic for increasing confinement and can be largely enhanced or suppressed, compared to the bulk case, by simply varying the slit or channel trasversal dimension. The observed knot population consists of knots that are far simpler than for DNA chains in spherical (i.e. cavities or capsids) confinement. These results suggest that nanoslits and nanochannels can be properly designed to produce open DNA chains hosting simple knots or to sieve DNA rings according to their knotted state. Finally we discuss the implications that the presence of knots may have on the dynamical properties of confined DNA chains such as chain elongation, injection/ejection processes and entanglement relaxation. We acknowledge financial support from the Italian ministry of education, grant PRIN 2010HXAW77.

Localization in finite vibroimpact chains: Discrete breathers and multibreathers.

PubMed

Grinberg, Itay; Gendelman, Oleg V

2016-09-01

We explore the dynamics of strongly localized periodic solutions (discrete solitons or discrete breathers) in a finite one-dimensional chain of oscillators. Localization patterns with both single and multiple localization sites (breathers and multibreathers) are considered. The model involves parabolic on-site potential with rigid constraints (the displacement domain of each particle is finite) and a linear nearest-neighbor coupling. When the particle approaches the constraint, it undergoes an inelastic impact according to Newton's impact model. The rigid nonideal impact constraints are the only source of nonlinearity and damping in the system. We demonstrate that this vibro-impact model allows derivation of exact analytic solutions for the breathers and multibreathers with an arbitrary set of localization sites, both in conservative and in forced-damped settings. Periodic boundary conditions are considered; exact solutions for other types of boundary conditions are also available. Local character of the nonlinearity permits explicit derivation of a monodromy matrix for the breather solutions. Consequently, the stability of the derived breather and multibreather solutions can be efficiently studied in the framework of simple methods of linear algebra, and with rather moderate computational efforts. One reveals that that the finiteness of the chain fragment and possible proximity of the localization sites strongly affect both the existence and the stability patterns of these localized solutions.

Tunnel current across linear homocatenated germanium chains

NASA Astrophysics Data System (ADS)

Matsuura, Yukihito

2014-01-01

The electronic transport properties of germanium oligomers catenating into linear chains (linear Ge chains) have been theoretically studied using first principle methods. The conduction mechanism of a Ge chain sandwiched between gold electrodes was analyzed based on the density of states and the eigenstates of the molecule in a two-probe environment. Like that of silicon chains (Si chains), the highest occupied molecular orbital of Ge chains contains the extended σ-conjugation of Ge 4p orbitals at energy levels close to the Fermi level; this is in contrast to the electronic properties of linear carbon chains. Furthermore, the conductance of a Ge chain is expected to decrease exponentially with molecular length L. The decay constant β, which is defined as e-βL, of a Ge chain is similar to that of a Si chain, whereas the conductance of the Ge chains is higher than that of Si chains even though the Ge-Ge bond length is longer than the Si-Si bond length.

Mechanism Underlying IκB Kinase Activation Mediated by the Linear Ubiquitin Chain Assembly Complex

PubMed Central

Fujita, Hiroaki; Akita, Mariko; Kato, Ryuichi; Sasaki, Yoshiteru; Wakatsuki, Soichi

2014-01-01

The linear ubiquitin chain assembly complex (LUBAC) ligase, consisting of HOIL-1L, HOIP, and SHARPIN, specifically generates linear polyubiquitin chains. LUBAC-mediated linear polyubiquitination has been implicated in NF-κB activation. NEMO, a component of the IκB kinase (IKK) complex, is a substrate of LUBAC, but the precise molecular mechanism underlying linear chain-mediated NF-κB activation has not been fully elucidated. Here, we demonstrate that linearly polyubiquitinated NEMO activates IKK more potently than unanchored linear chains. In mutational analyses based on the crystal structure of the complex between the HOIP NZF1 and NEMO CC2-LZ domains, which are involved in the HOIP-NEMO interaction, NEMO mutations that impaired linear ubiquitin recognition activity and prevented recognition by LUBAC synergistically suppressed signal-induced NF-κB activation. HOIP NZF1 bound to NEMO and ubiquitin simultaneously, and HOIP NZF1 mutants defective in interaction with either NEMO or ubiquitin could not restore signal-induced NF-κB activation. Furthermore, linear chain-mediated activation of IKK2 involved homotypic interaction of the IKK2 kinase domain. Collectively, these results demonstrate that linear polyubiquitination of NEMO plays crucial roles in IKK activation and that this modification involves the HOIP NZF1 domain and recognition of NEMO-conjugated linear ubiquitin chains by NEMO on another IKK complex. PMID:24469399

Monte Carlo simulation of star/linear and star/star blends with chemically identical monomers

NASA Astrophysics Data System (ADS)

Theodorakis, P. E.; Avgeropoulos, A.; Freire, J. J.; Kosmas, M.; Vlahos, C.

2007-11-01

The effects of chain size and architectural asymmetry on the miscibility of blends with chemically identical monomers, differing only in their molecular weight and architecture, are studied via Monte Carlo simulation by using the bond fluctuation model. Namely, we consider blends composed of linear/linear, star/linear and star/star chains. We found that linear/linear blends are more miscible than the corresponding star/star mixtures. In star/linear blends, the increase in the volume fraction of the star chains increases the miscibility. For both star/linear and star/star blends, the miscibility decreases with the increase in star functionality. When we increase the molecular weight of linear chains of star/linear mixtures the miscibility decreases. Our findings are compared with recent analytical and experimental results.

The effects of mixotrophy on the stability and dynamics of a simple planktonic food web

USGS Publications Warehouse

Jost, Christian; Lawrence, Cathryn A.; Campolongo, Francesca; Wouter, van de Bund; Hill, Sheryl; DeAngelis, Donald L.

2004-01-01

Recognition of the microbial loop as an important part of aquatic ecosystems disrupted the notion of simple linear food chains. However, current research suggests that even the microbial loop paradigm is a gross simplification of microbial interactions due to the presence of mixotrophs—organisms that both photosynthesize and graze. We present a simple food web model with four trophic species, three of them arranged in a food chain (nutrients–autotrophs–herbivores) and the fourth as a mixotroph with links to both the nutrients and the autotrophs. This model is used to study the general implications of inclusion of the mixotrophic link in microbial food webs and the specific predictions for a parameterization that describes open ocean mixed layer plankton dynamics. The analysis indicates that the system parameters reside in a region of the parameter space where the dynamics converge to a stable equilibrium rather than displaying periodic or chaotic solutions. However, convergence requires weeks to months, suggesting that the system would never reach equilibrium in the ocean due to alteration of the physical forcing regime. Most importantly, the mixotrophic grazing link seems to stabilize the system in this region of the parameter space, particularly when nutrient recycling feedback loops are included.

A Secondary Antibody-Detecting Molecular Weight Marker with Mouse and Rabbit IgG Fc Linear Epitopes for Western Blot Analysis

PubMed Central

Cheng, Ta-Chun; Tung, Yi-Ching; Chu, Pei-Yu; Chuang, Chih-Hung; Hsieh, Yuan-Chin; Huang, Chien-Chiao; Wang, Yeng-Tseng; Kao, Chien-Han; Roffler, Steve R.; Cheng, Tian-Lu

2016-01-01

Molecular weight markers that can tolerate denaturing conditions and be auto-detected by secondary antibodies offer great efficacy and convenience for Western Blotting. Here, we describe M&R LE protein markers which contain linear epitopes derived from the heavy chain constant regions of mouse and rabbit immunoglobulin G (IgG Fc LE). These markers can be directly recognized and stained by a wide range of anti-mouse and anti-rabbit secondary antibodies. We selected three mouse (M1, M2 and M3) linear IgG1 and three rabbit (R1, R2 and R3) linear IgG heavy chain epitope candidates based on their respective crystal structures. Western blot analysis indicated that M2 and R2 linear epitopes are effectively recognized by anti-mouse and anti-rabbit secondary antibodies, respectively. We fused the M2 and R2 epitopes (M&R LE) and incorporated the polypeptide in a range of 15–120 kDa auto-detecting markers (M&R LE protein marker). The M&R LE protein marker can be auto-detected by anti-mouse and anti-rabbit IgG secondary antibodies in standard immunoblots. Linear regression analysis of the M&R LE protein marker plotted as gel mobility versus the log of the marker molecular weights revealed good linearity with a correlation coefficient R2 value of 0.9965, indicating that the M&R LE protein marker displays high accuracy for determining protein molecular weights. This accurate, regular and auto-detected M&R LE protein marker may provide a simple, efficient and economical tool for protein analysis. PMID:27494183

A Secondary Antibody-Detecting Molecular Weight Marker with Mouse and Rabbit IgG Fc Linear Epitopes for Western Blot Analysis.

PubMed

Lin, Wen-Wei; Chen, I-Ju; Cheng, Ta-Chun; Tung, Yi-Ching; Chu, Pei-Yu; Chuang, Chih-Hung; Hsieh, Yuan-Chin; Huang, Chien-Chiao; Wang, Yeng-Tseng; Kao, Chien-Han; Roffler, Steve R; Cheng, Tian-Lu

2016-01-01

Molecular weight markers that can tolerate denaturing conditions and be auto-detected by secondary antibodies offer great efficacy and convenience for Western Blotting. Here, we describe M&R LE protein markers which contain linear epitopes derived from the heavy chain constant regions of mouse and rabbit immunoglobulin G (IgG Fc LE). These markers can be directly recognized and stained by a wide range of anti-mouse and anti-rabbit secondary antibodies. We selected three mouse (M1, M2 and M3) linear IgG1 and three rabbit (R1, R2 and R3) linear IgG heavy chain epitope candidates based on their respective crystal structures. Western blot analysis indicated that M2 and R2 linear epitopes are effectively recognized by anti-mouse and anti-rabbit secondary antibodies, respectively. We fused the M2 and R2 epitopes (M&R LE) and incorporated the polypeptide in a range of 15-120 kDa auto-detecting markers (M&R LE protein marker). The M&R LE protein marker can be auto-detected by anti-mouse and anti-rabbit IgG secondary antibodies in standard immunoblots. Linear regression analysis of the M&R LE protein marker plotted as gel mobility versus the log of the marker molecular weights revealed good linearity with a correlation coefficient R2 value of 0.9965, indicating that the M&R LE protein marker displays high accuracy for determining protein molecular weights. This accurate, regular and auto-detected M&R LE protein marker may provide a simple, efficient and economical tool for protein analysis.

Spectral likelihood expansions for Bayesian inference

NASA Astrophysics Data System (ADS)

Nagel, Joseph B.; Sudret, Bruno

2016-03-01

A spectral approach to Bayesian inference is presented. It pursues the emulation of the posterior probability density. The starting point is a series expansion of the likelihood function in terms of orthogonal polynomials. From this spectral likelihood expansion all statistical quantities of interest can be calculated semi-analytically. The posterior is formally represented as the product of a reference density and a linear combination of polynomial basis functions. Both the model evidence and the posterior moments are related to the expansion coefficients. This formulation avoids Markov chain Monte Carlo simulation and allows one to make use of linear least squares instead. The pros and cons of spectral Bayesian inference are discussed and demonstrated on the basis of simple applications from classical statistics and inverse modeling.

Research on allocation efficiency of the daisy chain allocation algorithm

NASA Astrophysics Data System (ADS)

Shi, Jingping; Zhang, Weiguo

2013-03-01

With the improvement of the aircraft performance in reliability, maneuverability and survivability, the number of the control effectors increases a lot. How to distribute the three-axis moments into the control surfaces reasonably becomes an important problem. Daisy chain method is simple and easy to be carried out in the design of the allocation system. But it can not solve the allocation problem for entire attainable moment subset. For the lateral-directional allocation problem, the allocation efficiency of the daisy chain can be directly measured by the area of its subset of attainable moments. Because of the non-linear allocation characteristic, the subset of attainable moments of daisy-chain method is a complex non-convex polygon, and it is difficult to solve directly. By analyzing the two-dimensional allocation problems with a "micro-element" idea, a numerical calculation algorithm is proposed to compute the area of the non-convex polygon. In order to improve the allocation efficiency of the algorithm, a genetic algorithm with the allocation efficiency chosen as the fitness function is proposed to find the best pseudo-inverse matrix.

Solid-State Powered X-band Accelerator

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

Othman, Mohamed A.K.; Nann, Emilio A.; Dolgashev, Valery A.

2017-03-06

In this report we disseminate the hot test results of an X-band 100-W solid state amplifier chain for linear accelerator (linac) applications. Solid state power amplifiers have become increasingly attractive solutions for achieving high power in radar and maritime applications. Here the performance of solid state amplifiers when driving an RF cavity is investigated. Commercially available, matched and fully-packaged GaN on SiC HEMTs are utilized, comprising a wideband driver stage and two power stages. The amplifier chain has a high poweradded- efficiency and is able to supply up to ~1.2 MV/m field gradient at 9.2 GHz in a simple testmore » cavity, with a peak power exceeding 100 W. These findings set forth the enabling technology for solid-state powered linacs.« less

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

Suhara, Tadahiro; Kanada-En'yo, Yoshiko

We investigate the linear-chain structures in highly excited states of {sup 14}C using a generalized molecular-orbital model, by which we incorporate an asymmetric configuration of three {alpha} clusters in the linear-chain states. By applying this model to the {sup 14}C system, we study the {sup 10}Be+{alpha} correlation in the linear-chain state of {sup 14}C. To clarify the origin of the {sup 10}Be+{alpha} correlation in the {sup 14}C linear-chain state, we analyze linear 3 {alpha} and 3{alpha} + n systems in a similar way. We find that a linear 3{alpha} system prefers the asymmetric 2{alpha} + {alpha} configuration, whose origin ismore » the many-body correlation incorporated by the parity projection. This configuration causes an asymmetric mean field for two valence neutrons, which induces the concentration of valence neutron wave functions around the correlating 2{alpha}. A linear-chain structure of {sup 16}C is also discussed.« less

Reduction in aggregation and energy transfer of quantum dots incorporated in polystyrene beads by kinetic entrapment due to cross-linking during polymerization.

PubMed

Vaidya, Shyam V; Couzis, Alex; Maldarelli, Charles

2015-03-17

We report the development of barcoded polystyrene microbeads, approximately 50 μm in diameter, which are encoded by incorporating multicolored semiconductor fluorescent nanocrystals (quantum dots or QDs) within the microbeads and using the emission spectrum of the embedded QDs as a spectral label. The polymer/nanocrystal bead composites are formed by polymerizing emulsified liquid droplets of styrene monomer and QDs suspended in an immiscible continuous phase (suspension polymerization). We focus specifically on the effect of divinylbenzene (DVB) added to cross-link the linearly growing styrene polymer chains and the effect of this cross-linking on the state of aggregation of the nanocrystals in the composite. Aggregated states of multicolor QDs give rise to nonradiative resonance energy transfer (RET) which distorts the emission label from a spectrum recorded in a reference solvent in which the nanocrystals are well dispersed and unaggregated. A simple barcode is chosen of a mixture of QDs emitting at 560 (yellow) and 620 nm (red). We find that for linear chain growth (no DVB), the QDs aggregate as is evident from the emission spectrum and the QD distribution as seen from confocal laser scanning microscopy (CLSM) and transmission electron microscopy (TEM) images. Increasing the extent of cross-linking by the addition of DVB is shown to significantly decrease the aggregation and provide a clear label. We suggest that in the absence of cross-linking, linearly growing polymer chains, through enthalpic and entropic effects, drive the nanocrystals into inclusions, while cross-linking kinetically entraps the particle and prevents their aggregation.

A mechanical comparison of linear and double-looped hung supplemental heavy chain resistance to the back squat: a case study.

PubMed

Neelly, Kurt R; Terry, Joseph G; Morris, Martin J

2010-01-01

A relatively new and scarcely researched technique to increase strength is the use of supplemental heavy chain resistance (SHCR) in conjunction with plate weights to provide variable resistance to free weight exercises. The purpose of this case study was to determine the actual resistance being provided by a double-looped versus a linear hung SHCR to the back squat exercise. The linear technique simply hangs the chain directly from the bar, whereas the double-looped technique uses a smaller chain to adjust the height of the looped chain. In both techniques, as the squat descends, chain weight is unloaded onto the floor, and as the squat ascends, chain weight is progressively loaded back as resistance. One experienced and trained male weight lifter (age = 33 yr; height = 1.83 m; weight = 111.4 kg) served as the subject. Plate weight was set at 84.1 kg, approximately 50% of the subject's 1 repetition maximum. The SHCR was affixed to load cells, sampling at a frequency of 500 Hz, which were affixed to the Olympic bar. Data were collected as the subject completed the back squat under the following conditions: double-looped 1 chain (9.6 kg), double-looped 2 chains (19.2 kg), linear 1 chain, and linear 2 chains. The double-looped SHCR resulted in a 78-89% unloading of the chain weight at the bottom of the squat, whereas the linear hanging SHCR resulted in only a 36-42% unloading. The double-looped technique provided nearly 2 times the variable resistance at the top of the squat compared with the linear hanging technique, showing that attention must be given to the technique used to hang SHCR.

Analysis of Nuclear Factor-κB (NF-κB) Essential Modulator (NEMO) Binding to Linear and Lysine-linked Ubiquitin Chains and Its Role in the Activation of NF-κB*

PubMed Central

Kensche, Tobias; Tokunaga, Fuminori; Ikeda, Fumiyo; Goto, Eiji; Iwai, Kazuhiro; Dikic, Ivan

2012-01-01

Nuclear factor-κB (NF-κB) essential modulator (NEMO), a component of the inhibitor of κB kinase (IKK) complex, controls NF-κB signaling by binding to ubiquitin chains. Structural studies of NEMO provided a rationale for the specific binding between the UBAN (ubiquitin binding in ABIN and NEMO) domain of NEMO and linear (Met-1-linked) di-ubiquitin chains. Full-length NEMO can also interact with Lys-11-, Lys-48-, and Lys-63-linked ubiquitin chains of varying length in cells. Here, we show that purified full-length NEMO binds preferentially to linear ubiquitin chains in competition with lysine-linked ubiquitin chains of defined length, including long Lys-63-linked deca-ubiquitins. Linear di-ubiquitins were sufficient to activate both the IKK complex in vitro and to trigger maximal NF-κB activation in cells. In TNFα-stimulated cells, NEMO chimeras engineered to bind exclusively to Lys-63-linked ubiquitin chains mediated partial NF-κB activation compared with cells expressing NEMO that binds to linear ubiquitin chains. We propose that NEMO functions as a high affinity receptor for linear ubiquitin chains and a low affinity receptor for long lysine-linked ubiquitin chains. This phenomenon could explain quantitatively distinct NF-κB activation patterns in response to numerous cell stimuli. PMID:22605335

Dynamics of a discrete chain of bi-stable elements: A biomimetic shock absorbing mechanism

NASA Astrophysics Data System (ADS)

Cohen, T.; Givli, S.

2014-03-01

A biomimetic shock absorbing mechanism, inspired by the bi-stable elongation behavior of the giant protein titin, is examined. A bi-stable element, composed of three mass particles with monotonous interaction forces, is suggested to facilitate an internal degree of freedom of finite mass which contributes significantly to dissipation upon unlocking of an internal link. An essential feature of the suggested element is that it undergoes reversible rapture and therefore retrieves its initial configuration once unloaded. The quasistatic and dynamic behaviors are investigated showing similarity to the common tri-linear bi-stable response, with two steady phases separated by a spinodal region. The dynamic behavior of a chain of elements is also examined, for several loading scenarios, showing that the suggested mechanism serves as an efficient shock absorber in a sub-critical dampening environment, as compared with a simple mass on spring system. Propagation of shock waves and refraction waves in an element chain is observed and the effect of natural imperfections is considered.

Representing Lumped Markov Chains by Minimal Polynomials over Field GF(q)

NASA Astrophysics Data System (ADS)

Zakharov, V. M.; Shalagin, S. V.; Eminov, B. F.

2018-05-01

A method has been proposed to represent lumped Markov chains by minimal polynomials over a finite field. The accuracy of representing lumped stochastic matrices, the law of lumped Markov chains depends linearly on the minimum degree of polynomials over field GF(q). The method allows constructing the realizations of lumped Markov chains on linear shift registers with a pre-defined “linear complexity”.

Propagation of transition fronts in nonlinear chains with non-degenerate on-site potentials

NASA Astrophysics Data System (ADS)

Shiroky, I. B.; Gendelman, O. V.

2018-02-01

We address the problem of transition front propagation in chains with a bi-stable nondegenerate on-site potential and a nonlinear gradient coupling. For generic nonlinear coupling, one encounters a special regime of transitions, characterized by extremely narrow fronts, far supersonic velocities of the front propagation, and long waves in the oscillatory tail. This regime can be qualitatively associated with a shock wave. The front propagation can be described with the help of a simple reduced-order model; the latter delivers a kinetic law, which is almost not sensitive to the fine details of the on-site potential. Besides, it is possible to predict all main characteristics of the transition front, including its velocity, as well as the frequency and the amplitude of the oscillatory tail. Numerical results are in good agreement with the analytical predictions. The suggested approach allows one to consider the effects of an external pre-load, the next-nearest-neighbor coupling and the on-site damping. When the damping is moderate, it is possible to consider the shock propagation in the damped chain as a perturbation of the undamped dynamics. This approach yields reasonable predictions. When the damping is high, the transition front enters a completely different asymptotic regime of a subsonic kink. The gradient nonlinearity generically turns negligible, and the propagating front converges to the regime described by a simple exact solution for a continuous model with linear coupling.

Making sense of enthalpy of vaporization trends for ionic liquids: new experimental and simulation data show a simple linear relationship and help reconcile previous data.

PubMed

Verevkin, Sergey P; Zaitsau, Dzmitry H; Emel'yanenko, Vladimir N; Yermalayeu, Andrei V; Schick, Christoph; Liu, Hongjun; Maginn, Edward J; Bulut, Safak; Krossing, Ingo; Kalb, Roland

2013-05-30

Vaporization enthalpy of an ionic liquid (IL) is a key physical property for applications of ILs as thermofluids and also is useful in developing liquid state theories and validating intermolecular potential functions used in molecular modeling of these liquids. Compilation of the data for a homologous series of 1-alkyl-3-methylimidazolium bis(trifluoromethane-sulfonyl)imide ([C(n)mim][NTf2]) ILs has revealed an embarrassing disarray of literature results. New experimental data, based on the concurring results from quartz crystal microbalance, thermogravimetric analyses, and molecular dynamics simulation have revealed a clear linear dependence of IL vaporization enthalpies on the chain length of the alkyl group on the cation. Ambiguity of the procedure for extrapolation of vaporization enthalpies to the reference temperature 298 K was found to be a major source of the discrepancies among previous data sets. Two simple methods for temperature adjustment of vaporization enthalpies have been suggested. Resulting vaporization enthalpies obey group additivity, although the values of the additivity parameters for ILs are different from those for molecular compounds.

Collapse transitions in thermosensitive multi-block copolymers: A Monte Carlo study

NASA Astrophysics Data System (ADS)

Rissanou, Anastassia N.; Tzeli, Despoina S.; Anastasiadis, Spiros H.; Bitsanis, Ioannis A.

2014-05-01

Monte Carlo simulations are performed on a simple cubic lattice to investigate the behavior of a single linear multiblock copolymer chain of various lengths N. The chain of type (AnBn)m consists of alternating A and B blocks, where A are solvophilic and B are solvophobic and N = 2nm. The conformations are classified in five cases of globule formation by the solvophobic blocks of the chain. The dependence of globule characteristics on the molecular weight and on the number of blocks, which participate in their formation, is examined. The focus is on relative high molecular weight blocks (i.e., N in the range of 500-5000 units) and very differing energetic conditions for the two blocks (very good—almost athermal solvent for A and bad solvent for B). A rich phase behavior is observed as a result of the alternating architecture of the multiblock copolymer chain. We trust that thermodynamic equilibrium has been reached for chains of N up to 2000 units; however, for longer chains kinetic entrapments are observed. The comparison among equivalent globules consisting of different number of B-blocks shows that the more the solvophobic blocks constituting the globule the bigger its radius of gyration and the looser its structure. Comparisons between globules formed by the solvophobic blocks of the multiblock copolymer chain and their homopolymer analogs highlight the important role of the solvophilic A-blocks.

A novel framework to simulating non-stationary, non-linear, non-Normal hydrological time series using Markov Switching Autoregressive Models

NASA Astrophysics Data System (ADS)

Birkel, C.; Paroli, R.; Spezia, L.; Tetzlaff, D.; Soulsby, C.

2012-12-01

In this paper we present a novel model framework using the class of Markov Switching Autoregressive Models (MSARMs) to examine catchments as complex stochastic systems that exhibit non-stationary, non-linear and non-Normal rainfall-runoff and solute dynamics. Hereby, MSARMs are pairs of stochastic processes, one observed and one unobserved, or hidden. We model the unobserved process as a finite state Markov chain and assume that the observed process, given the hidden Markov chain, is conditionally autoregressive, which means that the current observation depends on its recent past (system memory). The model is fully embedded in a Bayesian analysis based on Markov Chain Monte Carlo (MCMC) algorithms for model selection and uncertainty assessment. Hereby, the autoregressive order and the dimension of the hidden Markov chain state-space are essentially self-selected. The hidden states of the Markov chain represent unobserved levels of variability in the observed process that may result from complex interactions of hydroclimatic variability on the one hand and catchment characteristics affecting water and solute storage on the other. To deal with non-stationarity, additional meteorological and hydrological time series along with a periodic component can be included in the MSARMs as covariates. This extension allows identification of potential underlying drivers of temporal rainfall-runoff and solute dynamics. We applied the MSAR model framework to streamflow and conservative tracer (deuterium and oxygen-18) time series from an intensively monitored 2.3 km2 experimental catchment in eastern Scotland. Statistical time series analysis, in the form of MSARMs, suggested that the streamflow and isotope tracer time series are not controlled by simple linear rules. MSARMs showed that the dependence of current observations on past inputs observed by transport models often in form of the long-tailing of travel time and residence time distributions can be efficiently explained by non-stationarity either of the system input (climatic variability) and/or the complexity of catchment storage characteristics. The statistical model is also capable of reproducing short (event) and longer-term (inter-event) and wet and dry dynamical "hydrological states". These reflect the non-linear transport mechanisms of flow pathways induced by transient climatic and hydrological variables and modified by catchment characteristics. We conclude that MSARMs are a powerful tool to analyze the temporal dynamics of hydrological data, allowing for explicit integration of non-stationary, non-linear and non-Normal characteristics.

The E3 ligase HOIP specifies linear ubiquitin chain assembly through its RING-IBR-RING domain and the unique LDD extension

PubMed Central

Smit, Judith J; Monteferrario, Davide; Noordermeer, Sylvie M; van Dijk, Willem J; van der Reijden, Bert A; Sixma, Titia K

2012-01-01

Activation of the NF-κB pathway requires the formation of Met1-linked ‘linear' ubiquitin chains on NEMO, which is catalysed by the Linear Ubiquitin Chain Assembly Complex (LUBAC) E3 consisting of HOIP, HOIL-1L and Sharpin. Here, we show that both LUBAC catalytic activity and LUBAC specificity for linear ubiquitin chain formation are embedded within the RING-IBR-RING (RBR) ubiquitin ligase subunit HOIP. Linear ubiquitin chain formation by HOIP proceeds via a two-step mechanism involving both RING and HECT E3-type activities. RING1-IBR catalyses the transfer of ubiquitin from the E2 onto RING2, to transiently form a HECT-like covalent thioester intermediate. Next, the ubiquitin is transferred from HOIP onto the N-terminus of a target ubiquitin. This transfer is facilitated by a unique region in the C-terminus of HOIP that we termed ‘Linear ubiquitin chain Determining Domain' (LDD), which may coordinate the acceptor ubiquitin. Consistent with this mechanism, the RING2-LDD region was found to be important for NF-κB activation in cellular assays. These data show how HOIP combines a general RBR ubiquitin ligase mechanism with unique, LDD-dependent specificity for producing linear ubiquitin chains. PMID:22863777

Asymmetric simple exclusion process on chains with a shortcut.

PubMed

Bunzarova, Nadezhda; Pesheva, Nina; Brankov, Jordan

2014-03-01

We consider the asymmetric simple exclusion process (TASEP) on an open network consisting of three consecutively coupled macroscopic chain segments with a shortcut between the tail of the first segment and the head of the third one. The model was introduced by Y.-M. Yuan et al. [J. Phys. A 40, 12351 (2007)] to describe directed motion of molecular motors along twisted filaments. We report here unexpected results which revise the previous findings in the case of maximum current through the network. Our theoretical analysis, based on the effective rates' approximation, shows that the second (shunted) segment can exist in both low- and high-density phases, as well as in the coexistence (shock) phase. Numerical simulations demonstrate that the last option takes place in finite-size networks with head and tail chains of equal length, provided the injection and ejection rates at their external ends are equal and greater than one-half. Then the local density distribution and the nearest-neighbor correlations in the middle chain correspond to a shock phase with completely delocalized domain wall. Upon moving the shortcut to the head or tail of the network, the density profile takes a shape typical of a high- or low-density phase, respectively. Surprisingly, the main quantitative parameters of that shock phase are governed by a positive root of a cubic equation, the coefficients of which linearly depend on the probability of choosing the shortcut. Alternatively, they can be expressed in a universal way through the shortcut current. The unexpected conclusion is that a shortcut in the bulk of a single lane may create traffic jams.

Linear ubiquitin chains: enzymes, mechanisms and biology

PubMed Central

2017-01-01

Ubiquitination is a versatile post-translational modification that regulates a multitude of cellular processes. Its versatility is based on the ability of ubiquitin to form multiple types of polyubiquitin chains, which are recognized by specific ubiquitin receptors to induce the required cellular response. Linear ubiquitin chains are linked through Met 1 and have been established as important players of inflammatory signalling and apoptotic cell death. These chains are generated by a ubiquitin E3 ligase complex called the linear ubiquitin chain assembly complex (LUBAC) that is thus far the only E3 ligase capable of forming linear ubiquitin chains. The complex consists of three subunits, HOIP, HOIL-1L and SHARPIN, each of which have specific roles in the observed biological functions of LUBAC. Furthermore, LUBAC has been found to be associated with OTULIN and CYLD, deubiquitinases that disassemble linear chains and counterbalance the E3 ligase activity of LUBAC. Gene mutations in HOIP, HOIL-1L and OTULIN are found in human patients who suffer from autoimmune diseases, and HOIL-1L mutations are also found in myopathy patients. In this paper, we discuss the mechanisms of linear ubiquitin chain generation and disassembly by their respective enzymes and review our current understanding of their biological functions and association with human diseases. PMID:28446710

Linear ubiquitin chains: enzymes, mechanisms and biology.

PubMed

Rittinger, Katrin; Ikeda, Fumiyo

2017-04-01

Ubiquitination is a versatile post-translational modification that regulates a multitude of cellular processes. Its versatility is based on the ability of ubiquitin to form multiple types of polyubiquitin chains, which are recognized by specific ubiquitin receptors to induce the required cellular response. Linear ubiquitin chains are linked through Met 1 and have been established as important players of inflammatory signalling and apoptotic cell death. These chains are generated by a ubiquitin E3 ligase complex called the linear ubiquitin chain assembly complex (LUBAC) that is thus far the only E3 ligase capable of forming linear ubiquitin chains. The complex consists of three subunits, HOIP, HOIL-1L and SHARPIN, each of which have specific roles in the observed biological functions of LUBAC. Furthermore, LUBAC has been found to be associated with OTULIN and CYLD, deubiquitinases that disassemble linear chains and counterbalance the E3 ligase activity of LUBAC. Gene mutations in HOIP, HOIL-1L and OTULIN are found in human patients who suffer from autoimmune diseases, and HOIL-1L mutations are also found in myopathy patients. In this paper, we discuss the mechanisms of linear ubiquitin chain generation and disassembly by their respective enzymes and review our current understanding of their biological functions and association with human diseases. © 2017 The Authors.

Bayesian reconstruction of projection reconstruction NMR (PR-NMR).

PubMed

Yoon, Ji Won

2014-11-01

Projection reconstruction nuclear magnetic resonance (PR-NMR) is a technique for generating multidimensional NMR spectra. A small number of projections from lower-dimensional NMR spectra are used to reconstruct the multidimensional NMR spectra. In our previous work, it was shown that multidimensional NMR spectra are efficiently reconstructed using peak-by-peak based reversible jump Markov chain Monte Carlo (RJMCMC) algorithm. We propose an extended and generalized RJMCMC algorithm replacing a simple linear model with a linear mixed model to reconstruct close NMR spectra into true spectra. This statistical method generates samples in a Bayesian scheme. Our proposed algorithm is tested on a set of six projections derived from the three-dimensional 700 MHz HNCO spectrum of a protein HasA. Copyright © 2014 Elsevier Ltd. All rights reserved.

Reciprocal Sliding Friction Model for an Electro-Deposited Coating and Its Parameter Estimation Using Markov Chain Monte Carlo Method

PubMed Central

Kim, Kyungmok; Lee, Jaewook

2016-01-01

This paper describes a sliding friction model for an electro-deposited coating. Reciprocating sliding tests using ball-on-flat plate test apparatus are performed to determine an evolution of the kinetic friction coefficient. The evolution of the friction coefficient is classified into the initial running-in period, steady-state sliding, and transition to higher friction. The friction coefficient during the initial running-in period and steady-state sliding is expressed as a simple linear function. The friction coefficient in the transition to higher friction is described with a mathematical model derived from Kachanov-type damage law. The model parameters are then estimated using the Markov Chain Monte Carlo (MCMC) approach. It is identified that estimated friction coefficients obtained by MCMC approach are in good agreement with measured ones. PMID:28773359

A new way of visualising quantum fields

NASA Astrophysics Data System (ADS)

Linde, Helmut

2018-05-01

Quantum field theory (QFT) is the basis of some of the most fundamental theories in modern physics, but it is not an easy subject to learn. In the present article we intend to pave the way from quantum mechanics to QFT for students at early graduate or advanced undergraduate level. More specifically, we propose a new way of visualising the wave function Ψ of a linear chain of interacting quantum harmonic oscillators, which can be seen as a model for a simple one-dimensional bosonic quantum field. The main idea is to draw randomly chosen classical states of the chain superimposed upon each other and use a grey scale to represent the value of Ψ at the corresponding coordinates of the quantised system. Our goal is to establish a better intuitive understanding of the mathematical objects underlying quantum field theories and solid state physics.

Linear and nonlinear dynamics of isospectral granular chains

NASA Astrophysics Data System (ADS)

Chaunsali, R.; Xu, H.; Yang, J.; Kevrekidis, P. G.

2017-04-01

We study the dynamics of isospectral granular chains that are highly tunable due to the nonlinear Hertz contact law interaction between the granular particles. The system dynamics can thus be tuned easily from being linear to strongly nonlinear by adjusting the initial compression applied to the chain. In particular, we introduce both discrete and continuous spectral transformation schemes to generate a family of granular chains that are isospectral in their linear limit. Inspired by the principle of supersymmetry in quantum systems, we also introduce a methodology to add or remove certain eigenfrequencies, and we demonstrate numerically that the corresponding physical system can be constructed in the setting of one-dimensional granular crystals. In the linear regime, we highlight the similarities in the elastic wave transmission characteristics of such isospectral systems, and emphasize that the presented mathematical framework allows one to suitably tailor the wave transmission through a general class of granular chains, both ordered and disordered. Moreover, we show how the dynamic response of these structures deviates from its linear limit as we introduce Hertzian nonlinearity in the chain and how nonlinearity breaks the notion of linear isospectrality.

A kinetic theory description of the viscosity of dense fluids consisting of chain molecules.

PubMed

de Wijn, Astrid S; Vesovic, Velisa; Jackson, George; Trusler, J P Martin

2008-05-28

An expression for the viscosity of a dense fluid is presented that includes the effect of molecular shape. The molecules of the fluid are approximated by chains of equal-sized, tangentially jointed, rigid spheres. It is assumed that the collision dynamics in such a fluid can be approximated by instantaneous collisions between two rigid spheres belonging to different chains. The approach is thus analogous to that of Enskog for a fluid consisting of rigid spheres. The description is developed in terms of two molecular parameters, the diameter sigma of the spherical segment and the chain length (number of segments) m. It is demonstrated that an analysis of viscosity data of a particular pure fluid alone cannot be used to obtain independently effective values of both sigma and m. Nevertheless, the chain lengths of n-alkanes are determined by assuming that the diameter of each rigid sphere making up the chain can be represented by the diameter of a methane molecule. The effective chain lengths of n-alkanes are found to increase linearly with the number C of carbon atoms present. The dependence can be approximated by a simple relationship m=1+(C-1)3. The same relationship was reported within the context of a statistical associating fluid theory equation of state treatment of the fluid, indicating that both the equilibrium thermodynamic properties and viscosity yield the same value for the chain lengths of n-alkanes.

Surface structure evolution in a homologous series of ionic liquids.

PubMed

Haddad, Julia; Pontoni, Diego; Murphy, Bridget M; Festersen, Sven; Runge, Benjamin; Magnussen, Olaf M; Steinrück, Hans-Georg; Reichert, Harald; Ocko, Benjamin M; Deutsch, Moshe

2018-02-06

Interfaces of room temperature ionic liquids (RTILs) are important for both applications and basic science and are therefore intensely studied. However, the evolution of their interface structure with the cation's alkyl chain length [Formula: see text] from Coulomb to van der Waals interaction domination has not yet been studied for even a single broad homologous RTIL series. We present here such a study of the liquid-air interface for [Formula: see text], using angstrom-resolution X-ray methods. For [Formula: see text], a typical "simple liquid" monotonic surface-normal electron density profile [Formula: see text] is obtained, like those of water and organic solvents. For [Formula: see text], increasingly more pronounced nanoscale self-segregation of the molecules' charged moieties and apolar chains yields surface layering with alternating regions of headgroups and chains. The layering decays into the bulk over a few, to a few tens, of nanometers. The layering periods and decay lengths, their linear [Formula: see text] dependence, and slopes are discussed within two models, one with partial-chain interdigitation and the other with liquid-like chains. No surface-parallel long-range order is found within the surface layer. For [Formula: see text], a different surface phase is observed above melting. Our results also impact general liquid-phase issues like supramolecular self-aggregation and bulk-surface structure relations.

Macromolecular 'size' and 'hardness' drives structure in solvent-swollen blends of linear, cyclic, and star polymers.

PubMed

Gartner, Thomas E; Jayaraman, Arthi

2018-01-17

In this paper, we apply molecular simulation and liquid state theory to uncover the structure and thermodynamics of homopolymer blends of the same chemistry and varying chain architecture in the presence of explicit solvent species. We use hybrid Monte Carlo (MC)/molecular dynamics (MD) simulations in the Gibbs ensemble to study the swelling of ∼12 000 g mol -1 linear, cyclic, and 4-arm star polystyrene chains in toluene. Our simulations show that the macroscopic swelling response is indistinguishable between the various architectures and matches published experimental data for the solvent annealing of linear polystyrene by toluene vapor. We then use standard MD simulations in the NPT ensemble along with polymer reference interaction site model (PRISM) theory to calculate effective polymer-solvent and polymer-polymer Flory-Huggins interaction parameters (χ eff ) in these systems. As seen in the macroscopic swelling results, there are no significant differences in the polymer-solvent and polymer-polymer χ eff between the various architectures. Despite similar macroscopic swelling and effective interaction parameters between various architectures, the pair correlation function between chain centers-of-mass indicates stronger correlations between cyclic or star chains in the linear-cyclic blends and linear-star blends, compared to linear chain-linear chain correlations. Furthermore, we note striking similarities in the chain-level correlations and the radius of gyration of cyclic and 4-arm star architectures of identical molecular weight. Our results indicate that the cyclic and star chains are 'smaller' and 'harder' than their linear counterparts, and through comparison with MD simulations of blends of soft spheres with varying hardness and size we suggest that these macromolecular characteristics are the source of the stronger cyclic-cyclic and star-star correlations.

Global quantum discord and matrix product density operators

NASA Astrophysics Data System (ADS)

Huang, Hai-Lin; Cheng, Hong-Guang; Guo, Xiao; Zhang, Duo; Wu, Yuyin; Xu, Jian; Sun, Zhao-Yu

2018-06-01

In a previous study, we have proposed a procedure to study global quantum discord in 1D chains whose ground states are described by matrix product states [Z.-Y. Sun et al., Ann. Phys. 359, 115 (2015)]. In this paper, we show that with a very simple generalization, the procedure can be used to investigate quantum mixed states described by matrix product density operators, such as quantum chains at finite temperatures and 1D subchains in high-dimensional lattices. As an example, we study the global discord in the ground state of a 2D transverse-field Ising lattice, and pay our attention to the scaling behavior of global discord in 1D sub-chains of the lattice. We find that, for any strength of the magnetic field, global discord always shows a linear scaling behavior as the increase of the length of the sub-chains. In addition, global discord and the so-called "discord density" can be used to indicate the quantum phase transition in the model. Furthermore, based upon our numerical results, we make some reliable predictions about the scaling of global discord defined on the n × n sub-squares in the lattice.

Structural and optical properties of self-assembled chains of plasmonic nanocubes

DOE PAGES

Klinkova, Anna; Gang, Oleg; Therien-Aubin, Heloise; ...

2014-10-10

Solution-based linear self-assembly of metal nanoparticles offers a powerful strategy for creating plasmonic polymers, which, so far, have been formed from spherical nanoparticles and nanorods. Here, we report linear solution-based self-assembly of metal nanocubes (NCs), examine the structural characteristics of the NC chains and demonstrate their advanced optical characteristics. Predominant face-to-face assembly of large NCs coated with short polymer ligands led to a larger volume of hot spots in the chains, a nearly uniform E-field enhancement in the gaps between co-linear NCs and a new coupling mode for NC chains, in comparison with chains of nanospheres with similar dimensions, compositionmore » and surface chemistry. The NC chains exhibited a stronger surface enhanced Raman scattering (SERS) signal, in comparison with linear assemblies of nanospheres. The experimental results were in agreement with finite difference time domain (FDTD) simulations.« less

Dust coagulation in ISM

NASA Technical Reports Server (NTRS)

Chokshi, Arati; Tielens, Alexander G. G. M.; Hollenbach, David

1989-01-01

Coagulation is an important mechanism in the growth of interstellar and interplanetary dust particles. The microphysics of the coagulation process was theoretically analyzed as a function of the physical properties of the coagulating grains, i.e., their size, relative velocities, temperature, elastic properties, and the van der Waal interaction. Numerical calculations of collisions between linear chains provide the wave energy in individual particles and the spectrum of the mechanical vibrations set up in colliding particles. Sticking probabilities are then calculated using simple estimates for elastic deformation energies and for the attenuation of the wave energy due to absorption and scattering processes.

Bottlebrush-Guided Polymer Crystallization Resulting in Supersoft and Reversibly Moldable Physical Networks

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

Daniel, William F. M.; Xie, Guojun; Vatankhah Varnoosfaderani, Mohammad

The goal of this study is to use ABA triblock copolymers with central bottlebrush B segments and crystalline linear chain A segments to demonstrate the effect of side chains on the formation and mechanical properties of physical networks cross-linked by crystallites. For this purpose, a series of bottlebrush copolymers was synthesized consisting of central amorphous bottlebrush polymer segments with a varying degree of polymerization (DP) of poly(n-butyl acrylate) (PnBA) side chains and linear tail blocks of crystallizable poly(octadecyl acrylate-stat-docosyl acrylate) (poly(ODA-stat-DA)). The materials were generated by sequential atom transfer radical polymerization (ATRP) steps starting with a series of bifunctional macroinitiatorsmore » followed by the growth of two ODA-stat-DA linear-chain tails and eventually growing poly(nBA) side chains with increasing DPs. Crystallization of the poly(ODA-stat-DA) tails resulted in a series of reversible physical networks with bottlebrush strands bridging crystalline cross-links. They displayed very low moduli of elasticity of the order of 10 3–10 4 Pa. These distinct properties are due to the bottlebrush architecture, wherein densely grafted side chains play a dual role by facilitating disentanglement of the network strands and confining crystallization of the linear-chain tails. This combination leads to physical cross-linking of supersoft networks without percolation of the crystalline phase. The cross-link density was effectively controlled by the DP of the side chains with respect to the DP of the linear tails (n A). Furthermore, shorter side chains allowed for crystallization of the linear tails of neighboring bottlebrushes, while steric repulsion between longer side chains hindered the phase separation and crystallization process and prevented network formation.« less

Bottlebrush-Guided Polymer Crystallization Resulting in Supersoft and Reversibly Moldable Physical Networks

DOE PAGES

Daniel, William F. M.; Xie, Guojun; Vatankhah Varnoosfaderani, Mohammad; ...

2017-02-24

The goal of this study is to use ABA triblock copolymers with central bottlebrush B segments and crystalline linear chain A segments to demonstrate the effect of side chains on the formation and mechanical properties of physical networks cross-linked by crystallites. For this purpose, a series of bottlebrush copolymers was synthesized consisting of central amorphous bottlebrush polymer segments with a varying degree of polymerization (DP) of poly(n-butyl acrylate) (PnBA) side chains and linear tail blocks of crystallizable poly(octadecyl acrylate-stat-docosyl acrylate) (poly(ODA-stat-DA)). The materials were generated by sequential atom transfer radical polymerization (ATRP) steps starting with a series of bifunctional macroinitiatorsmore » followed by the growth of two ODA-stat-DA linear-chain tails and eventually growing poly(nBA) side chains with increasing DPs. Crystallization of the poly(ODA-stat-DA) tails resulted in a series of reversible physical networks with bottlebrush strands bridging crystalline cross-links. They displayed very low moduli of elasticity of the order of 10 3–10 4 Pa. These distinct properties are due to the bottlebrush architecture, wherein densely grafted side chains play a dual role by facilitating disentanglement of the network strands and confining crystallization of the linear-chain tails. This combination leads to physical cross-linking of supersoft networks without percolation of the crystalline phase. The cross-link density was effectively controlled by the DP of the side chains with respect to the DP of the linear tails (n A). Furthermore, shorter side chains allowed for crystallization of the linear tails of neighboring bottlebrushes, while steric repulsion between longer side chains hindered the phase separation and crystallization process and prevented network formation.« less

Asymmetric simple exclusion process on chains with a shortcut

NASA Astrophysics Data System (ADS)

Bunzarova, Nadezhda; Pesheva, Nina; Brankov, Jordan

2014-03-01

We consider the asymmetric simple exclusion process (TASEP) on an open network consisting of three consecutively coupled macroscopic chain segments with a shortcut between the tail of the first segment and the head of the third one. The model was introduced by Y.-M. Yuan et al. [J. Phys. A 40, 12351 (2007), 10.1088/1751-8113/40/41/006] to describe directed motion of molecular motors along twisted filaments. We report here unexpected results which revise the previous findings in the case of maximum current through the network. Our theoretical analysis, based on the effective rates' approximation, shows that the second (shunted) segment can exist in both low- and high-density phases, as well as in the coexistence (shock) phase. Numerical simulations demonstrate that the last option takes place in finite-size networks with head and tail chains of equal length, provided the injection and ejection rates at their external ends are equal and greater than one-half. Then the local density distribution and the nearest-neighbor correlations in the middle chain correspond to a shock phase with completely delocalized domain wall. Upon moving the shortcut to the head or tail of the network, the density profile takes a shape typical of a high- or low-density phase, respectively. Surprisingly, the main quantitative parameters of that shock phase are governed by a positive root of a cubic equation, the coefficients of which linearly depend on the probability of choosing the shortcut. Alternatively, they can be expressed in a universal way through the shortcut current. The unexpected conclusion is that a shortcut in the bulk of a single lane may create traffic jams.

Granular dynamics during impact.

PubMed

Nordstrom, K N; Lim, E; Harrington, M; Losert, W

2014-06-06

We study the impact of a projectile onto a bed of 3 mm grains immersed in an index-matched fluid. We vary the amount of prestrain on the sample, strengthening the force chains within the system. We find this affects only the prefactor of the linear depth-dependent term in the stopping force. We propose a simple model to account for the strain dependence of this term, owing to increased pressure in the pile. Interestingly, we find that the presence of the fluid does not affect the impact dynamics, suggesting that dynamic friction is not a factor. Using a laser sheet scanning technique to visualize internal grain motion, we measure the trajectory of each grain throughout an impact. Microscopically, our results indicate that weaker initial force chains result in more irreversible, plastic rearrangements, suggesting static friction between grains does play a substantial role in the energy dissipation.

Renormalized charge in a two-dimensional model of colloidal suspension from hypernetted chain approach.

PubMed

Camargo, Manuel; Téllez, Gabriel

2008-04-07

The renormalized charge of a simple two-dimensional model of colloidal suspension was determined by solving the hypernetted chain approximation and Ornstein-Zernike equations. At the infinite dilution limit, the asymptotic behavior of the correlation functions is used to define the effective interactions between the components of the system and these effective interactions were compared to those derived from the Poisson-Boltzmann theory. The results we obtained show that, in contrast to the mean-field theory, the renormalized charge does not saturate, but exhibits a maximum value and then decays monotonically as the bare charge increases. The results also suggest that beyond the counterion layer near to the macroion surface, the ionic cloud is not a diffuse layer which can be handled by means of the linearized theory, as the two-state model claims, but a more complex structure is settled by the correlations between microions.

Engineering single-polymer micelle shape using nonuniform spontaneous surface curvature

NASA Astrophysics Data System (ADS)

Moths, Brian; Witten, T. A.

2018-03-01

Conventional micelles, composed of simple amphiphiles, exhibit only a few standard morphologies, each characterized by its mean surface curvature set by the amphiphiles. Here we demonstrate a rational design scheme to construct micelles of more general shape from polymeric amphiphiles. We replace the many amphiphiles of a conventional micelle by a single flexible, linear, block copolymer chain containing two incompatible species arranged in multiple alternating segments. With suitable segment lengths, the chain exhibits a condensed spherical configuration in solution, similar to conventional micelles. Our design scheme posits that further shapes are attained by altering the segment lengths. As a first study of the power of this scheme, we demonstrate the capacity to produce long-lived micelles of horseshoe form using conventional bead-spring simulations in two dimensions. Modest changes in the segment lengths produce smooth changes in the micelle's shape and stability.

Bacterial Expression of a Single-Chain Variable Fragment (scFv) Antibody against Ganoderic Acid A: A Cost-Effective Approach for Quantitative Analysis Using the scFv-Based Enzyme-Linked Immunosorbent Assay.

PubMed

Yusakul, Gorawit; Nuntawong, Poomraphie; Sakamoto, Seiichi; Ratnatilaka Na Bhuket, Pahweenvaj; Kohno, Toshitaka; Kikkawa, Nao; Rojsitthisak, Pornchai; Shimizu, Kuniyoshi; Tanaka, Hiroyuki; Morimoto, Satoshi

2017-01-01

Due to the highly specific binding between an antibody and its target, superior analytical performances was obtained by immunoassays for phytochemical analysis over conventional chromatographic techniques. Here, we describe a simple method for producing a functional single-chain variable fragment (scFv) antibody against ganoderic acid A (GAA), a pharmacologically active metabolite from Ganoderma lingzhi. The Escherichia coli BL21(DE3) strain produced a large amount of anti-GAA scFv. However, in vitro refolding steps, which partially recovered the reactivity of the scFv, were required. Interestingly, the functional scFv was expressed as a soluble and active form in the cytoplasm of an engineered E. coli SHuffle ® strain. Purified anti-GAA scFv, which yielded 2.56 mg from 1 L of culture medium, was obtained from simple and inexpensive procedures for expression and purification. The anti-GAA scFv-based indirect competitive enzyme-linked immunosorbent assay (icELISA) exhibited high sensitivity (linearity: 0.078-1.25 µg/mL) with precision (CV: ≤6.20%) and reliability (recovery: 100.1-101.8%) for GAA determination. In summary, the approach described here is an inexpensive, simple, and efficient expression system that extends the application of anti-GAA scFv-based immunoassays. In addition, when in vitro refolding steps can be skipped, the cost and complexity of scFv antibody production can be minimized.

Structure of the conversion laws in quantum integrable spin chains with short range interactions

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

Grabowski, M.P.; Mathieu, P.

1995-11-01

The authors present a detailed analysis of the structure of the conservation laws in quantum integrable chains of the XYZ-type and in the Hubbard model. The essential tool for the former class of models is the boost operator, which provides a recursive way of calculating the integrals of motion. With its help, they establish the general form of the XYZ conserved charges in terms of simple polynomials in spin variables and derive recursion relations for the relative coefficients of these polynomials. Although these relations are difficult to solve in general, a subset of the coefficients can be determined. Moreover, formore » two submodels of the XYZ chain, namely the XXX and XY cases, all the charges can be calculated in closed form. Using this approach, the authors rederive the known expressions for the XY charges in a novel way. For the XXX case. a simple description of conserved charges is found in terms of a Catalan tree. This construction is generalized for the su(M) invariant integrable chain. They also investigate the circumstances permitting the existence of a recursive (ladder) operator in general quantum integrable systems. They indicate that a quantum ladder operator can be traced back to the presence of a Hamiltonian mastersymmetry of degree one in the classical continuous version of the model. In this way, quantum chains endowed with a recursive structure can be identified from the properties of their classical relatives. The authors also show that in the quantum continuous limits of the XYZ model, the ladder property of the boost operator disappears. For the Hubbard model they demonstrate the nonexistence of a ladder operator. Nevertheless, the general structure of the conserved charges is indicated, and the expression for the terms linear in the model`s free parameter for all charges is derived in closed form. 62 refs., 4 figs.« less

Electronic band gaps of confined linear carbon chains ranging from polyyne to carbyne

NASA Astrophysics Data System (ADS)

Shi, Lei; Rohringer, Philip; Wanko, Marius; Rubio, Angel; Waßerroth, Sören; Reich, Stephanie; Cambré, Sofie; Wenseleers, Wim; Ayala, Paola; Pichler, Thomas

2017-12-01

Ultralong linear carbon chains of more than 6000 carbon atoms have recently been synthesized within double-walled carbon nanotubes (DWCNTs), and they show a promising route to one-atom-wide semiconductors with a direct band gap. Theoretical studies predicted that this band gap can be tuned by the length of the chains, the end groups, and their interactions with the environment. However, different density functionals lead to very different values of the band gap of infinitely long carbyne. In this work, we applied resonant Raman excitation spectroscopy with more than 50 laser wavelengths to determine the band gap of long carbon chains encapsulated inside DWCNTs. The experimentally determined band gaps ranging from 2.253 to 1.848 eV follow a linear relation with Raman frequency. This lower bound is the smallest band gap of linear carbon chains observed so far. The comparison with experimental data obtained for short chains in gas phase or in solution demonstrates the effect of the DWCNT encapsulation, leading to an essential downshift of the band gap. This is explained by the interaction between the carbon chain and the host tube, which greatly modifies the chain's bond-length alternation.

Confined dynamics of grafted polymer chains in solutions of linear polymer

DOE PAGES

Poling-Skutvik, Ryan D.; Olafson, Katy N.; Narayanan, Suresh; ...

2017-09-11

Here, we measure the dynamics of high molecular weight polystyrene grafted to silica nanoparticles dispersed in semidilute solutions of linear polymer. Structurally, the linear free chains do not penetrate the grafted corona but increase the osmotic pressure of the solution, collapsing the grafted polymer and leading to eventual aggregation of the grafted particles at high matrix concentrations. Dynamically, the relaxations of the grafted polymer are controlled by the solvent viscosity according to the Zimm model on short time scales. On longer time scales, the grafted chains are confined by neighboring grafted chains, preventing full relaxation over the experimental time scale.more » Adding free linear polymer to the solution does not affect the initial Zimm relaxations of the grafted polymer but does increase the confinement of the grafted chains. Finally, our results elucidate the physics underlying the slow relaxations of grafted polymer.« less

Confined dynamics of grafted polymer chains in solutions of linear polymer

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

Poling-Skutvik, Ryan D.; Olafson, Katy N.; Narayanan, Suresh

Here, we measure the dynamics of high molecular weight polystyrene grafted to silica nanoparticles dispersed in semidilute solutions of linear polymer. Structurally, the linear free chains do not penetrate the grafted corona but increase the osmotic pressure of the solution, collapsing the grafted polymer and leading to eventual aggregation of the grafted particles at high matrix concentrations. Dynamically, the relaxations of the grafted polymer are controlled by the solvent viscosity according to the Zimm model on short time scales. On longer time scales, the grafted chains are confined by neighboring grafted chains, preventing full relaxation over the experimental time scale.more » Adding free linear polymer to the solution does not affect the initial Zimm relaxations of the grafted polymer but does increase the confinement of the grafted chains. Finally, our results elucidate the physics underlying the slow relaxations of grafted polymer.« less

Surface structure evolution in a homologous series of ionic liquids

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

Haddad, Julia; Pontoni, Diego; Murphy, Bridget M.

Interfaces of room temperature ionic liquids (RTILs) are important for both applications and basic science and are therefore intensely studied. However, the evolution of their interface structure with the cation’s alkyl chain length n from Coulomb to van der Waals interaction domination has not yet been studied for even a single broad homologous RTIL series. We present in this paper such a study of the liquid–air interface for n = 2 to 22, using angstrom-resolution X-ray methods. For n < 6, a typical “simple liquid” monotonic surface-normal electron density profile ρ e more » ( z ) is obtained, like those of water and organic solvents. For n > 6, increasingly more pronounced nanoscale self-segregation of the molecules’ charged moieties and apolar chains yields surface layering with alternating regions of headgroups and chains. The layering decays into the bulk over a few, to a few tens, of nanometers. The layering periods and decay lengths, their linear n dependence, and slopes are discussed within two models, one with partial-chain interdigitation and the other with liquid-like chains. No surface-parallel long-range order is found within the surface layer. For n = 22, a different surface phase is observed above melting. Finally, our results also impact general liquid-phase issues like supramolecular self-aggregation and bulk–surface structure relations.« less

Thermodynamics and mechanics of stretch-induced crystallization in rubbers

NASA Astrophysics Data System (ADS)

Guo, Qiang; Zaïri, Fahmi; Guo, Xinglin

2018-05-01

The aim of the present paper is to provide a quantitative prediction of the stretch-induced crystallization in natural rubber, the exclusive reason for its history-dependent thermomechanical features. A constitutive model based on a micromechanism inspired molecular chain approach is formulated within the context of the thermodynamic framework. The molecular configuration of the partially crystallized single chain is analyzed and calculated by means of some statistical mechanical methods. The random thermal oscillation of the crystal orientation, considered as a continuous random variable, is treated by means of a representative angle. The physical expression of the chain free energy is derived according to a two-step strategy by separating crystallization and stretching. This strategy ensures that the stretch-induced part of the thermodynamic crystallization force is null at the initial instant and allows, without any additional constraint, the formulation of a simple linear relationship for the crystallinity evolution law. The model contains very few physically interpretable material constants to simulate the complex mechanism: two chain-scale constants, one crystallinity kinetics constant, three thermodynamic constants related to the newly formed crystallites, and a function controlling the crystal orientation with respect to the chain. The model is used to discuss some important aspects of the micromechanism and the macroresponse under the equilibrium state and the nonequilibrium state involved during stretching and recovery, and continuous relaxation.

Surface structure evolution in a homologous series of ionic liquids

DOE PAGES

Haddad, Julia; Pontoni, Diego; Murphy, Bridget M.; ...

2018-01-22

Interfaces of room temperature ionic liquids (RTILs) are important for both applications and basic science and are therefore intensely studied. However, the evolution of their interface structure with the cation’s alkyl chain length n from Coulomb to van der Waals interaction domination has not yet been studied for even a single broad homologous RTIL series. We present in this paper such a study of the liquid–air interface for n = 2 to 22, using angstrom-resolution X-ray methods. For n < 6, a typical “simple liquid” monotonic surface-normal electron density profile ρ e more » ( z ) is obtained, like those of water and organic solvents. For n > 6, increasingly more pronounced nanoscale self-segregation of the molecules’ charged moieties and apolar chains yields surface layering with alternating regions of headgroups and chains. The layering decays into the bulk over a few, to a few tens, of nanometers. The layering periods and decay lengths, their linear n dependence, and slopes are discussed within two models, one with partial-chain interdigitation and the other with liquid-like chains. No surface-parallel long-range order is found within the surface layer. For n = 22, a different surface phase is observed above melting. Finally, our results also impact general liquid-phase issues like supramolecular self-aggregation and bulk–surface structure relations.« less

Protein side chain rotational isomerization: A minimum perturbation mapping study

NASA Astrophysics Data System (ADS)

Haydock, Christopher

1993-05-01

A theory of the rotational isomerization of the indole side chain of tryptophan-47 of variant-3 scorpion neurotoxin is presented. The isomerization potential energy, entropic part of the isomerization free energy, isomer probabilities, transition state theory reaction rates, and indole order parameters are calculated from a minimum perturbation mapping over tryptophan-47 χ1×χ2 torsion space. A new method for calculating the fluorescence anisotropy from molecular dynamics simulations is proposed. The method is based on an expansion that separates transition dipole orientation from chromophore dynamics. The minimum perturbation potential energy map is inverted and applied as a bias potential for a 100 ns umbrella sampling simulation. The entropic part of the isomerization free energy as calculated by minimum perturbation mapping and umbrella sampling are in fairly close agreement. Throughout, the approximation is made that two glutamine and three tyrosine side chains neighboring tryptophan-47 are truncated at the Cβ atom. Comparison with the previous combination thermodynamic perturbation and umbrella sampling study suggests that this truncated neighbor side chain approximation leads to at least a qualitatively correct theory of tryptophan-47 rotational isomerization in the wild type variant-3 scorpion neurotoxin. Analysis of van der Waals interactions in a transition state region indicates that for the simulation of barrier crossing trajectories a linear combination of three specially defined dihedral angles will be superior to a simple side chain dihedral reaction coordinate.

Simple and novel electrochemical sensor for the determination of tetracycline based on iron/zinc cations-exchanged montmorillonite catalyst.

PubMed

Gan, Tian; Shi, Zhaoxia; Sun, Junyong; Liu, Yanming

2014-04-01

A simple and novel electrochemical sensor for the determination of tetracycline (TC), a kind of antibiotic that may induce residue in the food chain, was developed by the modification of iron/zinc cation-exchanged montmorillonite (Fe/Zn-MMT) catalyst on glassy carbon electrode (GCE). The morphology and the structure of the Fe/Zn-MMT nanomaterial were characterized by scanning electron microscopy and X-ray diffraction, respectively. The results of electrochemical experiments demonstrated that the sensor exhibited excellent electrocatalytic activity to the oxidation of TC in the presence of sodium dodecyl sulfate. The sensor displayed a wide linear range from 0.30 to 52.0 μM and a low detection limit of 0.10 μM by using the derivative differential pulse voltammetry. Moreover, the electrochemical sensor was applied to the detection of TC in feedstuff and meat samples. Copyright © 2014 Elsevier B.V. All rights reserved.

Temperature-dependent layer breathing modes in two-dimensional materials

NASA Astrophysics Data System (ADS)

Maity, Indrajit; Maiti, Prabal K.; Jain, Manish

2018-04-01

Relative out-of-plane displacements of the constituent layers of two-dimensional materials give rise to unique low-frequency breathing modes. By computing the height-height correlation functions from molecular dynamics simulations, we show that the layer breathing modes (LBMs) can be mapped consistently to vibrations of a simple linear chain model. Our calculated thickness dependence of LBM frequencies for few-layer (FL) graphene and molybdenum disulfide (MoS2) are in excellent agreement with available experiments. Our results show a redshift of LBM frequency with an increase in temperature, which is a direct consequence of anharmonicities present in the interlayer interaction. We also predict the thickness and temperature dependence of LBM frequencies for FL hexagonal boron nitride. Our Rapid Communication provides a simple and efficient way to probe the interlayer interaction for layered materials and their heterostructures with the inclusion of anharmonic effects.

Lattice model of linear telechelic polymer melts. II. Influence of chain stiffness on basic thermodynamic properties

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

Xu, Wen-Sheng, E-mail: wsxu@uchicago.edu; Freed, Karl F., E-mail: freed@uchicago.edu; Department of Chemistry, The University of Chicago, Chicago, Illinois 60637

2015-07-14

The lattice cluster theory (LCT) for semiflexible linear telechelic melts, developed in Paper I, is applied to examine the influence of chain stiffness on the average degree of self-assembly and the basic thermodynamic properties of linear telechelic polymer melts. Our calculations imply that chain stiffness promotes self-assembly of linear telechelic polymer melts that assemble on cooling when either polymer volume fraction ϕ or temperature T is high, but opposes self-assembly when both ϕ and T are sufficiently low. This allows us to identify a boundary line in the ϕ-T plane that separates two regions of qualitatively different influence of chainmore » stiffness on self-assembly. The enthalpy and entropy of self-assembly are usually treated as adjustable parameters in classical Flory-Huggins type theories for the equilibrium self-assembly of polymers, but they are demonstrated here to strongly depend on chain stiffness. Moreover, illustrative calculations for the dependence of the entropy density of linear telechelic polymer melts on chain stiffness demonstrate the importance of including semiflexibility within the LCT when exploring the nature of glass formation in models of linear telechelic polymer melts.« less

On the polymer physics origins of protein folding thermodynamics.

PubMed

Taylor, Mark P; Paul, Wolfgang; Binder, Kurt

2016-11-07

A remarkable feature of the spontaneous folding of many small proteins is the striking similarity in the thermodynamics of the folding process. This process is characterized by simple two-state thermodynamics with large and compensating changes in entropy and enthalpy and a funnel-like free energy landscape with a free-energy barrier that varies linearly with temperature. One might attribute the commonality of this two-state folding behavior to features particular to these proteins (e.g., chain length, hydrophobic/hydrophilic balance, attributes of the native state) or one might suspect that this similarity in behavior has a more general polymer-physics origin. Here we show that this behavior is also typical for flexible homopolymer chains with sufficiently short range interactions. Two-state behavior arises from the presence of a low entropy ground (folded) state separated from a set of high entropy disordered (unfolded) states by a free energy barrier. This homopolymer model exhibits a funneled free energy landscape that reveals a complex underlying dynamics involving competition between folding and non-folding pathways. Despite the presence of multiple pathways, this simple physics model gives the robust result of two-state thermodynamics for both the cases of folding from a basin of expanded coil states and from a basin of compact globule states.

On the polymer physics origins of protein folding thermodynamics

NASA Astrophysics Data System (ADS)

Taylor, Mark P.; Paul, Wolfgang; Binder, Kurt

2016-11-01

A remarkable feature of the spontaneous folding of many small proteins is the striking similarity in the thermodynamics of the folding process. This process is characterized by simple two-state thermodynamics with large and compensating changes in entropy and enthalpy and a funnel-like free energy landscape with a free-energy barrier that varies linearly with temperature. One might attribute the commonality of this two-state folding behavior to features particular to these proteins (e.g., chain length, hydrophobic/hydrophilic balance, attributes of the native state) or one might suspect that this similarity in behavior has a more general polymer-physics origin. Here we show that this behavior is also typical for flexible homopolymer chains with sufficiently short range interactions. Two-state behavior arises from the presence of a low entropy ground (folded) state separated from a set of high entropy disordered (unfolded) states by a free energy barrier. This homopolymer model exhibits a funneled free energy landscape that reveals a complex underlying dynamics involving competition between folding and non-folding pathways. Despite the presence of multiple pathways, this simple physics model gives the robust result of two-state thermodynamics for both the cases of folding from a basin of expanded coil states and from a basin of compact globule states.

Methodical fitting for mathematical models of rubber-like materials

NASA Astrophysics Data System (ADS)

Destrade, Michel; Saccomandi, Giuseppe; Sgura, Ivonne

2017-02-01

A great variety of models can describe the nonlinear response of rubber to uniaxial tension. Yet an in-depth understanding of the successive stages of large extension is still lacking. We show that the response can be broken down in three steps, which we delineate by relying on a simple formatting of the data, the so-called Mooney plot transform. First, the small-to-moderate regime, where the polymeric chains unfold easily and the Mooney plot is almost linear. Second, the strain-hardening regime, where blobs of bundled chains unfold to stiffen the response in correspondence to the `upturn' of the Mooney plot. Third, the limiting-chain regime, with a sharp stiffening occurring as the chains extend towards their limit. We provide strain-energy functions with terms accounting for each stage that (i) give an accurate local and then global fitting of the data; (ii) are consistent with weak nonlinear elasticity theory and (iii) can be interpreted in the framework of statistical mechanics. We apply our method to Treloar's classical experimental data and also to some more recent data. Our method not only provides models that describe the experimental data with a very low quantitative relative error, but also shows that the theory of nonlinear elasticity is much more robust that seemed at first sight.

Equivalence between a generalized dendritic network and a set of one-dimensional networks as a ground of linear dynamics.

PubMed

Koda, Shin-ichi

2015-05-28

It has been shown by some existing studies that some linear dynamical systems defined on a dendritic network are equivalent to those defined on a set of one-dimensional networks in special cases and this transformation to the simple picture, which we call linear chain (LC) decomposition, has a significant advantage in understanding properties of dendrimers. In this paper, we expand the class of LC decomposable system with some generalizations. In addition, we propose two general sufficient conditions for LC decomposability with a procedure to systematically realize the LC decomposition. Some examples of LC decomposable linear dynamical systems are also presented with their graphs. The generalization of the LC decomposition is implemented in the following three aspects: (i) the type of linear operators; (ii) the shape of dendritic networks on which linear operators are defined; and (iii) the type of symmetry operations representing the symmetry of the systems. In the generalization (iii), symmetry groups that represent the symmetry of dendritic systems are defined. The LC decomposition is realized by changing the basis of a linear operator defined on a dendritic network into bases of irreducible representations of the symmetry group. The achievement of this paper makes it easier to utilize the LC decomposition in various cases. This may lead to a further understanding of the relation between structure and functions of dendrimers in future studies.

Characteristic α and 6He decays of linear-chain structures in 16C

NASA Astrophysics Data System (ADS)

Baba, T.; Kimura, M.

2018-05-01

The linear-chain states of 16C and their decay modes are theoretically investigated by using the antisymmetrized molecular dynamics. It is found that the positive-parity linear-chain states have the (3/2π-) 2(1/2σ-) 2 configuration and primary decay to 12Be(21+) as well as to 12Be(g.s.) by α -particle emission. Moreover, we show that they also decay via the 6He+10Be channel. In the negative-parity states, it is found that two types of linear chains exist. One has the valence neutrons occupying the molecular orbits (3/2π-) 2(1 /2σ-) (3 /2π+) , while the other's configuration cannot be explained in terms of the molecular orbits because of the strong parity mixing. Both configurations constitute the rotational bands with a large moment of inertia and intraband E 2 transitions. Their α and 6He reduced widths are sufficiently large to be distinguished from other noncluster states although they are smaller than those of the positive-parity linear chain.

Algebraic Bethe ansatz for the sℓ (2) Gaudin model with boundary

NASA Astrophysics Data System (ADS)

Cirilo António, N.; Manojlović, N.; Ragoucy, E.; Salom, I.

2015-04-01

Following Sklyanin's proposal in the periodic case, we derive the generating function of the Gaudin Hamiltonians with boundary terms. Our derivation is based on the quasi-classical expansion of the linear combination of the transfer matrix of the XXX Heisenberg spin chain and the central element, the so-called Sklyanin determinant. The corresponding Gaudin Hamiltonians with boundary terms are obtained as the residues of the generating function. By defining the appropriate Bethe vectors which yield strikingly simple off shell action of the generating function, we fully implement the algebraic Bethe ansatz, obtaining the spectrum of the generating function and the corresponding Bethe equations.

Combining two-directional synthesis and tandem reactions. Part 21: Exploitation of a dimeric macrocycle for chain terminus differentiation and synthesis of an sp(3)-rich library.

PubMed

Storr, Thomas E; Cully, Sarah J; Rawling, Michael J; Lewis, William; Hamza, Daniel; Jones, Geraint; Stockman, Robert A

2015-06-01

The application of a tandem condensation/cyclisation/[3+2]-cycloaddition/elimination reaction gives an sp(3)-rich tricyclic pyrazoline scaffold with two ethyl esters in a single step from a simple linear starting material. The successive hydrolysis and cyclisation (with Boc anhydride) of these 3-dimensional architectures, generates unprecedented 16-membered macrocyclic bisanhydrides (characterised by XRD). Selective amidations could then be achieved by ring opening with a primary amine followed by HATU-promoted amide coupling to yield an sp(3)-rich natural product-like library. Copyright © 2015 Elsevier Ltd. All rights reserved.

Flexible polyelectrolyte chain in a strong electrolyte solution: Insight into equilibrium properties and force-extension behavior from mesoscale simulation

NASA Astrophysics Data System (ADS)

Malekzadeh Moghani, Mahdy; Khomami, Bamin

2016-01-01

Macromolecules with ionizable groups are ubiquitous in biological and synthetic systems. Due to the complex interaction between chain and electrostatic decorrelation lengths, both equilibrium properties and micro-mechanical response of dilute solutions of polyelectrolytes (PEs) are more complex than their neutral counterparts. In this work, the bead-rod micromechanical description of a chain is used to perform hi-fidelity Brownian dynamics simulation of dilute PE solutions to ascertain the self-similar equilibrium behavior of PE chains with various linear charge densities, scaling of the Kuhn step length (lE) with salt concentration cs and the force-extension behavior of the PE chain. In accord with earlier theoretical predictions, our results indicate that for a chain with n Kuhn segments, lE ˜ cs-0.5 as linear charge density approaches 1/n. Moreover, the constant force ensemble simulation results accurately predict the initial non-linear force-extension region of PE chain recently measured via single chain experiments. Finally, inspired by Cohen's extraction of Warner's force law from the inverse Langevin force law, a novel numerical scheme is developed to extract a new elastic force law for real chains from our discrete set of force-extension data similar to Padè expansion, which accurately depicts the initial non-linear region where the total Kuhn length is less than the thermal screening length.

Flexible polyelectrolyte chain in a strong electrolyte solution: Insight into equilibrium properties and force-extension behavior from mesoscale simulation.

PubMed

Malekzadeh Moghani, Mahdy; Khomami, Bamin

2016-01-14

Macromolecules with ionizable groups are ubiquitous in biological and synthetic systems. Due to the complex interaction between chain and electrostatic decorrelation lengths, both equilibrium properties and micro-mechanical response of dilute solutions of polyelectrolytes (PEs) are more complex than their neutral counterparts. In this work, the bead-rod micromechanical description of a chain is used to perform hi-fidelity Brownian dynamics simulation of dilute PE solutions to ascertain the self-similar equilibrium behavior of PE chains with various linear charge densities, scaling of the Kuhn step length (lE) with salt concentration cs and the force-extension behavior of the PE chain. In accord with earlier theoretical predictions, our results indicate that for a chain with n Kuhn segments, lE ∼ cs (-0.5) as linear charge density approaches 1/n. Moreover, the constant force ensemble simulation results accurately predict the initial non-linear force-extension region of PE chain recently measured via single chain experiments. Finally, inspired by Cohen's extraction of Warner's force law from the inverse Langevin force law, a novel numerical scheme is developed to extract a new elastic force law for real chains from our discrete set of force-extension data similar to Padè expansion, which accurately depicts the initial non-linear region where the total Kuhn length is less than the thermal screening length.

Nonstoichiometric control of tunnel-filling order, thermal expansion, and dielectric relaxation in tetragonal tungsten Bronzes Ba0.5-xTaO3-x.

PubMed

Pan, Fengjuan; Li, Xiaohui; Lu, Fengqi; Wang, Xiaoming; Cao, Jiang; Kuang, Xiaojun; Véron, Emmanuel; Porcher, Florence; Suchomel, Matthew R; Wang, Jing; Allix, Mathieu

2015-09-21

Ordering of interpolated Ba(2+) chains and alternate Ta-O rows (TaO)(3+) in the pentagonal tunnels of tetragonal tungsten bronzes (TTB) is controlled by the nonstoichiometry in the highly nonstoichiometric Ba0.5-xTaO3-x system. In Ba0.22TaO2.72, the filling of Ba(2+) and (TaO)(3+) groups is partially ordered along the ab-plane of the simple TTB structure, resulting in a √2-type TTB superstructure (Pbmm), while in Ba0.175TaO2.675, the pentagonal tunnel filling is completely ordered along the b-axis of the simple TTB structure, leading to a triple TTB superstructure (P21212). Both superstructures show completely empty square tunnels favoring Ba(2+) conduction and feature unusual accommodation of Ta(5+) cations in the small triangular tunnels. In contrast with stoichiometric Ba6GaTa9O30, which shows linear thermal expansion of the cell parameters and monotonic decrease of permittivity with temperature within 100-800 K, these TTB superstructures and slightly nonstoichiometric simple TTB Ba0.4TaO2.9 display abnormally broad and frequency-dependent extrinsic dielectric relaxations in 10(3)-10(5) Hz above room temperature, a linear deviation of the c-axis thermal expansion around 600 K, and high dielectric permittivity ∼60-95 at 1 MHz at room temperature.

DOS cones along atomic chains

NASA Astrophysics Data System (ADS)

Kwapiński, Tomasz

2017-03-01

The electron transport properties of a linear atomic chain are studied theoretically within the tight-binding Hamiltonian and the Green’s function method. Variations of the local density of states (DOS) along the chain are investigated. They are crucial in scanning tunnelling experiments and give important insight into the electron transport mechanism and charge distribution inside chains. It is found that depending on the chain parity the local DOS at the Fermi level can form cone-like structures (DOS cones) along the chain. The general condition for the local DOS oscillations is obtained and the linear behaviour of the local density function is confirmed analytically. DOS cones are characterized by a linear decay towards the chain which is in contrast to the propagation properties of charge density waves, end states and Friedel oscillations in one-dimensional systems. We find that DOS cones can appear due to non-resonant electron transport, the spin-orbit scattering or for chains fabricated on a substrate with localized electrons. It is also shown that for imperfect chains (e.g. with a reduced coupling strength between two neighboring sites) a diamond-like structure of the local DOS along the chain appears.

Novel linear piezoelectric motor for precision position stage

NASA Astrophysics Data System (ADS)

Chen, Chao; Shi, Yunlai; Zhang, Jun; Wang, Junshan

2016-03-01

Conventional servomotor and stepping motor face challenges in nanometer positioning stages due to the complex structure, motion transformation mechanism, and slow dynamic response, especially directly driven by linear motor. A new butterfly-shaped linear piezoelectric motor for linear motion is presented. A two-degree precision position stage driven by the proposed linear ultrasonic motor possesses a simple and compact configuration, which makes the system obtain shorter driving chain. Firstly, the working principle of the linear ultrasonic motor is analyzed. The oscillation orbits of two driving feet on the stator are produced successively by using the anti-symmetric and symmetric vibration modes of the piezoelectric composite structure, and the slider pressed on the driving feet can be propelled twice in only one vibration cycle. Then with the derivation of the dynamic equation of the piezoelectric actuator and transient response model, start-upstart-up and settling state characteristics of the proposed linear actuator is investigated theoretically and experimentally, and is applicable to evaluate step resolution of the precision platform driven by the actuator. Moreover the structure of the two-degree position stage system is described and a special precision displacement measurement system is built. Finally, the characteristics of the two-degree position stage are studied. In the closed-loop condition the positioning accuracy of plus or minus <0.5 μm is experimentally obtained for the stage propelled by the piezoelectric motor. A precision position stage based the proposed butterfly-shaped linear piezoelectric is theoretically and experimentally investigated.

Going the Extra Mile: Enabling Joint Logistics for the Tactical War Fighter

DTIC Science & Technology

2010-05-04

few of the links when relocating hubs. Chains v. Networks Supply Chain Too brittle , long CPL, low clustering, simple pattern, simple control...Mass Service Perspective Efficiency Highly Optimized Brittle , Rigid Supply Chains vs Networked Cross-Service Mutual Support Cross-Enterprise...Storage and Distribution Centei\\" Army Logistician 39, no. 6 (November-December 2007): 40. 68 Glen R Dowling, "Army and Marine Joint Ammunition

Sampling rare fluctuations of discrete-time Markov chains

NASA Astrophysics Data System (ADS)

Whitelam, Stephen

2018-03-01

We describe a simple method that can be used to sample the rare fluctuations of discrete-time Markov chains. We focus on the case of Markov chains with well-defined steady-state measures, and derive expressions for the large-deviation rate functions (and upper bounds on such functions) for dynamical quantities extensive in the length of the Markov chain. We illustrate the method using a series of simple examples, and use it to study the fluctuations of a lattice-based model of active matter that can undergo motility-induced phase separation.

Sampling rare fluctuations of discrete-time Markov chains.

PubMed

Whitelam, Stephen

2018-03-01

We describe a simple method that can be used to sample the rare fluctuations of discrete-time Markov chains. We focus on the case of Markov chains with well-defined steady-state measures, and derive expressions for the large-deviation rate functions (and upper bounds on such functions) for dynamical quantities extensive in the length of the Markov chain. We illustrate the method using a series of simple examples, and use it to study the fluctuations of a lattice-based model of active matter that can undergo motility-induced phase separation.

Comparison between culture and a multiplex quantitative real-time polymerase chain reaction assay detecting Ureaplasma urealyticum and U. parvum.

PubMed

Frølund, Maria; Björnelius, Eva; Lidbrink, Peter; Ahrens, Peter; Jensen, Jørgen Skov

2014-01-01

A novel multiplex quantitative real-time polymerase chain reaction (qPCR) for simultaneous detection of U. urealyticum and U. parvum was developed and compared with quantitative culture in Shepard's 10 C medium for ureaplasmas in urethral swabs from 129 men and 66 women, and cervical swabs from 61 women. Using culture as the gold standard, the sensitivity of the qPCR was 96% and 95% for female urethral and cervical swabs, respectively. In male urethral swabs the sensitivity was 89%. The corresponding specificities were 100%, 87% and 99%. The qPCR showed a linear increasing DNA copy number with increasing colour-changing units. Although slightly less sensitive than culture, this multiplex qPCR assay detecting U. urealyticum and U. parvum constitutes a simple and fast alternative to the traditional methods for identification of ureaplasmas and allows simultaneous species differentiation and quantitation in clinical samples. Furthermore, specimens overgrown by other bacteria using the culture method can be evaluated in the qPCR.

All-carbon sp-sp2 hybrid structures: Geometrical properties, current rectification, and current amplification

PubMed Central

Zhang, Zhenhua; Zhang, Junjun; Kwong, Gordon; Li, Ji; Fan, Zhiqiang; Deng, Xiaoqing; Tang, Guiping

2013-01-01

All-carbon sp-sp2 hybrid structures comprised of a zigzag-edged trigonal graphene (ZTG)and carbon chains are proposed and constructed as nanojunctions. It has been found that such simple hybrid structures possess very intriguing propertiesapp:addword:intriguing. The high-performance rectifying behaviors similar to macroscopic p-n junction diodes, such as a nearly linear positive-bias I-V curve (metallic behavior), a very small leakage current under negative bias (insulating behavior), a rather low threshold voltage, and a large bias region contributed to a rectification, can be predicted. And also, a transistor can be built by such a hybrid structure, which can show an extremely high current amplification. This is because a sp-hybrid carbon chain has a special electronic structure which can limit the electronic resonant tunneling of the ZTG to a unique and favorable situation. These results suggest that these hybrid structures might promise importantly potential applications for developing nano-scale integrated circuits. PMID:23999318

Phenotyping polyclonal kappa and lambda light chain molecular mass distributions in patient serum using mass spectrometry.

PubMed

Barnidge, David R; Dasari, Surendra; Ramirez-Alvarado, Marina; Fontan, Adrian; Willrich, Maria A V; Tschumper, Renee C; Jelinek, Diane F; Snyder, Melissa R; Dispenzieri, Angela; Katzmann, Jerry A; Murray, David L

2014-11-07

We previously described a microLC-ESI-Q-TOF MS method for identifying monoclonal immunoglobulins in serum and then tracking them over time using their accurate molecular mass. Here we demonstrate how the same methodology can be used to identify and characterize polyclonal immunoglobulins in serum. We establish that two molecular mass distributions observed by microLC-ESI-Q-TOF MS are from polyclonal kappa and lambda light chains using a combination of theoretical molecular masses from gene sequence data and the analysis of commercially available purified polyclonal IgG kappa and IgG lambda from normal human serum. A linear regression comparison of kappa/lambda ratios for 74 serum samples (25 hypergammaglobulinemia, 24 hypogammaglobulinemia, 25 normal) determined by microflowLC-ESI-Q-TOF MS and immunonephelometry had a slope of 1.37 and a correlation coefficient of 0.639. In addition to providing kappa/lambda ratios, the same microLC-ESI-Q-TOF MS analysis can determine the molecular mass for oligoclonal light chains observed above the polyclonal background in patient samples. In 2 patients with immune disorders and hypergammaglobulinemia, we observed a skewed polyclonal molecular mass distribution which translated into biased kappa/lambda ratios. Mass spectrometry provides a rapid and simple way to combine the polyclonal kappa/lambda light chain abundance ratios with the identification of dominant monoclonal as well as oligoclonal light chain immunoglobulins. We anticipate that this approach to evaluating immunoglobulin light chains will lead to improved understanding of immune deficiencies, autoimmune diseases, and antibody responses.

Interfacial free energy governs single polystyrene chain collapse in water and aqueous solutions.

PubMed

Li, Isaac T S; Walker, Gilbert C

2010-05-12

The hydrophobic interaction is significantly responsible for driving protein folding and self-assembly. To understand it, the thermodynamics, the role of water structure, the dewetting process surrounding hydrophobes, and related aspects have undergone extensive investigations. Here, we examine the hypothesis that polymer-solvent interfacial free energy is adequate to describe the energetics of the collapse of a hydrophobic homopolymer chain at fixed temperature, which serves as a much simplified model for studying the hydrophobic collapse of a protein. This implies that changes in polymer-solvent interfacial free energy should be directly proportional to the force to extend a collapsed polymer into a bad solvent. To test this hypothesis, we undertook single-molecule force spectroscopy on a collapsed, single, polystyrene chain in water-ethanol and water-salt mixtures where we measured the monomer solvation free energy from an ensemble average conformations. Different proportions within the binary mixture were used to create solvents with different interfacial free energies with polystyrene. In these mixed solvents, we observed a linear correlation between the interfacial free energy and the force required to extend the chain into solution, which is a direct measure of the solvation free energy per monomer on a single chain at room temperature. A simple analytical model compares favorably with the experimental results. This knowledge supports a common assumption that explicit water solvent may not be necessary for cases whose primary concerns are hydrophobic interactions and hydrophobic hydration.

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.

Rheology modification with ring polymers

NASA Astrophysics Data System (ADS)

Vlassopoulos, Dimitris

It is now established that experimental unconcatenated ring polymers can be purified effectively by means of fractionation at the critical condition. For molecular weights well above the entanglement threshold, purified rings relax stress via power-law (with an exponent of about -0.4), sharply departing from their linear counterparts. Experimental results are in harmony with modeling predictions and simulations. Here, we present results from recent interdisciplinary efforts and discuss two challenges: (i) the nonlinear shear rheology of purified ring melts is also very different from that of unlinked chains. Whereas the latter exhibit features that can be explained, to a first approach, in the framework in the tube model, the former behave akin to unentangled chains with finite extensibility and exhibit much small deformation at steady state. (ii) blends of rings and linear polymers exhibit unique features in different regimes: The addition of minute amounts of linear chains drastically affects ring dynamics. This relates to ring purity and the ability of unlinked linear chains to thread rings. With the help of simulations, it is possible to rationalize the observed surprisingly slow viscoelastic relaxation, which is attributed to ring-linear and ring-ring penetrations. On the other hand, adding small amounts of rings to linear polymers of different molecular weights influences their linear and nonlinear rheology in an unprecedented way. The blend viscosity exceeds that of the slower component (linear) in this non-interacting mixture, and its dependencies on composition and molecular weight ratio are examined, whereas the role of molecular architecture is also addressed. Consequently, closing the ends of a linear chain can serve as a powerful means for molecular manipulation of its rheology. This presentation reflects collaborative efforts with S. Costanzo, Z-C. Yan, R. Pasquino, M. Kaliva, S. Kamble, Y. Jeong, P. Lutz, J. Allgaier, T. Chang, D. Talikis, V. Mavrantzas and M. Rubinstein.

Shear and elongational rheology of photo-oxidative degraded HDPE and LLDPE

NASA Astrophysics Data System (ADS)

Wagner, Manfred Hermann; Zheng, Wang; Wang, Peng; Talamante, Sebastián Ramos; Narimissa, Esmaeil

2017-05-01

The effect of photo-oxidative degradation of high-density polyethylene (HDPE) and linear low-density polyethylene (LLDPE) was investigated by linear and non-linear rheological measurements. The linear-viscoelastic rheological measurements were performed at different temperatures, while the elongational viscosity was measured at 170°C and at different strain rates. The rheological data are indicative of structural changes caused by photo-oxidative degradation including formation of long-chain branches (LCB), cross-linking, and chain scission, and they revealed a cyclic and continuing competition between chain scission and LCB/gel formation. These findings are supported by additional FTIR measurements and direct measurements of the gel content of the degraded samples.

Advanced statistics: linear regression, part I: simple linear regression.

PubMed

Marill, Keith A

2004-01-01

Simple linear regression is a mathematical technique used to model the relationship between a single independent predictor variable and a single dependent outcome variable. In this, the first of a two-part series exploring concepts in linear regression analysis, the four fundamental assumptions and the mechanics of simple linear regression are reviewed. The most common technique used to derive the regression line, the method of least squares, is described. The reader will be acquainted with other important concepts in simple linear regression, including: variable transformations, dummy variables, relationship to inference testing, and leverage. Simplified clinical examples with small datasets and graphic models are used to illustrate the points. This will provide a foundation for the second article in this series: a discussion of multiple linear regression, in which there are multiple predictor variables.

Chain-Length-Dependent Exciton Dynamics in Linear Oligothiophenes Probed Using Ensemble and Single-Molecule Spectroscopy.

PubMed

Kim, Tae-Woo; Kim, Woojae; Park, Kyu Hyung; Kim, Pyosang; Cho, Jae-Won; Shimizu, Hideyuki; Iyoda, Masahiko; Kim, Dongho

2016-02-04

Exciton dynamics in π-conjugated molecular systems is highly susceptible to conformational disorder. Using time-resolved and single-molecule spectroscopic techniques, the effect of chain length on the exciton dynamics in a series of linear oligothiophenes, for which the conformational disorder increased with increasing chain length, was investigated. As a result, extraordinary features of the exciton dynamics in longer-chain oligothiophene were revealed. Ultrafast fluorescence depolarization processes were observed due to exciton self-trapping in longer and bent chains. Increase in exciton delocalization during dynamic planarization processes was also observed in the linear oligothiophenes via time-resolved fluorescence spectra but was restricted in L-10T because of its considerable conformational disorder. Exciton delocalization was also unexpectedly observed in a bent chain using single-molecule fluorescence spectroscopy. Such delocalization modulates the fluorescence spectral shape by attenuating the 0-0 peak intensity. Collectively, these results provide significant insights into the exciton dynamics in conjugated polymers.

Opening-assisted coherent transport in the semiclassical regime

NASA Astrophysics Data System (ADS)

Zhang, Yang; Celardo, G. Luca; Borgonovi, Fausto; Kaplan, Lev

2017-02-01

We study quantum enhancement of transport in open systems in the presence of disorder and dephasing. Quantum coherence effects may significantly enhance transport in open systems even in the semiclassical regime (where the decoherence rate is greater than the intersite hopping amplitude), as long as the disorder is sufficiently strong. When the strengths of disorder and dephasing are fixed, there is an optimal opening strength at which the coherent transport enhancement is optimized. Analytic results are obtained in two simple paradigmatic tight-binding models of large systems: the linear chain and the fully connected network. The physical behavior is also reflected in the Fenna-Matthews-Olson (FMO) photosynthetic complex, which may be viewed as intermediate between these paradigmatic models.

Charge-screening role of c -axis atomic displacements in YBa 2 Cu 3 O 6 + x and related superconductors

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

Božin, E. S.; Huq, A.; Shen, Bing

2016-02-01

The importance of charge reservoir layers for supplying holes to the CuO 2 planes of cuprate superconductors has long been recognized. Less attention has been paid to the screening of the charge transfer by the intervening ionic layers. We address this issue in the case of YBa 2 Cu 3 O 6 + x , where CuO chains supply the holes for the planes. We present a simple dielectric-screening model that gives a linear correlation between the relative displacements of ions along the c axis, determined by neutron powder diffraction, and the hole density of the planes. Applying this modelmore » to the temperature-dependent shifts of ions along the c axis, we infer a charge transfer of 5–10% of the hole density from the planes to the chains on warming from the superconducting transition to room temperature. Given the significant coupling of c -axis displacements to the average charge density, we point out the relevance of local displacements for screening charge modulations and note recent evidence for dynamic screening of in-plane quasiparticles. This line of argument leads us to a simple model for atomic displacements and charge modulation that is consistent with images from scanning-tunneling microscopy for underdoped Bi 2 Sr 2 CaCu 2 O 8 + δ .« less

Charge-screening role of c -axis atomic displacements in YBa 2 Cu 3 O 6 + x and related superconductors

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

Božin, E. S.; Huq, A.; Shen, Bing

2016-02-01

The importance of charge reservoir layers for supplying holes to the CuO2 planes of cuprate superconductors has long been recognized. Less attention has been paid to the screening of the charge transfer by the intervening ionic layers.We address this issue in the case of YBa2Cu3O6+x , where CuO chains supply the holes for the planes. We present a simple dielectric-screening model that gives a linear correlation between the relative displacements of ions along the c axis, determined by neutron powder diffraction, and the hole density of the planes. Applying this model to the temperature-dependent shifts of ions along the cmore » axis, we infer a charge transfer of 5–10% of the hole density from the planes to the chains on warming from the superconducting transition to room temperature. Given the significant coupling of c-axis displacements to the average charge density, we point out the relevance of local displacements for screening charge modulations and note recent evidence for dynamic screening of in-plane quasiparticles. This line of argument leads us to a simple model for atomic displacements and charge modulation that is consistent with images from scanning-tunneling microscopy for underdoped Bi2Sr2CaCu2O8+δ .« less

Charge-screening role of c-axis atomic displacements in YBa 2Cu 3O 6+x and related superconductors

DOE PAGES

E. S. Bozin; Huq, A.; Shen, Bing; ...

2016-02-29

The importance of charge reservoir layers for supplying holes to the CuO 2 planes of cuprate superconductors has long been recognized. Less attention has been paid to the screening of the charge transfer by the intervening ionic layers. We address this issue in the case of YBa 2Cu 3O 6+x, where CuO chains supply the holes for the planes. We present a simple dielectric-screening model that gives a linear correlation between the relative displacements of ions along the c axis, determined by neutron powder diffraction, and the hole density of the planes. Applying this model to the temperature-dependent shifts ofmore » ions along the c axis, we infer a charge transfer of 5-10% of the hole density from the planes to the chains on warming from the superconducting transition to room temperature. Given the significant coupling of c-axis displacements to the average charge density, we point out the relevance of local displacements for screening charge modulations and note recent evidence for dynamic screening of in-plane quasiparticles. Furthermore, this line of argument leads us to a simple model for atomic displacements and charge modulation that is consistent with images from scanning-tunneling microscopy for underdoped Bi 2Sr 2CaCu 2O 8+δ.« less

Exotic states of matter with polariton chains

NASA Astrophysics Data System (ADS)

Kalinin, Kirill P.; Lagoudakis, Pavlos G.; Berloff, Natalia G.

2018-04-01

We consider linear periodic chains of exciton-polariton condensates formed by pumping polaritons nonresonantly into a linear network. To the leading order such a sequence of condensates establishes relative phases as to minimize a classical one-dimensional X Y Hamiltonian with nearest and next-to-nearest neighbors. We show that the low-energy states of polaritonic linear chains demonstrate various classical regimes: ferromagnetic, antiferromagnetic, and frustrated spiral phases where quantum or thermal fluctuations are expected to give rise to a spin-liquid state. At the same time nonlinear interactions at higher pumping intensities bring about phase chaos and novel exotic phases.

Dispersive liquid-liquid microextraction applied to isolation and concentration of alkylphenols and their short-chained ethoxylates in water samples.

PubMed

Zgoła-Grześkowiak, Agnieszka

2010-03-12

Dispersive liquid-liquid microextraction (DLLME) coupled with high-performance liquid chromatography with fluorescence detector was applied for the determination of alkylphenols and their short-chained ethoxylates in water samples. Development of DLLME procedure included optimisation of some important parameters such as kind and volume of extracting and dispersing solvents. Under optimised conditions 50 microL of trichloroethylene in 1.5 mL of acetone were rapidly injected into 5 mL of a water sample. After centrifuging the organic phase containing the analytes was taken for evaporation with a gentle nitrogen purge and reconstituted to 50 microL of acetonitrile. The aliquot of this solution was analysed with the use of HPLC. For octylphenol (OP) and octylphenol ethoxylates (OPEOs) linearity was satisfactory in the range 8-1000 microg L(-1) and for nonylphenol (NP) and nonylphenol ethoxylates (NPEOs) linearity was in the range from 50 to about 3000 microg L(-1). Limit of quantitation was 0.1 microg L(-1) for OP and OPEOs and 0.3 microg L(-1) for NP and NPEOs. Satisfactory recoveries between 66 and 79% were obtained for environmental samples. The results showed that DLLME is a simple, rapid and sensitive analytical method for the preconcentration of trace amounts of alkylphenols and their ethoxylates in environmental water samples. Copyright (c) 2010 Elsevier B.V. All rights reserved.

The effect of polymer architecture on the interdiffusion in thin polymer films

NASA Astrophysics Data System (ADS)

Caglayan, Ayse; Yuan, Guangcui; Satija, Sushil K.; Uhrig, David; Hong, Kunlun; Akgun, Bulent

Branched polymer chains have been traditionally used in industrial applications as additives. Recently they have found applications in electrochromic displays, lithography, biomedical coatings and targeting multidrug resistant bacteria. In some of these applications where they are confined in thin layers, it is important to understand the relation between the mobility and polymer chain architecture to optimize the processing conditions. Earlier interdiffusion measurements on linear and cyclic polymer chains demonstrated the key role of chain architecture on mobility. We have determined the vertical diffusion coefficients of the star polystyrene chains in thin films as a function of number of polymer arms, molecular weight per arm, and film thickness using neutron reflectivity (NR) and compare our results with linear chains of identical total molecular weight. Bilayer samples of 4-arm and 8-arm protonated polystyrenes (hPS) and deuterated polystyrenes (dPS) were used to elucidate the effect of polymer chain architecture on polymer diffusion. NR measurements indicate that the mobility of polymer chains in thin films get faster as the number of polymer arms increases and the arm molecular weight decreases. Both star polymers showed faster interdiffusion compared to their linear analog. Diffusion coefficient of branched PS chains has a weak dependence on the film thickness.

Does linear separability really matter? Complex visual search is explained by simple search

PubMed Central

Vighneshvel, T.; Arun, S. P.

2013-01-01

Visual search in real life involves complex displays with a target among multiple types of distracters, but in the laboratory, it is often tested using simple displays with identical distracters. Can complex search be understood in terms of simple searches? This link may not be straightforward if complex search has emergent properties. One such property is linear separability, whereby search is hard when a target cannot be separated from its distracters using a single linear boundary. However, evidence in favor of linear separability is based on testing stimulus configurations in an external parametric space that need not be related to their true perceptual representation. We therefore set out to assess whether linear separability influences complex search at all. Our null hypothesis was that complex search performance depends only on classical factors such as target-distracter similarity and distracter homogeneity, which we measured using simple searches. Across three experiments involving a variety of artificial and natural objects, differences between linearly separable and nonseparable searches were explained using target-distracter similarity and distracter heterogeneity. Further, simple searches accurately predicted complex search regardless of linear separability (r = 0.91). Our results show that complex search is explained by simple search, refuting the widely held belief that linear separability influences visual search. PMID:24029822

Determination of the linear coefficient of thermal expansion in polymer films at the nanoscale: influence of the composition of EVA copolymers and the molecular weight of PMMA.

PubMed

González-Benito, J; Castillo, E; Cruz-Caldito, J F

2015-07-28

Nanothermal-expansion of poly(ethylene-co-vinylacetate), EVA, and poly(methyl methacrylate), PMMA, in the form of films was measured to finally obtain linear coefficients of thermal expansion, CTEs. The simple deflection of a cantilever in an atomic force microscope, AFM, was used to monitor thermal expansions at the nanoscale. The influences of: (a) the structure of EVA in terms of its composition (vinylacetate content) and (b) the size of PMMA chains in terms of the molecular weight were studied. To carry out this, several polymer samples were used, EVA copolymers with different weight percents of the vinylacetate comonomer (12, 18, 25 and 40%) and PMMA polymers with different weight average molecular weights (33.9, 64.8, 75.600 and 360.0 kg mol(-1)). The dependencies of the vinyl acetate weight fraction of EVA and the molecular weight of PMMA on their corresponding CTEs were analyzed to finally explain them using new, intuitive and very simple models based on the rule of mixtures. In the case of EVA copolymers a simple equation considering the weighted contributions of each comonomer was enough to estimate the final CTE above the glass transition temperature. On the other hand, when the molecular weight dependence is considered the free volume concept was used as novelty. The expansion of PMMA, at least at the nanoscale, was well and easily described by the sum of the weighted contributions of the occupied and free volumes, respectively.

Exploring the role of internal friction in the dynamics of unfolded proteins using simple polymer models.

PubMed

Cheng, Ryan R; Hawk, Alexander T; Makarov, Dmitrii E

2013-02-21

Recent experiments showed that the reconfiguration dynamics of unfolded proteins are often adequately described by simple polymer models. In particular, the Rouse model with internal friction (RIF) captures internal friction effects as observed in single-molecule fluorescence correlation spectroscopy (FCS) studies of a number of proteins. Here we use RIF, and its non-free draining analog, Zimm model with internal friction, to explore the effect of internal friction on the rate with which intramolecular contacts can be formed within the unfolded chain. Unlike the reconfiguration times inferred from FCS experiments, which depend linearly on the solvent viscosity, the first passage times to form intramolecular contacts are shown to display a more complex viscosity dependence. We further describe scaling relationships obeyed by contact formation times in the limits of high and low internal friction. Our findings provide experimentally testable predictions that can serve as a framework for the analysis of future studies of contact formation in proteins.

Inhibition of telomerase by linear-chain fatty acids: a structural analysis.

PubMed Central

Oda, Masako; Ueno, Takamasa; Kasai, Nobuyuki; Takahashi, Hirotada; Yoshida, Hiromi; Sugawara, Fumio; Sakaguchi, Kengo; Hayashi, Hideya; Mizushina, Yoshiyuki

2002-01-01

In the present study, we have found that mono-unsaturated linear-chain fatty acids in the cis configuration with C(18) hydrocarbon chains (i.e. oleic acid) strongly inhibited the activity of human telomerase in a cell-free enzymic assay, with an IC(50) value of 8.6 microM. Interestingly, fatty acids with hydrocarbon chain lengths below 16 or above 20 carbons substantially decreased the potency of inhibition of telomerase. Moreover, the cis-mono-unsaturated C(18) linear-chain fatty acid oleic acid was the strongest inhibitor of all the fatty acids tested. A kinetic study revealed that oleic acid competitively inhibited the activity of telomerase ( K (i)=3.06 microM) with respect to the telomerase substrate primer. The energy-minimized three-dimensional structure of the linear-chain fatty acid was calculated and modelled. A molecule width of 11.53-14.26 A (where 1 A=0.1 nm) in the C(16) to C(20) fatty acid structure was suggested to be important for telomerase inhibition. The three-dimensional structure of the telomerase active site (i.e. the substrate primer-binding site) appears to have a pocket that could bind oleic acid, with the pocket being 8.50 A long and 12.80 A wide. PMID:12121150

Intrinsic viscosity and the electrical polarizability of arbitrarily shaped objects

NASA Astrophysics Data System (ADS)

Mansfield, Marc L.; Douglas, Jack F.; Garboczi, Edward J.

2001-12-01

The problem of calculating the electric polarizability tensor αe of objects of arbitrary shape has been reformulated in terms of path integration and implemented computationally. The method simultaneously yields the electrostatic capacity C and the equilibrium charge density. These functionals of particle shape are important in many materials science applications, including the conductivity and viscosity of filled materials and suspensions. The method has been validated through comparison with exact results (for the sphere, the circular disk, touching spheres, and tori), it has been found that 106 trajectories yield an accuracy of about four and three significant figures for C and αe, respectively. The method is fast: For simple objects, 106 trajectories require about 1 min on a PC. It is also versatile: Switching from one object to another is easy. Predictions have also been made for regular polygons, polyhedra, and right circular cylinders, since these shapes are important in applications and since numerical calculations of high stated accuracy are available. Finally, the path-integration method has been applied to estimate transport properties of both linear flexible polymers (random walk chains of spheres) and lattice model dendrimer molecules. This requires probing of an ensemble of objects. For linear chains, the distribution function of C and of the trace (αe), are found to be universal in a size coordinate reduced by the chain radius of gyration. For dendrimers, these distribution functions become increasingly sharp with generation number. It has been found that C and αe provide important information about the distribution of molecular size and shape and that they are important for estimating the Stokes friction and intrinsic viscosity of macromolecules.

Linear viscoelasticity and thermorheological simplicity of n-hexadecane fluids under oscillatory shear via non-equilibrium molecular dynamics simulations.

PubMed

Tseng, Huan-Chang; Wu, Jiann-Shing; Chang, Rong-Yeu

2010-04-28

A small amplitude oscillatory shear flows with the classic characteristic of a phase shift when using non-equilibrium molecular dynamics simulations for n-hexadecane fluids. In a suitable range of strain amplitude, the fluid possesses significant linear viscoelastic behavior. Non-linear viscoelastic behavior of strain thinning, which means the dynamic modulus monotonously decreased with increasing strain amplitudes, was found at extreme strain amplitudes. Under isobaric conditions, different temperatures strongly affected the range of linear viscoelasticity and the slope of strain thinning. The fluid's phase states, containing solid-, liquid-, and gel-like states, can be distinguished through a criterion of the viscoelastic spectrum. As a result, a particular condition for the viscoelastic behavior of n-hexadecane molecules approaching that of the Rouse chain was obtained. Besides, more importantly, evidence of thermorheologically simple materials was presented in which the relaxation modulus obeys the time-temperature superposition principle. Therefore, using shift factors from the time-temperature superposition principle, the estimated Arrhenius flow activation energy was in good agreement with related experimental values. Furthermore, one relaxation modulus master curve well exhibited both transition and terminal zones. Especially regarding non-equilibrium thermodynamic states, variations in the density, with respect to frequencies, were revealed.

Nanoprobe diffusion in entangled polymer solutions: Linear vs. unconcatenated ring chains

NASA Astrophysics Data System (ADS)

Nahali, Negar; Rosa, Angelo

2018-05-01

We employ large-scale molecular dynamics computer simulations to study the problem of nanoprobe diffusion in entangled solutions of linear polymers and unknotted and unconcatenated circular (ring) polymers. By tuning both the diameter of the nanoprobe and the density of the solution, we show that nanoprobes of diameter smaller than the entanglement distance (tube diameter) of the solution display the same (Rouse-like) behavior in solutions of both polymer architectures. Instead, nanoprobes with larger diameters appear to diffuse markedly faster in solutions of rings than in solutions of linear chains. Finally, by analysing the distribution functions of spatial displacements, we find that nanoprobe motion in rings' solutions shows both Gaussian and ergodic behaviors, in all regimes considered, while, in solutions of linear chains, nanoprobes exceeding the size of the tube diameter show a transition to non-Gaussian and non-ergodic motion. Our results emphasize the role of chain architecture in the motion of nanoprobes dispersed in polymer solutions.

Optimal Linear Responses for Markov Chains and Stochastically Perturbed Dynamical Systems

NASA Astrophysics Data System (ADS)

Antown, Fadi; Dragičević, Davor; Froyland, Gary

2018-03-01

The linear response of a dynamical system refers to changes to properties of the system when small external perturbations are applied. We consider the little-studied question of selecting an optimal perturbation so as to (i) maximise the linear response of the equilibrium distribution of the system, (ii) maximise the linear response of the expectation of a specified observable, and (iii) maximise the linear response of the rate of convergence of the system to the equilibrium distribution. We also consider the inhomogeneous, sequential, or time-dependent situation where the governing dynamics is not stationary and one wishes to select a sequence of small perturbations so as to maximise the overall linear response at some terminal time. We develop the theory for finite-state Markov chains, provide explicit solutions for some illustrative examples, and numerically apply our theory to stochastically perturbed dynamical systems, where the Markov chain is replaced by a matrix representation of an approximate annealed transfer operator for the random dynamical system.

Excess entropy scaling for the segmental and global dynamics of polyethylene melts.

PubMed

Voyiatzis, Evangelos; Müller-Plathe, Florian; Böhm, Michael C

2014-11-28

The range of validity of the Rosenfeld and Dzugutov excess entropy scaling laws is analyzed for unentangled linear polyethylene chains. We consider two segmental dynamical quantities, i.e. the bond and the torsional relaxation times, and two global ones, i.e. the chain diffusion coefficient and the viscosity. The excess entropy is approximated by either a series expansion of the entropy in terms of the pair correlation function or by an equation of state for polymers developed in the context of the self associating fluid theory. For the whole range of temperatures and chain lengths considered, the two estimates of the excess entropy are linearly correlated. The scaled bond and torsional relaxation times fall into a master curve irrespective of the chain length and the employed scaling scheme. Both quantities depend non-linearly on the excess entropy. For a fixed chain length, the reduced diffusion coefficient and viscosity scale linearly with the excess entropy. An empirical reduction to a chain length-independent master curve is accessible for both dynamic quantities. The Dzugutov scheme predicts an increased value of the scaled diffusion coefficient with increasing chain length which contrasts physical expectations. The origin of this trend can be traced back to the density dependence of the scaling factors. This finding has not been observed previously for Lennard-Jones chain systems (Macromolecules, 2013, 46, 8710-8723). Thus, it limits the applicability of the Dzugutov approach to polymers. In connection with diffusion coefficients and viscosities, the Rosenfeld scaling law appears to be of higher quality than the Dzugutov approach. An empirical excess entropy scaling is also proposed which leads to a chain length-independent correlation. It is expected to be valid for polymers in the Rouse regime.

Continuously Variable Transmission

NASA Technical Reports Server (NTRS)

Grana, D. C.

1985-01-01

Chain slides along two cones, in novel transmission concept. Transmission includes chain drive between two splined shafts. Chain sprockets follow surfaces of two cones. As one chain sprocket moves toward smaller diameter other chain sprocket moves toward larger diameter, thereby changing "gear" ratio. Movement initiated by tension applied to chain by planetary gear mechanism. Device positive, simple, and efficient over wide range of speed ratios.

Detections of Long Carbon Chains CH_{3}CCCCH, C_{6}H, LINEAR-C_{6}H_{2} and C_{7}H in the Low-Mass Star Forming Region L1527

NASA Astrophysics Data System (ADS)

Araki, Mitsunori; Takano, Shuro; Sakai, Nami; Yamamoto, Satoshi; Oyama, Takahiro; Kuze, Nobuhiko; Tsukiyama, Koichi

2017-06-01

Carbon chains in the warm carbon chain chemistry (WCCC) region has been searched in the 42-44 GHz region by using Green Bank 100 m telescope. Long carbon chains C_{7}H, C_{6}H, CH_{3}CCCCH, and linear-C_{6}H_{2} and cyclic species C_{3}H and C_{3}H_{2}O have been detected in the low-mass star forming region L1527, performing the WCCC. C_{7}H was detected for the first time in molecular clouds. The column density of C_{7}H is derived to be 6.2 × 10^{10} cm^{-2} by using the detected J = 24.5-23.5 and 25.5-24.5 rotational lines. The ^{2}Π_{1/2} electronic state of C_{6}H, locating 21.6 K above the ^{2}Π_{3/2} electronic ground state, and the K_a = 0 line of the para species of linear-C_{6}H_{2} were also detected firstly in molecular clouds. The column densities of the ^{2}Π_{1/2} and ^{2}Π_{3/2} states of C_{6}H in L1527 were derived to be 1.6 × 10^{11} and 1.1 × 10^{12} cm^{-2}, respectively. The total column density of linear-C_{6}H_{2} is obtained to be 1.86 × 10^{11} cm^{-2}. While the abundance ratios of carbon chains in between L1527 and the starless dark cloud Taurus Molecular Cloud-1 Cyanopolyyne Peak (TMC-1 CP) have a trend of decrease by extension of carbon-chain length, column densities of CH_{3}CCCCH and C_{6}H are on the trend. However, the column densities of linear-C_{6}H_{2}, and C_{7}H are as abundant as those of TMC-1 CP in spite of long carbon chain, i.e., they are not on the trend. The abundances of linear-C_{6}H_{2} and C_{7}H show that L1527 is rich for long carbon chains as well as TMC-1 CP.

Influence of chain topology on polymer crystallization: poly(ethylene oxide) (PEO) rings vs. linear chains.

PubMed

Zardalidis, George; Mars, Julian; Allgaier, Jürgen; Mezger, Markus; Richter, Dieter; Floudas, George

2016-10-04

The absence of entanglements, the more compact structure and the faster diffusion in melts of cyclic poly(ethylene oxide) (PEO) chains have consequences on their crystallization behavior at the lamellar and spherulitic length scales. Rings with molecular weight below the entanglement molecular weight (M < M e ), attain the equilibrium configuration composed from twice-folded chains with a lamellar periodicity that is half of the corresponding linear chains. Rings with M > M e undergo distinct step-like conformational changes to a crystalline lamellar with the equilibrium configuration. Rings melt from this configuration in the absence of crystal thickening in sharp contrast to linear chains. In general, rings more easily attain their extended equilibrium configuration due to strained segments and the absence of entanglements. In addition, rings have a higher equilibrium melting temperature. At the level of the spherulitic superstructure, growth rates are much faster for rings reflecting the faster diffusion and more compact structure. With respect to the segmental dynamics in their semi-crystalline state, ring PEOs with a steepness index of ∼34 form some of the "strongest" glasses.

A generalized electro-elastic theory of polymer networks

NASA Astrophysics Data System (ADS)

Cohen, Noy

2018-01-01

A rigorous multi-scale analysis of the electromechanical coupling in dielectric polymers is conducted. The body couples stemming from a misalignment between the electric field and the electric-dipole density vector are studied and the conservation laws for polymer networks are derived. Using variational principles, expressions for the polarization and the stress are determined. Interestingly, it is found that the stress tensor resulting from coupled loadings in which the electric field is misaligned with the principal stretch directions is not symmetric and the asymmetry arises from the body couples. Next, the electro-mechanical response of a chain is analyzed. The deformations of the individual polymer chains are related to the macroscopic deformation via two highly non-linear constraints - the first pertaining to the compatibility of the local deformations with the imposed macroscopic one and the second stems from the symmetric part of the stress at equilibrium. In accord with the proposed framework, an amended three-chains model is introduced. The predictions of this model are found to be in excellent agreement with experimental findings. Lastly, the behavior of a polymer subjected to a simple shear and an electric field is studied. The offset between the electric field and the principal directions gives rise to body couples, a polarization that is not aligned with the electric field, and an asymmetric stress tensor.

Easy preparation of a large-size random gene mutagenesis library in Escherichia coli.

PubMed

You, Chun; Percival Zhang, Y-H

2012-09-01

A simple and fast protocol for the preparation of a large-size mutant library for directed evolution in Escherichia coli was developed based on the DNA multimers generated by prolonged overlap extension polymerase chain reaction (POE-PCR). This protocol comprised the following: (i) a linear DNA mutant library was generated by error-prone PCR or shuffling, and a linear vector backbone was prepared by regular PCR; (ii) the DNA multimers were generated based on these two DNA templates by POE-PCR; and (iii) the one restriction enzyme-digested DNA multimers were ligated to circular plasmids, followed by transformation to E. coli. Because the ligation efficiency of one DNA fragment was several orders of magnitude higher than that of two DNA fragments for typical mutant library construction, it was very easy to generate a mutant library with a size of more than 10(7) protein mutants per 50 μl of the POE-PCR product. Via this method, four new fluorescent protein mutants were obtained based on monomeric cherry fluorescent protein. This new protocol was simple and fast because it did not require labor-intensive optimizations in restriction enzyme digestion and ligation, did not involve special plasmid design, and enabled constructing a large-size mutant library for directed enzyme evolution within 1 day. Copyright © 2012 Elsevier Inc. All rights reserved.

Linear-to-λ-Shape P-O-P Bond Transmutation in Polyphosphates with Infinite (PO3)∞ Chain.

PubMed

Wang, Ying; Li, Lin; Han, Shujuan; Lei, Bing-Hua; Abudoureheman, Maierhaba; Yang, Zhihua; Pan, Shilie

2017-09-05

A new metal polyphosphate, α-CsBa 2 (PO 3 ) 5 , exhibiting the first example of a linear P-O-P bond angle in a one-dimensional (PO 3 ) ∞ chain has been reported. Interestingly, α → β phase transition occurs in CsBa 2 (PO 3 ) 5 along with the P-O-P bonds varying from linear to λ-shape, suggesting that α-CsBa 2 (PO 3 ) 5 with unfavorable linear P-O-P bonds is more stable at ambient temperature.

Non-Linear Dynamics of Saturn's Rings

NASA Astrophysics Data System (ADS)

Esposito, L. W.

2016-12-01

Non-linear processes can explain why Saturn's rings are so active and dynamic. Ring systems differ from simple linear systems in two significant ways: 1. They are systems of granular material: where particle-to-particle collisions dominate; thus a kinetic, not a fluid description needed. Stresses are strikingly inhomogeneous and fluctuations are large compared to equilibrium. 2. They are strongly forced by resonances: which drive a non-linear response, that push the system across thresholds that lead to persistent states. Some of this non-linearity is captured in a simple Predator-Prey Model: Periodic forcing from the moon causes streamline crowding; This damps the relative velocity. About a quarter phase later, the aggregates stir the system to higher relative velocity and the limit cycle repeats each orbit, with relative velocity ranging from nearly zero to a multiple of the orbit average. Summary of Halo Results: A predator-prey model for ring dynamics produces transient structures like `straw' that can explain the halo morphology and spectroscopy: Cyclic velocity changes cause perturbed regions to reach higher collision speeds at some orbital phases, which preferentially removes small regolith particles; surrounding particles diffuse back too slowly to erase the effect: this gives the halo morphology; this requires energetic collisions (v ≈ 10m/sec, with throw distances about 200km, implying objects of scale R ≈ 20km).Transform to Duffing Eqn : With the coordinate transformation, z = M2/3, the Predator-Prey equations can be combined to form a single second-order differential equation with harmonic resonance forcing.Ring dynamics and history implications: Moon-triggered clumping explains both small and large particles at resonances. We calculate the stationary size distribution using a cell-to-cell mapping procedure that converts the phase-plane trajectories to a Markov chain. Approximating it as an asymmetric random walk with reflecting boundaries determines the power law index, using results of numerical simulations in the tidal environment. Aggregates can explain many dynamic aspects of the rings and can renew rings by shielding and recycling the material within them, depending on how long the mass is sequestered. We can ask: Are Saturn's rings a chaotic non-linear driven system?

Simplicial Descent Categories

NASA Astrophysics Data System (ADS)

Rodriguez Gonzalez, Beatriz

2008-04-01

Much of the homotopical and homological structure of the categories of chain complexes and topological spaces can be deduced from the existence and properties of the 'simple' functors Tot : {double chain complexes} -> {chain complexes} and geometric realization : {sSets} -> {Top}, or similarly, Tot : {simplicial chain complexes} -> {chain complexes} and | | : {sTop} -> {Top}. The purpose of this thesis is to abstract this situation, and to this end we introduce the notion of '(co)simplicial descent category'. It is inspired by Guillen-Navarros's '(cubical) descent categories'. The key ingredients in a (co)simplicial descent category D are a class E of morphisms in D, called equivalences, and a 'simple' functor s : {(co)simplicial objects in D} -> D. They must satisfy axioms like 'Eilenberg-Zilber', 'exactness' and 'acyclicity'. This notion covers a wide class of examples, as chain complexes, sSets, topological spaces, filtered cochain complexes (where E = filtered quasi-isomorphisms or E = E_2-isomorphisms), commutative differential graded algebras (with s = Navarro's Thom-Whitney simple), DG-modules over a DG-category and mixed Hodge complexes, where s = Deligne's simple. From the simplicial descent structure we obtain homotopical structure on D, as cone and cylinder objects. We use them to i) explicitly describe the morphisms of HoD=D[E^{-1}] similarly to the case of calculus of fractions; ii) endow HoD with a non-additive pre-triangulated structure, that becomes triangulated in the stable additive case. These results use the properties of a 'total functor', which associates to any biaugmented bisimplicial object a simplicial object. It is the simplicial analogue of the total chain complex of a double complex, and it is left adjoint to Illusie's 'decalage' functor.

Effect of short-chain branching on interfacial polymer structure and dynamics under shear flow.

PubMed

Jeong, Sohdam; Kim, Jun Mo; Cho, Soowon; Baig, Chunggi

2017-11-22

We present a detailed analysis on the effect of short-chain branches on the structure and dynamics of interfacial chains using atomistic nonequilibrium molecular dynamics simulations of confined polyethylene melts in a wide range of shear rates. The intrinsically fast random motions of the short branches constantly disturb the overall chain conformation, leading to a more compact and less deformed chain structure of the short-chain branched (SCB) polymer against the imposed flow field in comparison with the corresponding linear polymer. Moreover, such highly mobile short branches along the backbone of the SCB polymer lead to relatively weaker out-of-plane wagging dynamics of interfacial chains, with highly curvy backbone structures in the intermediate flow regime. In conjunction with the contribution of short branches (as opposed to that of the backbone) to the total interfacial friction between the chains and the wall, the SCB polymer shows a nearly constant behavior in the degree of slip (d s ) with respect to shear rate in the weak-to-intermediate flow regimes. On the contrary, in the strong flow regime where irregular chain rotation and tumbling dynamics occur via intensive dynamical collisions between interfacial chains and the wall, an enhancement effect on the chain detachment from the wall, caused by short branches, leads to a steeper increase in d s for the SCB polymer than for the linear polymer. Remarkably, the SCB chains at the interface exhibit two distinct types of rolling mechanisms along the backbone, with a half-dumbbell mesoscopic structure at strong flow fields, in addition to the typical hairpin-like tumbling behavior displayed by the linear chains.

FAST TRACK COMMUNICATION: Exact and simple results for the XYZ and strongly interacting fermion chains

NASA Astrophysics Data System (ADS)

Fendley, Paul; Hagendorf, Christian

2010-10-01

We conjecture exact and simple formulas for some physical quantities in two quantum chains. A classic result of this type is Onsager, Kaufman and Yang's formula for the spontaneous magnetization in the Ising model, subsequently generalized to the chiral Potts models. We conjecture that analogous results occur in the XYZ chain when the couplings obey JxJy + JyJz + JxJz = 0, and in a related fermion chain with strong interactions and supersymmetry. We find exact formulas for the magnetization and gap in the former, and the staggered density in the latter, by exploiting the fact that certain quantities are independent of finite-size effects.

Guggenheim's rule and the enthalpy of vaporization of simple and polar fluids, molten salts, and room temperature ionic liquids.

PubMed

Weiss, Volker C

2010-07-22

One of Guggenheim's many corresponding-states rules for simple fluids implies that the molar enthalpy of vaporization (determined at the temperature at which the pressure reaches 1/50th of its critical value, which approximately coincides with the normal boiling point) divided by the critical temperature has a value of roughly 5.2R, where R is the universal gas constant. For more complex fluids, such as strongly polar and ionic fluids, one must expect deviations from Guggenheim's rule. Such a deviation has far-reaching consequences for other empirical rules related to the vaporization of fluids, namely Guldberg's rule and Trouton's rule. We evaluate these characteristic quantities for simple fluids, polar fluids, hydrogen-bonding fluids, simple inorganic molten salts, and room temperature ionic liquids (RTILs). For the ionic fluids, the critical parameters are not accessible to direct experimental observation; therefore, suitable extrapolation schemes have to be applied. For the RTILs [1-n-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imides, where the alkyl chain is ethyl, butyl, hexyl, or octyl], the critical temperature is estimated by extrapolating the surface tension to zero using Guggenheim's and Eotvos' rules; the critical density is obtained using the linear-diameter rule. It is shown that the RTILs adhere to Guggenheim's master curve for the reduced surface tension of simple and moderately polar fluids, but that they deviate significantly from his rule for the reduced enthalpy of vaporization of simple fluids. Consequences for evaluating the Trouton constant of RTILs, the value of which has been discussed controversially in the literature, are indicated.

Application of the compensated arrhenius formalism to dielectric relaxation.

PubMed

Petrowsky, Matt; Frech, Roger

2009-12-17

The temperature dependence of the dielectric rate constant, defined as the reciprocal of the dielectric relaxation time, is examined for several groups of organic solvents. Early studies of linear alcohols using a simple Arrhenius equation found that the activation energy was dependent on the chain length of the alcohol. This paper re-examines the earlier data using a compensated Arrhenius formalism that assumes the presence of a temperature-dependent static dielectric constant in the exponential prefactor. Scaling temperature-dependent rate constants to isothermal rate constants so that the dielectric constant dependence is removed results in calculated energies of activation E(a) in which there is a small increase with chain length. These energies of activation are very similar to those calculated from ionic conductivity data using compensated Arrhenius formalism. This treatment is then extended to dielectic relaxation data for n-alkyl bromides, n-nitriles, and n-acetates. The exponential prefactor is determined by dividing the temperature-dependent rate constants by the Boltzmann term exp(-E(a)/RT). Plotting the prefactors versus the static dielectric constant places the data on a single master curve for each group of solvents.

Supplementing Menu Labeling With Calorie Recommendations to Test for Facilitation Effects

PubMed Central

Wisdom, Jessica; Wansink, Brian; Loewenstein, George

2013-01-01

Objectives. We examined the effect on food purchases of adding recommended calorie intake per day or per meal to the mandated calorie information posted on chain restaurant menus. Methods. Before and after New York City implemented calorie posting on chain restaurant menus in 2008, we provided daily, per-meal, or no calorie recommendations to randomized subsets of adult lunchtime customers (n = 1121) entering 2 McDonald’s restaurants, in Manhattan and Brooklyn, and collected receipts and survey responses as they exited. In linear and logistic regressions, with adjustment for gender, race, age, and day, we tested for simple differences in calories consumed and interactions between variables. Results. Posting calorie benchmarks had no direct impact, nor did it moderate the impact of calorie labels on food purchases. The recommendation appeared to promote a slight increase in calorie intake, attributable to increased purchases of higher-calorie entrées. Conclusions. These results do not support the introduction of calorie recommendations as a means of enhancing the impact of posted calorie information or reducing the contribution of restaurant dining to the obesity epidemic. PMID:23865657

Precise fabrication of a 5 nm graphene nanopore with a helium ion microscope for biomolecule detection

NASA Astrophysics Data System (ADS)

Deng, Yunsheng; Huang, Qimeng; Zhao, Yue; Zhou, Daming; Ying, Cuifeng; Wang, Deqiang

2017-01-01

We report a scalable method to fabricate high-quality graphene nanopores for biomolecule detection using a helium ion microscope (HIM). HIM milling shows promising capabilities for precisely controlling the size and shape, and may allow for the potential production of nanopores at wafer scale. Nanopores could be fabricated at different sizes ranging from 5 to 30 nm in diameter in few minutes. Compared with the current solid-state nanopore fabrication techniques, e.g. transmission electron microscopy, HIM is fast. Furthermore, we investigated the exposure-time dependence of graphene nanopore formation: the rate of pore expansion did not follow a simple linear relationship with exposure time, but a fast expansion rate at short exposure time and a slow rate at long exposure time. In addition, we performed biomolecule detection with our patterned graphene nanopore. The ionic current signals induced by 20-base single-stranded DNA homopolymers could be used as a basis for homopolymer differentiation. However, the charge interaction of homopolymer chains with graphene nanopores, and the conformations of homopolymer chains need to be further considered to improve the accuracy of discrimination.

A microanalytical method for ammonium and short-chain primary aliphatic amines using precolumn derivatization and capillary liquid chromatography.

PubMed

Moliner-Martínez, Y; Herráez-Hernández, R; Campíns-Falcó, P

2007-09-14

A new microscale method is presented for the determination of ammonium and primary short-chain aliphatic amines (methylamine, ethylamine, propylamine, n-butylamine and n-pentylamine) in water. The assay uses precolumn derivatization with the reagent o-phthaldialdehyde (OPA) in combination with the thiol N-acetyl-L-cysteine (NAC), and capillary liquid chromatography with UV detection at 330 nm. The described method is very simple and rapid as no preconcentration of the analytes is necessary, and the volume of sample required is only 0.1 mL. Under the proposed conditions good linearity has been obtained up to a concentration of the analytes of 10.0 mgL(-1), the limits of detection being of 8-50 microgL(-1). No matrix effect was found, and recoveries between 97 and 110% were obtained. The precision of the method was good, and the achieved variation coefficients were below 12%. The reliability of the proposed approach has been tested by analyzing a microsample of fogwater collected from leaf surfaces.

Concentrated Solutions of Single-Chain Nanoparticles: A Simple Model for Intrinsically Disordered Proteins under Crowding Conditions.

PubMed

Moreno, Angel J; Lo Verso, Federica; Arbe, Arantxa; Pomposo, José A; Colmenero, Juan

2016-03-03

By means of large-scale computer simulations and small-angle neutron scattering (SANS), we investigate solutions of single-chain nanoparticles (SCNPs), covering the whole concentration range from infinite dilution to melt density. The analysis of the conformational properties of the SCNPs reveals that these synthetic nano-objects share basic ingredients with intrinsically disordered proteins (IDPs), as topological polydispersity, generally sparse conformations, and locally compact domains. We investigate the role of the architecture of the SCNPs in their collapse behavior under macromolecular crowding. Unlike in the case of linear macromolecules, which experience the usual transition from self-avoiding to Gaussian random-walk conformations, crowding leads to collapsed conformations of SCNPs resembling those of crumpled globules. This behavior is already found at volume fractions (about 30%) that are characteristic of crowding in cellular environments. The simulation results are confirmed by the SANS experiments. Our results for SCNPs--a model system free of specific interactions--propose a general scenario for the effect of steric crowding on IDPs: collapse from sparse conformations at high dilution to crumpled globular conformations in cell environments.

Sensitive SERS detection of lead ions via DNAzyme based quadratic signal amplification.

PubMed

Tian, Aihua; Liu, Yu; Gao, Jian

2017-08-15

Highly sensitive detection of Pb 2+ is very necessary for water quality control, clinical toxicology, and industrial monitoring. In this work, a simple and novel DNAzyme-based SERS quadratic amplification method is developed for the detection of Pb 2+ . This strategy possesses some remarkable features compared to the conventional DNAzyme-based SERS methods, which are as follows: (i) Coupled DNAzyme-activated hybridization chain reaction (HCR) with bio barcodes; a quadratic amplification method is designed using the unique catalytic selectivity of DNAzyme. The SERS signal is significantly amplified. This method is rapid with a detection time of 2h. (ii) The problem of high background induced by excess bio barcodes is circumvented by using magnetic beads (MBs) as the carrier of signal-output products, and this sensing system is simple in design and can easily be carried out by simple mixing and incubation. Given the unique and attractive characteristics, a simple and universal strategy is designed to accomplish sensitive detection of Pb 2+ . The detection limit of Pb 2+ via SERS detection is 70 fM, with the linear range from 1.0×10 -13 M to 1.0×10 -7 M. The method can be further extended to the quantitative detection of a variety of targets by replacing the lead-responsive DNAzyme with other functional DNA. Copyright © 2017 Elsevier B.V. All rights reserved.

Unexpected power-law stress relaxation of entangled ring polymers

PubMed Central

KAPNISTOS, M.; LANG, M.; PYCKHOUT-HINTZEN, W.; RICHTER, D.; CHO, D.; CHANG, T.

2016-01-01

After many years of intense research, most aspects of the motion of entangled polymers have been understood. Long linear and branched polymers have a characteristic entanglement plateau and their stress relaxes by chain reptation or branch retraction, respectively. In both mechanisms, the presence of chain ends is essential. But how do entangled polymers without ends relax their stress? Using properly purified high-molar-mass ring polymers, we demonstrate that these materials exhibit self-similar dynamics, yielding a power-law stress relaxation. However, trace amounts of linear chains at a concentration almost two decades below their overlap cause an enhanced mechanical response. An entanglement plateau is recovered at higher concentrations of linear chains. These results constitute an important step towards solving an outstanding problem of polymer science and are useful for manipulating properties of materials ranging from DNA to polycarbonate. They also provide possible directions for tuning the rheology of entangled polymers. PMID:18953345

Crystal structure and magnetic properties of a unique 3D coordination polymer constructed from flexible aliphatic tricarballylic acid ligands featuring linear trimeric Manganese(II)-based, metal carboxylate chains

NASA Astrophysics Data System (ADS)

Zou, Hua-Hong; Zhang, Shu-Hua; Zeng, Ming-Hua; Zhou, Yan-Ling; Liang, Hong

2008-08-01

A novel linear trimeric-based, Mn(II)-carboxylate chain well separated by long-linking flexible aliphatic tricarballylic acid ligands in a 3D coordination polymer [Mn 3(C 6H 5O 6) 2(H 2O) 4] n ( 1, C 6H 5O 6dbnd CH (COO -)(CH 2COO -) 2, TCA) exhibits low-dimensional antiferromagnetic order at 3.0 K. Such magnetic behavior is arises from the alternate Antiferro-Antiferro-Antiferro' ( J1J1J2) repeating interactions sequence, based on the nature of the binding modes of Mn(II)-carboxylate chain and the effect of interchains arrangement of 1. The reported carboxylate-bridged metal chain systems display a new structurally authenticated example of linear homometallic spin arranged antiferromagnet among metal carboxylates.

The electrical response of turtle cones to flashes and steps of light.

PubMed

Baylor, D A; Hodgkin, A L; Lamb, T D

1974-11-01

1. The linear response of turtle cones to weak flashes or steps of light was usually well fitted by equations based on a chain of six or seven reactions with time constants varying over about a 6-fold range.2. The temperature coefficient (Q(10)) of the reciprocal of the time to peak of the response to a flash was 1.8 (15-25 degrees C), corresponding to an activation energy of 10 kcal/mole.3. Electrical measurements with one internal electrode and a balancing circuit gave the following results on red-sensitive cones of high resistance: resistance across cell surface in dark 50-170 MOmega; time constant in dark 4-6.5 msec. The effect of a bright light was to increase the resistance and time constant by 10-30%.4. If the cell time constant, resting potential and maximum hyperpolarization are known, the fraction of ionic channels blocked by light at any instant can be calculated from the hyperpolarization and its rate of change. At times less than 50 msec the shape of this relation is consistent with the idea that the concentration of a blocking molecule which varies linearly with light intensity is in equilibrium with the fraction of ionic channels blocked.5. The rising phase of the response to flashes and steps of light covering a 10(5)-fold range of intensities is well fitted by a theory in which the essential assumptions are that (i) light starts a linear chain of reactions leading to the production of a substance which blocks ionic channels in the outer segment, (ii) an equilibrium between the blocking molecules and unblocked channels is established rapidly, and (iii) the electrical properties of the cell can be represented by a simple circuit with a time constant in the dark of about 6 msec.6. Deviations from the simple theory which occur after 50 msec are attributed partly to a time-dependent desensitization mechanism and partly to a change in saturation potential resulting from a voltage-dependent change in conductance.7. The existence of several components in the relaxation of the potential to its resting level can be explained by supposing that the ;substance' which blocks light sensitive ionic channels is inactivated in a series of steps.

Tuning the thermal conductivity of solar cell polymers through side chain engineering.

PubMed

Guo, Zhi; Lee, Doyun; Liu, Yi; Sun, Fangyuan; Sliwinski, Anna; Gao, Haifeng; Burns, Peter C; Huang, Libai; Luo, Tengfei

2014-05-07

Thermal transport is critical to the performance and reliability of polymer-based energy devices, ranging from solar cells to thermoelectrics. This work shows that the thermal conductivity of a low band gap conjugated polymer, poly(4,8-bis-alkyloxybenzo[1,2-b:4,5-b']dithiophene-2,6-diyl-alt-(alkylthieno[3,4-b]thiophene-2-carboxylate)-2,6-diyl) (PBDTTT), for photovoltaic applications can be actively tuned through side chain engineering. Compared to the original polymer modified with short branched side chains, the engineered polymer using all linear and long side chains shows a 160% increase in thermal conductivity. The thermal conductivity of the polymer exhibits a good correlation with the side chain lengths as well as the crystallinity of the polymer characterized using small-angle X-ray scattering (SAXS) experiments. Molecular dynamics simulations and atomic force microscopy are used to further probe the molecular level local order of different polymers. It is found that the linear side chain modified polymer can facilitate the formation of more ordered structures, as compared to the branched side chain modified ones. The effective medium theory modelling also reveals that the long linear side chain enables a larger heat carrier propagation length and the crystalline phase in the bulk polymer increases the overall thermal conductivity. It is concluded that both the length of the side chains and the induced polymer crystallization are important for thermal transport. These results offer important guidance for actively tuning the thermal conductivity of conjugated polymers through molecular level design.

Dynamics of a linear system coupled to a chain of light nonlinear oscillators analyzed through a continuous approximation

NASA Astrophysics Data System (ADS)

Charlemagne, S.; Ture Savadkoohi, A.; Lamarque, C.-H.

2018-07-01

The continuous approximation is used in this work to describe the dynamics of a nonlinear chain of light oscillators coupled to a linear main system. A general methodology is applied to an example where the chain has local nonlinear restoring forces. The slow invariant manifold is detected at fast time scale. At slow time scale, equilibrium and singular points are sought around this manifold in order to predict periodic regimes and strongly modulated responses of the system. Analytical predictions are in good accordance with numerical results and represent a potent tool for designing nonlinear chains for passive control purposes.

Long-Chain Perfluoroalkyl acids (PFAAs) Affect the Bioconcentration and Tissue Distribution of Short-Chain PFAAs in Zebrafish (Danio rerio).

PubMed

Wen, Wu; Xia, Xinghui; Hu, Diexuan; Zhou, Dong; Wang, Haotian; Zhai, Yawei; Lin, Hui

2017-11-07

Short- and long-chain perfluoroalkyl acids (PFAAs), ubiquitously coexisting in the environment, can be accumulated in organisms by binding with proteins and their binding affinities generally increase with their chain length. Therefore, we hypothesized that long-chain PFAAs will affect the bioconcentration of short-chain PFAAs in organisms. To testify this hypothesis, the bioconcentration and tissue distribution of five short-chain PFAAs (linear C-F = 3-6) were investigated in zebrafish in the absence and presence of six long-chain PFAAs (linear C-F = 7-11). The results showed that the concentrations of the short-chain PFAAs in zebrafish tissues increased with exposure time until steady states reached in the absence of long-chain PFAAs. However, in the presence of long-chain PFAAs, these short-chain PFAAs in tissues increased until peak values reached and then decreased until steady states, and the uptake and elimination rate constants of short-chain PFAAs declined in all tissues and their BCF ss decreased by 24-89%. The inhibitive effect of long-chain PFAAs may be attributed to their competition for transporters and binding sites of proteins in zebrafish with short-chain PFAAs. These results suggest that the effect of long-chain PFAAs on the bioconcentration of short-chain PFAAs should be taken into account in assessing the ecological and environmental effects of short-chain PFAAs.

Chemical association in simple models of molecular and ionic fluids. III. The cavity function

NASA Astrophysics Data System (ADS)

Zhou, Yaoqi; Stell, George

1992-01-01

Exact equations which relate the cavity function to excess solvation free energies and equilibrium association constants are rederived by using a thermodynamic cycle. A zeroth-order approximation, derived previously by us as a simple interpolation scheme, is found to be very accurate if the associative bonding occurs on or near the surface of the repulsive core of the interaction potential. If the bonding radius is substantially less than the core radius, the approximation overestimates the association degree and the association constant. For binary association, the zeroth-order approximation is equivalent to the first-order thermodynamic perturbation theory (TPT) of Wertheim. For n-particle association, the combination of the zeroth-order approximation with a ``linear'' approximation (for n-particle distribution functions in terms of the two-particle function) yields the first-order TPT result. Using our exact equations to go beyond TPT, near-exact analytic results for binary hard-sphere association are obtained. Solvent effects on binary hard-sphere association and ionic association are also investigated. A new rule which generalizes Le Chatelier's principle is used to describe the three distinct forms of behaviors involving solvent effects that we find. The replacement of the dielectric-continuum solvent model by a dipolar hard-sphere model leads to improved agreement with an experimental observation. Finally, equation of state for an n-particle flexible linear-chain fluid is derived on the basis of a one-parameter approximation that interpolates between the generalized Kirkwood superposition approximation and the linear approximation. A value of the parameter that appears to be near optimal in the context of this application is obtained from comparison with computer-simulation data.

The Ultra-filtration of Macromolecules with Different Conformations and Configurations through Nanopores

NASA Astrophysics Data System (ADS)

Ge, Hui

This Ph. D. thesis presents our study on the ultrafiltration of polymers with different configurations and conformations; namly, theoretically, the passing of polymer chains through a nanopore under an elongational flow filed has been studied for years, but experimental studies are rare because of two following reasons: (1) lacks a precise method to investigate how individual single polymer chain pass through a nanopore; (2) it is difficult, if not impossible, to obtain a set of polymer samples with a narrow molar mass distribution and a uniform structures; except for linear chains. The central question in this study is to find the critical (minimum) flow rate (qc) for each kind of chains, at which the chains can pass through a given nanopore. A comparison of the measured and calculated qc leads to a better understanding how different chains are deformed, stretched and pulled through a nanopore. We have developed a novel method of combinating static and dynamic laser light scattering (LLS) to precisely measure the relative retention concentration ((C0 - C)/C0). Chapter 1 briefly introduces the theoretical background of how applications and lists some of resent research progresses in this area. Polymer with various configurations and conformations pass through nanopores; including polymer linear chains, stars polymer, branched polymers, polymer micelles are introduced. Among them, the de Gennes and Brochard-Wyart's predictions of polymer linear and star chains passing through nanopores are emphasized, in which they predicted that qc of linear chain is qc ≃ kBT/(3pieta), where kB, T and eta are the Boltzmann constant, the absolutely temperature, and the viscosity of solvent, respectively, independent of both the chain length and the pore size; and for star chains passing through nanopores, there exist a optimal entering arm numbers, namely, the star chains passing through nanopores. Chapter 2 details basic theory of static and dynamic laser light scattering (LLS), including its instrumentation and our ultrafiltration setup. Chapter 3 briefly introduces the sample preparation, including the history and mechanism of anionic living polymerization, as well as how we used a novel home-made set-up to prepare linear polystyrene with different chain lengths and star polystyrene with various arm numbers and lengths. Chapter 4 summarizes our measured critical flow rates (qc) of linear polymer chains with different lengths for nanopores with different sizes, since the flow rate is directly related to the hydrodynamic force, we have developed a sensitive method (down to tens fN) to directly assess how much the hydrodynamic force (Fh) is required to overcome the weak entropy elasticity and stretch individual coiled chains in solution. Our method is completely different from the using existing optical tweezers or AFM, because they measure the relatively stronger enthalpy elasticity. Our results confirm that qc is indeed independent of the chain length, but decreases as the pore size increases. The value of qc is ˜10--200 times smaller than kBT/(3pieta). Such a discrepancy has been attributed to the rough assumption made by de Gennes and his coworkers; namely, each chain segment "blob" confined inside the pore is not a hard sphere so that the effective length along the flow direction is much longer than the pore diameter. Finally, using the solution temperature, we varied the chain conformation, our result shows that q c has a minimum which is near, but not exactly located at the theta temperature, might leading to a better way to determine the true ideal state of a polymer solution, at which all viral coefficients, not only the second vanish. Chapter 5 uses polymer solutions made of different mixtures of linear and star chains, we have demonstrated that flushing these solution mixtures through a nanopore with a properly chosen flow rate can effectively and cleanly separate linear and star chains no matter whether linear chains are larger or smaller than star chains. Chapter 6 further investigates how star-like polystyrene pass through a given nanopore under the flow field. Star polystyrene chains with different arm lengths (LA) and numbers (f) passing through a nanopore (20 nm) under an elongational flow field was investigated in terms of the flow-rate dependent relative retention ((C0 - C)/C0), where C 0 and C are the polymer concentrations before and after the ultrafiltration. Our results reveal that for a given arm length (LA), the critical flow rate (qc,star), below which star chains are blocked, dramatically increases with the total arm numbers (f); but for a given f, is nearly independent on LA, contradictory to the previous prediction made by de Gennes and Brochard-Wyart. We have revised their theory in the region fin < fout and also accounted for the effective length of each blob, where fin and fout are the numbers of arms inside and outside the pore, respectively. In the revision, we show that qc,star is indeed independent of LA but related to f and f in in two different ways, depending on whether fin ≤ f/2 or ≥ f/2. A comparison of our experimental and calculated results reveals that most of star chains pass through the nanopores with fin ˜ f/2. Further study of the temperature dependent (C0 - C)/C 0 of polystyrene in cyclohexane reveals that there exists a minimum of qc,star at ˜38 °C, close to its theta temperature (-34.5 °C).

Comparison of the Single Molecule Dynamics of Linear and Circular DNAs in Planar Extensional Flows

NASA Astrophysics Data System (ADS)

Li, Yanfei; Hsiao, Kai-Wen; Brockman, Christopher; Yates, Daniel; McKenna, Gregory; Schroeder, Charles; San Francisco, Michael; Kornfield, Julie; Anderson, Rae

2015-03-01

Chain topology has a profound impact on the flow behaviors of single macromolecules. The absence of free ends separates circular polymers from other chain architectures, i.e., linear, star, and branched. In the present work, we study the single chain dynamics of large circular and linear DNA molecules by comparing the relaxation dynamics, steady state coil-stretch transition, and transient molecular individualism behaviors for the two types of macromolecules. To this end, large circular DNA molecules were biologically synthesized and studied in a microfluidic device that has a cross-slot geometry to develop a stagnation point extensional flow. Although the relaxation time of rings scales in the same way as for the linear analog, the circular polymers show quantitatively different behaviors in the steady state extension and qualitatively different behaviors during a transient stretch. The existence of some commonality between these two topologies is proposed. Texas Tech University John R. Bradford Endowment.

Linear and Nonlinear Elasticity of Networks Made of Comb-like Polymers and Bottle-Brushes

NASA Astrophysics Data System (ADS)

Liang, H.; Dobrynin, A.; Everhart, M.; Daniel, W.; Vatankhah-Varnoosfaderani, M.; Sheiko, S.

We study mechanical properties of networks made of combs and bottle-brushes by computer simulations, theoretical calculations and experimental techniques. The networks are prepared by cross-linking backbones of combs or bottle-brushes with linear chains. This results in ``hybrid'' networks consisting of linear chains and strands of combs or bottle-brushes. In the framework of the phantom network model, the network modulus at small deformations G0 can be represented as a sum of contributions from linear chains, G0 , l, and strands of comb or bottle-brush, G0 , bb. If the length of extended backbone between crosslinks, Rmax, is much longer than the Kuhn length, bk, the modulus scales with the degree of polymerization of the side chains, nsc, and number of monomers between side chains, ng, as G0 , bb (nsc/ng + 1)-1. In the limit when bk becomes of the order of Rmax, the combs and bottle-brushes can be considered as semiflexible chains, resulting in a network modulus to be G0 , bb (nsc/ng + 1)-1(nsc2/2/ng) . In the nonlinear deformation regime, the strain-hardening behavior is described by the nonlinear network deformation model, which predicts that the true stress is a universal function of the structural modulus, G, first strain invariant, I1, and deformation ratio, β. The results of the computer simulations and predictions of the theoretical model are in a good agreement with experimental results. NSF DMR-1409710, DMR-1407645, DMR-1624569, DMR-1436201.

Self-Consistent Field Theories for the Role of Large Length-Scale Architecture in Polymers

NASA Astrophysics Data System (ADS)

Wu, David

At large length-scales, the architecture of polymers can be described by a coarse-grained specification of the distribution of branch points and monomer types within a molecule. This includes molecular topology (e.g., cyclic or branched) as well as distances between branch points or chain ends. Design of large length-scale molecular architecture is appealing because it offers a universal strategy, independent of monomer chemistry, to tune properties. Non-linear analogs of linear chains differ in molecular-scale properties, such as mobility, entanglements, and surface segregation in blends that are well-known to impact rheological, dynamical, thermodynamic and surface properties including adhesion and wetting. We have used Self-Consistent Field (SCF) theories to describe a number of phenomena associated with large length-scale polymer architecture. We have predicted the surface composition profiles of non-linear chains in blends with linear chains. These predictions are in good agreement with experimental results, including from neutron scattering, on a range of well-controlled branched (star, pom-pom and end-branched) and cyclic polymer architectures. Moreover, the theory allows explanation of the segregation and conformations of branched polymers in terms of effective surface potentials acting on the end and branch groups. However, for cyclic chains, which have no end or junction points, a qualitatively different topological mechanism based on conformational entropy drives cyclic chains to a surface, consistent with recent neutron reflectivity experiments. We have also used SCF theory to calculate intramolecular and intermolecular correlations for polymer chains in the bulk, dilute solution, and trapped at a liquid-liquid interface. Predictions of chain swelling in dilute star polymer solutions compare favorably with existing PRISM theory and swelling at an interface helps explain recent measurements of chain mobility at an oil-water interface. In collaboration with: Renfeng Hu, Colorado School of Mines, and Mark Foster, University of Akron. This work was supported by NSF Grants No. CBET- 0730692 and No. CBET-0731319.

Structure of Irreversibly Adsorbed Star Polymers

NASA Astrophysics Data System (ADS)

Akgun, Bulent; Aykan, Meryem Seyma; Canavar, Seda; Satija, Sushil K.; Uhrig, David; Hong, Kunlun

Formation of irreversibly adsorbed polymer chains on solid substrates have a huge impact on the wetting, glass transition, aging and polymer chain mobility in thin films. In recent years there has been many reports on the formation, kinetics and dynamics of these layers formed by linear homopolymers. Recent studies showed that by varying the number of polymer arms and arm molecular weight one can tune the glass transition temperature of thin polymer films. Using polymer architecture as a tool, the behavior of thin films can be tuned between the behavior of linear chains and soft colloids. We have studied the effect of polymer chain architecture on the structure of dead layer using X-ray reflectivity (XR) and atomic force microscopy. Layer thicknesses and densities of flattened and loosely adsorbed chains has been measured for linear, 4-arm, and 8-arm star polymers with identical total molecular weight as a function of substrate surface energy, annealing temperature and annealing time. Star polymers have been synthesized using anionic polymerization. XR measurements showed that 8-arm star PS molecules form the densest and the thickest dead layers among these three molecules.

Life cycle cost optimization of biofuel supply chains under uncertainties based on interval linear programming.

PubMed

Ren, Jingzheng; Dong, Liang; Sun, Lu; Goodsite, Michael Evan; Tan, Shiyu; Dong, Lichun

2015-01-01

The aim of this work was to develop a model for optimizing the life cycle cost of biofuel supply chain under uncertainties. Multiple agriculture zones, multiple transportation modes for the transport of grain and biofuel, multiple biofuel plants, and multiple market centers were considered in this model, and the price of the resources, the yield of grain and the market demands were regarded as interval numbers instead of constants. An interval linear programming was developed, and a method for solving interval linear programming was presented. An illustrative case was studied by the proposed model, and the results showed that the proposed model is feasible for designing biofuel supply chain under uncertainties. Copyright © 2015 Elsevier Ltd. All rights reserved.

A biological phantom for evaluation of CT image reconstruction algorithms

NASA Astrophysics Data System (ADS)

Cammin, J.; Fung, G. S. K.; Fishman, E. K.; Siewerdsen, J. H.; Stayman, J. W.; Taguchi, K.

2014-03-01

In recent years, iterative algorithms have become popular in diagnostic CT imaging to reduce noise or radiation dose to the patient. The non-linear nature of these algorithms leads to non-linearities in the imaging chain. However, the methods to assess the performance of CT imaging systems were developed assuming the linear process of filtered backprojection (FBP). Those methods may not be suitable any longer when applied to non-linear systems. In order to evaluate the imaging performance, a phantom is typically scanned and the image quality is measured using various indices. For reasons of practicality, cost, and durability, those phantoms often consist of simple water containers with uniform cylinder inserts. However, these phantoms do not represent the rich structure and patterns of real tissue accurately. As a result, the measured image quality or detectability performance for lesions may not reflect the performance on clinical images. The discrepancy between estimated and real performance may be even larger for iterative methods which sometimes produce "plastic-like", patchy images with homogeneous patterns. Consequently, more realistic phantoms should be used to assess the performance of iterative algorithms. We designed and constructed a biological phantom consisting of porcine organs and tissue that models a human abdomen, including liver lesions. We scanned the phantom on a clinical CT scanner and compared basic image quality indices between filtered backprojection and an iterative reconstruction algorithm.

Simple method for production of internal control DNA for Mycobacterium tuberculosis polymerase chain reaction assays.

PubMed Central

deWit, D; Wootton, M; Allan, B; Steyn, L

1993-01-01

A simple method for the production of internal control DNA for two well-established Mycobacterium tuberculosis polymerase chain reaction assays is described. The internal controls were produced from Mycobacterium kansasii DNA with the same primers but at a lower annealing temperature than that used in the standard assays. In both assays, therefore, the internal control DNA has the same primer-binding sequences at the target DNA. One-microgram quantities of internal control DNA which was not contaminated with target DNA could easily be produced by this method. The inclusion of the internal control in the reaction mixture did not affect the efficiency of amplification of the target DNA. The method is simple and rapid and should be adaptable to most M. tuberculosis polymerase chain reaction assays. Images PMID:8370752

Improved zeolite regeneration processes for preparing saturated branched-chain fatty acids

USDA-ARS?s Scientific Manuscript database

Ferrierite zeolite solid is an excellent catalyst for the skeletal isomerization of unsaturated linear-chain fatty acids (i.e., oleic acid) to unsaturated branched-chain fatty acids (i.e., iso-oleic acid) follow by hydrogenation to give saturated branched-chain fatty acids (i.e., isostearic acid). ...

Quantum conductance oscillation in linear monatomic silicon chains

NASA Astrophysics Data System (ADS)

Liu, Fu-Ti; Cheng, Yan; Yang, Fu-Bin; Chen, Xiang-Rong

2014-02-01

The conductance of linear silicon atomic chains with n=1-8 atoms sandwiched between Au electrodes is investigated by using the density functional theory combined with non-equilibrium Green's function. The results show that the conductance oscillates with a period of two atoms as the number of atoms in the chain is varied. We optimize the geometric structure of nanoscale junctions in different distances, and obtain that the average bond-length of silicon atoms in each chain at equilibrium positions is 2.15±0.03 Å. The oscillation of average Si-Si bond-length can explain the conductance oscillation from the geometric structure of atomic chains. We calculate the transmission spectrum of the chains in the equilibrium positions, and explain the conductance oscillation from the electronic structure. The transport channel is mainly contributed by px and py orbital electrons of silicon atoms. The even-odd oscillation is robust under external voltage up to 1.2 V.

A simple bias correction in linear regression for quantitative trait association under two-tail extreme selection.

PubMed

Kwan, Johnny S H; Kung, Annie W C; Sham, Pak C

2011-09-01

Selective genotyping can increase power in quantitative trait association. One example of selective genotyping is two-tail extreme selection, but simple linear regression analysis gives a biased genetic effect estimate. Here, we present a simple correction for the bias.

Synthesis and antimalarial activity of new chloroquine analogues carrying a multifunctional linear side chain.

PubMed

Iwaniuk, Daniel P; Whetmore, Eric D; Rosa, Nicholas; Ekoue-Kovi, Kekeli; Alumasa, John; de Dios, Angel C; Roepe, Paul D; Wolf, Christian

2009-09-15

We report the synthesis and in vitro antimalarial activity of several new 4-amino- and 4-alkoxy-7-chloroquinolines carrying a linear dibasic side chain. Many of these chloroquine analogues have submicromolar antimalarial activity versus HB3 (chloroquine sensitive) and Dd2 (chloroquine resistant strain of Plasmodium falciparum) and low resistance indices were obtained in most cases. Importantly, compounds 11-15 and 24 proved to be more potent against Dd2 than chloroquine. Branching of the side chain structure proved detrimental to the activity against the CQR strain.

Practical Session: Simple Linear Regression

NASA Astrophysics Data System (ADS)

Clausel, M.; Grégoire, G.

2014-12-01

Two exercises are proposed to illustrate the simple linear regression. The first one is based on the famous Galton's data set on heredity. We use the lm R command and get coefficients estimates, standard error of the error, R2, residuals …In the second example, devoted to data related to the vapor tension of mercury, we fit a simple linear regression, predict values, and anticipate on multiple linear regression. This pratical session is an excerpt from practical exercises proposed by A. Dalalyan at EPNC (see Exercises 1 and 2 of http://certis.enpc.fr/~dalalyan/Download/TP_ENPC_4.pdf).

Prebiotic hydrocarbon synthesis in impacting reduced astrophysical icy mixtures

DOE PAGES

Koziol, Lucas; Goldman, Nir

2015-04-21

We present results of prebiotic organic synthesis in shock-compressed reducing mixtures of simple ices from quantum molecular dynamics simulations extended to close to chemical equilibrium timescales. Given the relative abundance of carbon in reduced forms in astrophysical ices as well as the tendency of these mixtures to form complex hydrocarbons under the presence of external stimuli, it is possible that cometary impacts on a planetary surface could have yielded a larger array of prebiotic organic compounds than previously investigated. We find that the high pressures and temperatures due to shock compression yield a large assortment of carbon- and nitrogen-bonded extendedmore » structures that are highly reactive with short molecular lifetimes. Expansion and cooling causes these materials to break apart and form a wide variety of stable, potentially life-building compounds, including long-chain linear and branched hydrocarbons, large heterocyclic compounds, and a variety of different amines and exotic amino acids. Lastly, our results help provide a bottom-up understanding of hydrocarbon impact synthesis on the early Earth and its role in producing life-building molecules from simple starting materials.« less

Prebiotic hydrocarbon synthesis in impacting reduced astrophysical icy mixtures

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

Koziol, Lucas; Goldman, Nir

We present results of prebiotic organic synthesis in shock-compressed reducing mixtures of simple ices from quantum molecular dynamics simulations extended to close to chemical equilibrium timescales. Given the relative abundance of carbon in reduced forms in astrophysical ices as well as the tendency of these mixtures to form complex hydrocarbons under the presence of external stimuli, it is possible that cometary impacts on a planetary surface could have yielded a larger array of prebiotic organic compounds than previously investigated. We find that the high pressures and temperatures due to shock compression yield a large assortment of carbon- and nitrogen-bonded extendedmore » structures that are highly reactive with short molecular lifetimes. Expansion and cooling causes these materials to break apart and form a wide variety of stable, potentially life-building compounds, including long-chain linear and branched hydrocarbons, large heterocyclic compounds, and a variety of different amines and exotic amino acids. Lastly, our results help provide a bottom-up understanding of hydrocarbon impact synthesis on the early Earth and its role in producing life-building molecules from simple starting materials.« less

From Comb-like Polymers to Bottle-Brushes

NASA Astrophysics Data System (ADS)

Liang, Heyi; Cao, Zhen; Dobrynin, Andrey; Sheiko, Sergei

We use a combination of the coarse-grained molecular dynamics simulations and scaling analysis to study conformations of bottle-brushes and comb-like polymers in a melt. Our analysis show that bottle-brushes and comb-like polymers can be in four different conformation regimes depending on the number of monomers between grafted side chains and side chain degree of polymerization. In loosely-grafted comb regime (LC) the degree of polymerization between side chains is longer than side chain degree of polymerization, such that the side chains belonging to the same macromolecule do not overlap. Crossover to a new densely-grafted comb regime (DC) takes place when side chains begin to overlap reducing interpenetration of side chains belonging to different macromolecules. In these two regimes both side-chains and backbone behave as unperturbed linear chains with the effective Kuhn length of the backbone being close to that of linear chain. Further decrease spacer degree of polymerization results in crossover to loosely-grafted bottle-brush regime (LB). In this regime, the bottle-brush backbone is stretched while the side-chains still maintain ideal chain conformation. Finally, for even shorter spacer between grafted side chains, which corresponds to densely-grafted bottle-brush regime (DB), the backbone adopts a fully extended chain conformation, and side-chains begin to stretch to maintain a constant monomer density. NSF DMR-1409710, DMR-1407645, DMR-1624569, DMR-1436201.

Linear rheology and structure of molecular bottlebrushes with short side chains

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

López-Barrón, Carlos R., E-mail: carlos.r.lopez-barron@exxonmobil.com; Brant, Patrick; Crowther, Donna J.

We investigate the microstructure and linear viscoelasticity of model molecular bottlebrushes (BBs) using rheological and small-angle X-ray and neutron scattering measurements. Our polymers have short atactic polypropylene (aPP) side chains of molecular weight ranging from 119 g/mol to 259 g/mol and narrow molecular weight distribution (M{sub w}/M{sub n} 1.02–1.05). The side chain molecular weights are a small fraction of the entanglement molecular weight of the corresponding linear polymer (M{sub e,aPP}= 7.05 kg/mol), and as such, they are unentangled. The morphology of the aPP BBs is characterized as semiflexible thick chains with small side chain interdigitation. Their dynamic master curves, obtained by time-temperature superposition,more » reveal two sequential relaxation processes corresponding to the segmental relaxation and the relaxation of the BB backbone. Due to the short length of the side chains, their fast relaxation could not be distinguished from the glassy relaxation. The fractional free volume is an increasing function of the side chain length (N{sub SC}). Therefore, the glassy behavior of these polymers as well as their molecular friction and dynamic properties are influenced by their N{sub SC} values. The apparent flow activation energies are a decreasing function of N{sub SC}, and their values explain the differences in zero-shear viscosity measured at different temperatures.« less

Nonequilibrium generalised Langevin equation for the calculation of heat transport properties in model 1D atomic chains coupled to two 3D thermal baths.

PubMed

Ness, H; Stella, L; Lorenz, C D; Kantorovich, L

2017-04-28

We use a generalised Langevin equation scheme to study the thermal transport of low dimensional systems. In this approach, the central classical region is connected to two realistic thermal baths kept at two different temperatures [H. Ness et al., Phys. Rev. B 93, 174303 (2016)]. We consider model Al systems, i.e., one-dimensional atomic chains connected to three-dimensional baths. The thermal transport properties are studied as a function of the chain length N and the temperature difference ΔT between the baths. We calculate the transport properties both in the linear response regime and in the non-linear regime. Two different laws are obtained for the linear conductance versus the length of the chains. For large temperatures (T≳500 K) and temperature differences (ΔT≳500 K), the chains, with N>18 atoms, present a diffusive transport regime with the presence of a temperature gradient across the system. For lower temperatures (T≲500 K) and temperature differences (ΔT≲400 K), a regime similar to the ballistic regime is observed. Such a ballistic-like regime is also obtained for shorter chains (N≤15). Our detailed analysis suggests that the behaviour at higher temperatures and temperature differences is mainly due to anharmonic effects within the long chains.

Intrachain exciton dynamics in conjugated polymer chains in solution.

PubMed

Tozer, Oliver Robert; Barford, William

2015-08-28

We investigate exciton dynamics on a polymer chain in solution induced by the Brownian rotational motion of the monomers. Poly(para-phenylene) is chosen as the model system and excitons are modeled via the Frenkel exciton Hamiltonian. The Brownian fluctuations of the torsional modes were modeled via the Langevin equation. The rotation of monomers in polymer chains in solution has a number of important consequences for the excited state properties. First, the dihedral angles assume a thermal equilibrium which causes off-diagonal disorder in the Frenkel Hamiltonian. This disorder Anderson localizes the Frenkel exciton center-of-mass wavefunctions into super-localized local exciton ground states (LEGSs) and higher-energy more delocalized quasi-extended exciton states (QEESs). LEGSs correspond to chromophores on polymer chains. The second consequence of rotations-that are low-frequency-is that their coupling to the exciton wavefunction causes local planarization and the formation of an exciton-polaron. This torsional relaxation causes additional self-localization. Finally, and crucially, the torsional dynamics cause the Frenkel Hamiltonian to be time-dependent, leading to exciton dynamics. We identify two distinct types of dynamics. At low temperatures, the torsional fluctuations act as a perturbation on the polaronic nature of the exciton state. Thus, the exciton dynamics at low temperatures is a small-displacement diffusive adiabatic motion of the exciton-polaron as a whole. The temperature dependence of the diffusion constant has a linear dependence, indicating an activationless process. As the temperature increases, however, the diffusion constant increases at a faster than linear rate, indicating a second non-adiabatic dynamics mechanism begins to dominate. Excitons are thermally activated into higher energy more delocalized exciton states (i.e., LEGSs and QEESs). These states are not self-localized by local torsional planarization. During the exciton's temporary occupation of a LEGS-and particularly a quasi-band QEES-its motion is semi-ballistic with a large group velocity. After a short period of rapid transport, the exciton wavefunction collapses again into an exciton-polaron state. We present a simple model for the activated dynamics which is in agreement with the data.

Controllable Nanoparticle Assembly and Actuation with Modified Dipole Potentials in Simulation

NASA Astrophysics Data System (ADS)

Dempster, Joshua

Science at the nanoscale poses several recurring difficulties. How can we control the assembly of objects too small for direct manipulation to be practical? How can we extend that control to in vivo systems so we can make use of nanotechnology in medicine? And how can we recreate the extraordinary capacities of Nature: healing, replication, growth, adaptation, self-regulation? One of the most powerful tools for addressing these challenges is the simple, familiar dipole moment. Since their debut as fuel control devices at NASA in the early sixties, possible applications for dipole suspensions have grown to areas far beyond what their creators envisioned. A multitude of ambitious new medical and mechanical applications make use of dipolar colloids. Dipoles are attractive from a practical standpoint because one can use fields to control not just their orientation and location, but also their mutual interactions. From a physical standpoint, dipoles are compelling as an exceptionally simple form of symmetry-breaking that leads to a variety of complex phenomena. This thesis studies the assembly and control of spherical colloids with a dipolar interaction modified by additional conditions using simulations. Three cases are examined in detail. The first is the case of an electrical dipole moment created by regions of opposite charge density on the surface of a colloid. Here the dipole potential is modified by strong screening. Such a system is interesting as a model for certain proteins in a high-salt solution and suggests possible uses for inverse Janus colloids. The resulting phases have little resemblance to the usual dipole phases and can be controlled with small quantities of homogeneously charged particles. In the second case, superparamagnetic dipoles are linked into chains. Such chains have been realized in a wide variety of experimental schemes. A general theory is developed for the equilibrium shapes of the chains in a precessing field when their endpoints are fixed. This theory reveals that the chains are good candidates for contracting muscles in microscopic devices with a conveniently harmonic form for their potentials. Ensembles of free chains can be put to more elaborate uses. To illustrate, a regime is designed that spins the chains into a self-healing cross-linked gel. Finally, we will turn to self-replication. Decorating a permanent dipole with a single permanent binding site is enough to enable self-replication using dimers as the template. A periodic magnetic drive provides the energy to drive replication. Several theoretical principles regarding the statistics of linear self-replicators are deduced and used to optimize the dipole replicating system.

Viscous bursting of suspended films

NASA Astrophysics Data System (ADS)

Debrégeas, G.; Martin, P.; Brochard-Wyart, F.

1995-11-01

Soap films break up by an inertial process. We present here the first observations on freely suspended films of long-chain polymers, where viscous effects are dominant and no surfactant is present. A hole is nucleated at time 0 and grows up to a radius R(t) at time t. A surprising feature is that the liquid from the hole is not collected into a rim (as it is in soap films): The liquid spreads out without any significant change of the film thickness. The radius R(t) grows exponentially with time, R~exp(t/τ) [while in soap films R(t) is linear]. The rise time τ~ηe/2γ where η is viscosity, e is thickness (in the micron range), and γ is surface tension. A simple model is developed to explain this growth law.

Determination of the pKa of the N-terminal amino group of ubiquitin by NMR

PubMed Central

Oregioni, Alain; Stieglitz, Benjamin; Kelly, Geoffrey; Rittinger, Katrin; Frenkiel, Tom

2017-01-01

Ubiquitination regulates nearly every aspect of cellular life. It is catalysed by a cascade of three enzymes and results in the attachment of the C-terminal carboxylate of ubiquitin to a lysine side chain in the protein substrate. Chain extension occurs via addition of subsequent ubiquitin molecules to either one of the seven lysine residues of ubiquitin, or via its N-terminal α-amino group to build linear ubiquitin chains. The pKa of lysine side chains is around 10.5 and hence E3 ligases require a mechanism to deprotonate the amino group at physiological pH to produce an effective nucleophile. In contrast, the pKa of N-terminal α-amino groups of proteins can vary significantly, with reported values between 6.8 and 9.1, raising the possibility that linear chain synthesis may not require a general base. In this study we use NMR spectroscopy to determine the pKa for the N-terminal α-amino group of methionine1 of ubiquitin for the first time. We show that it is 9.14, one of the highest pKa values ever reported for this amino group, providing a rational for the observed need for a general base in the E3 ligase HOIP, which synthesizes linear ubiquitin chains. PMID:28252051

Star Polymers.

PubMed

Ren, Jing M; McKenzie, Thomas G; Fu, Qiang; Wong, Edgar H H; Xu, Jiangtao; An, Zesheng; Shanmugam, Sivaprakash; Davis, Thomas P; Boyer, Cyrille; Qiao, Greg G

2016-06-22

Recent advances in controlled/living polymerization techniques and highly efficient coupling chemistries have enabled the facile synthesis of complex polymer architectures with controlled dimensions and functionality. As an example, star polymers consist of many linear polymers fused at a central point with a large number of chain end functionalities. Owing to this exclusive structure, star polymers exhibit some remarkable characteristics and properties unattainable by simple linear polymers. Hence, they constitute a unique class of technologically important nanomaterials that have been utilized or are currently under audition for many applications in life sciences and nanotechnologies. This article first provides a comprehensive summary of synthetic strategies towards star polymers, then reviews the latest developments in the synthesis and characterization methods of star macromolecules, and lastly outlines emerging applications and current commercial use of star-shaped polymers. The aim of this work is to promote star polymer research, generate new avenues of scientific investigation, and provide contemporary perspectives on chemical innovation that may expedite the commercialization of new star nanomaterials. We envision in the not-too-distant future star polymers will play an increasingly important role in materials science and nanotechnology in both academic and industrial settings.

Long-Term Supplementation with Chromium Malate Improves Short Chain Fatty Acid Content in Sprague-Dawley Rats.

PubMed

Wu, Huiyu; Feng, Weiwei; Mao, Guanghua; Zhao, Ting; Wu, Xiangyang; Wang, Songmei; Zou, Yanmin; Yang, Liuqing; Wang, Liang

2016-11-01

Our previous study showed that chromium malate improved the composition of intestinal flora, glycometabolism, glycometabolism-related enzymes, and lipid metabolism in type 2 diabetes mellitus (T2DM) rats. The present study was designed to evaluate the effect of chromium malate with long-term supplementation on short chain fatty acid (SCFA) content in Sprague-Dawley rats. The samples were analyzed by gas chromatography with high linearity (R 2  ≥ 0.9995), low quantification limit (0.011-0.070 mM), and satisfactory recoveries. The method was simple and environmentally friendly. The acetic content in cecum of 3-month control group was significantly higher than that of 1-year control group. When compared with 1-year control group, chromium malate (at a dose of 20.0 μg Cr/kg bw) could significantly increase acetic, propionic, i-butyric butyric, butyric, i-valeric, valeric, and n-caproic levels. The acetic, propionic, i-butyric, valeric, and n-caproic contents of 1-year chromium malate group (at a dose of 20.0 μg Cr/kg bw) had a significant improvement when compared with 1-year chromium picolinate group. Acetic, propionic, and butyric contained approximately 91.65 % of the total SCFAs in 1-year group. The results indicated that the improvement of chromium malate on short chain fatty acid content change was better than that of chromium picolinate.

RP-HPLC-fluorescence analysis of aliphatic aldehydes: application to aldehyde-generating enzymes HACL1 and SGPL1

PubMed Central

Mezzar, Serena; de Schryver, Evelyn; Van Veldhoven, Paul P.

2014-01-01

Long-chain aldehydes are commonly produced in various processes, such as peroxisomal α-oxidation of long-chain 3-methyl-branched and 2-hydroxy fatty acids and microsomal breakdown of phosphorylated sphingoid bases. The enzymes involved in the aldehyde-generating steps of these processes are 2-hydroxyacyl-CoA lyase (HACL1) and sphingosine-1-phosphate lyase (SGPL1), respectively. In the present work, nonradioactive assays for these enzymes were developed employing the Hantzsch reaction. Tridecanal (C13-al) and heptadecanal (C17-al) were selected as model compounds and cyclohexane-1,3-dione as 1,3-diketone, and the fluorescent derivatives were analyzed by reversed phase (RP)-HPLC. Assay mixture composition, as well as pH and heating, were optimized for C13-al and C17-al. Under optimized conditions, these aldehydes could be quantified in picomolar range and different long-chain aldehyde derivatives were well resolved with a linear gradient elution by RP-HPLC. Aldehydes generated by recombinant enzymes could easily be detected via this method. Moreover, the assay allowed to document activity or deficiency in tissue homogenates and fibroblast lysates without an extraction step. In conclusion, a simple, quick, and cheap assay for the study of HACL1 and SGPL1 activities was developed, without relying on expensive mass spectrometric detectors or radioactive substrates. PMID:24323699

A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data.

PubMed

Lartillot, Nicolas

2014-02-15

Correlation between life history or ecological traits and genomic features such as nucleotide or amino acid composition can be used for reconstructing the evolutionary history of the traits of interest along phylogenies. Thus far, however, such ancestral reconstructions have been done using simple linear regression approaches that do not account for phylogenetic inertia. These reconstructions could instead be seen as a genuine comparative regression problem, such as formalized by classical generalized least-square comparative methods, in which the trait of interest and the molecular predictor are represented as correlated Brownian characters coevolving along the phylogeny. Here, a Bayesian sampler is introduced, representing an alternative and more efficient algorithmic solution to this comparative regression problem, compared with currently existing generalized least-square approaches. Technically, ancestral trait reconstruction based on a molecular predictor is shown to be formally equivalent to a phylogenetic Kalman filter problem, for which backward and forward recursions are developed and implemented in the context of a Markov chain Monte Carlo sampler. The comparative regression method results in more accurate reconstructions and a more faithful representation of uncertainty, compared with simple linear regression. Application to the reconstruction of the evolution of optimal growth temperature in Archaea, using GC composition in ribosomal RNA stems and amino acid composition of a sample of protein-coding genes, confirms previous findings, in particular, pointing to a hyperthermophilic ancestor for the kingdom. The program is freely available at www.phylobayes.org.

Tuning conductivity in boron nanowire by edge geometry

NASA Astrophysics Data System (ADS)

Bhuyan, Prabal Dev; Gupta, Sanjeev K.; Sonvane, Yogesh; Gajjar, P. N.

2018-04-01

In present study, we have investigated electronic and temperature dependent transport properties of carbyne like linear chain and ribbon like zigzag structures of Boron (B) nanowire. The linear chain structure showed higher electric and thermal conductivity, as it is sp-hybridized, than its counterpart ribbon (R) structure. However the conductivity of ribbon structure increases with increases in width due to edge geometry effect. The ribbon (3R) structure showed high electric and thermal conductivity of 8.0×1019 1/Ω m s and 0.59×1015 W/ m K respectively. Interestingly we have observed that B linear chain showed higher thermal conductivity of 0.23×1015 W/ m K than its ribbon R and 2R structure above 600K. Because of high Seebeck co-efficient of boron chain and ribbon (R) structures at low temperature, they could find applications in thermoelectric sensors. Our results show that tuning conductivity property of boron nanowire could be of great interest in research for future electric connector in nanodevices.

Target Specificity of the E3 Ligase LUBAC for Ubiquitin and NEMO Relies on Different Minimal Requirements*

PubMed Central

Smit, Judith J.; van Dijk, Willem J.; El Atmioui, Dris; Merkx, Remco; Ovaa, Huib; Sixma, Titia K.

2013-01-01

The ubiquitination of NEMO with linear ubiquitin chains by the E3-ligase LUBAC is important for the activation of the canonical NF-κB pathway. NEMO ubiquitination requires a dual target specificity of LUBAC, priming on a lysine on NEMO and chain elongation on the N terminus of the priming ubiquitin. Here we explore the minimal requirements for these specificities. Effective linear chain formation requires a precise positioning of the ubiquitin N-terminal amine in a negatively charged environment on the top of ubiquitin. Whereas the RBR-LDD region on HOIP is sufficient for targeting the ubiquitin N terminus, the priming lysine modification on NEMO requires catalysis by the RBR domain of HOIL-1L as well as the catalytic machinery of the RBR-LDD domains of HOIP. Consequently, target specificity toward NEMO is determined by multiple LUBAC components, whereas linear ubiquitin chain elongation is realized by a specific interplay between HOIP and ubiquitin. PMID:24030825

Data on pigments and long-chain fatty compounds identified in Dietzia sp. A14101 grown on simple and complex hydrocarbons

PubMed Central

Hvidsten, Ina; Mjøs, Svein Are; Bødtker, Gunhild; Barth, Tanja

2015-01-01

This data article provides: 1. An overview of tentatively identified long chain compounds in Dietzia sp. A14101 grown on simple and complex hydrocarbons; 2. Preliminary Identification of pigments in bacterial material obtained from incubation with a hydrocarbon (dodecane, n-C12) as the only carbon and energy source; 3. Some pictures to illustrate the cell surface charge test. PMID:26442286

A Bayes linear Bayes method for estimation of correlated event rates.

PubMed

Quigley, John; Wilson, Kevin J; Walls, Lesley; Bedford, Tim

2013-12-01

Typically, full Bayesian estimation of correlated event rates can be computationally challenging since estimators are intractable. When estimation of event rates represents one activity within a larger modeling process, there is an incentive to develop more efficient inference than provided by a full Bayesian model. We develop a new subjective inference method for correlated event rates based on a Bayes linear Bayes model under the assumption that events are generated from a homogeneous Poisson process. To reduce the elicitation burden we introduce homogenization factors to the model and, as an alternative to a subjective prior, an empirical method using the method of moments is developed. Inference under the new method is compared against estimates obtained under a full Bayesian model, which takes a multivariate gamma prior, where the predictive and posterior distributions are derived in terms of well-known functions. The mathematical properties of both models are presented. A simulation study shows that the Bayes linear Bayes inference method and the full Bayesian model provide equally reliable estimates. An illustrative example, motivated by a problem of estimating correlated event rates across different users in a simple supply chain, shows how ignoring the correlation leads to biased estimation of event rates. © 2013 Society for Risk Analysis.

How can we make stable linear monoatomic chains? Gold-cesium binary subnanowires as an example of a charge-transfer-driven approach to alloying.

PubMed

Choi, Young Cheol; Lee, Han Myoung; Kim, Woo Youn; Kwon, S K; Nautiyal, Tashi; Cheng, Da-Yong; Vishwanathan, K; Kim, Kwang S

2007-02-16

On the basis of first-principles calculations of clusters and one dimensional infinitely long subnanowires of the binary systems, we find that alkali-noble metal alloy wires show better linearity and stability than either pure alkali metal or noble metal wires. The enhanced alternating charge buildup on atoms by charge transfer helps the atoms line up straight. The cesium doped gold wires showing significant charge transfer from cesium to gold can be stabilized as linear or circular monoatomic chains.

A Linear Regression and Markov Chain Model for the Arabian Horse Registry

DTIC Science & Technology

1993-04-01

as a tax deduction? Yes No T-4367 68 26. Regardless of previous equine tax deductions, do you consider your current horse activities to be... (Mark one...E L T-4367 A Linear Regression and Markov Chain Model For the Arabian Horse Registry Accesion For NTIS CRA&I UT 7 4:iC=D 5 D-IC JA" LI J:13tjlC,3 lO...the Arabian Horse Registry, which needed to forecast its future registration of purebred Arabian horses . A linear regression model was utilized to

Suspended chains damp wind-induced oscillations of tall flexible structures

NASA Technical Reports Server (NTRS)

Reed, W. H., III

1968-01-01

Hanging-chain system, which is a form of impact damper, suppresses wind-induced bending oscillations of tall cylindrical antenna masts. A cluster of chains enclosed in a neoprene shroud is suspended inside the tip of the antenna mast, forming a simple method of damping structural vibrations.

Using Games to Teach Markov Chains

ERIC Educational Resources Information Center

Johnson, Roger W.

2003-01-01

Games are promoted as examples for classroom discussion of stationary Markov chains. In a game context Markov chain terminology and results are made concrete, interesting, and entertaining. Game length for several-player games such as "Hi Ho! Cherry-O" and "Chutes and Ladders" is investigated and new, simple formulas are given. Slight…

CudaChain: an alternative algorithm for finding 2D convex hulls on the GPU.

PubMed

Mei, Gang

2016-01-01

This paper presents an alternative GPU-accelerated convex hull algorithm and a novel S orting-based P reprocessing A pproach (SPA) for planar point sets. The proposed convex hull algorithm termed as CudaChain consists of two stages: (1) two rounds of preprocessing performed on the GPU and (2) the finalization of calculating the expected convex hull on the CPU. Those interior points locating inside a quadrilateral formed by four extreme points are first discarded, and then the remaining points are distributed into several (typically four) sub regions. For each subset of points, they are first sorted in parallel; then the second round of discarding is performed using SPA; and finally a simple chain is formed for the current remaining points. A simple polygon can be easily generated by directly connecting all the chains in sub regions. The expected convex hull of the input points can be finally obtained by calculating the convex hull of the simple polygon. The library Thrust is utilized to realize the parallel sorting, reduction, and partitioning for better efficiency and simplicity. Experimental results show that: (1) SPA can very effectively detect and discard the interior points; and (2) CudaChain achieves 5×-6× speedups over the famous Qhull implementation for 20M points.

Atoms-in-molecules study of the genetically encoded amino acids. III. Bond and atomic properties and their correlations with experiment including mutation-induced changes in protein stability and genetic coding.

PubMed

Matta, Chérif F; Bader, Richard F W

2003-08-15

This article presents a study of the molecular charge distributions of the genetically encoded amino acids (AA), one that builds on the previous determination of their equilibrium geometries and the demonstrated transferability of their common geometrical parameters. The properties of the charge distributions are characterized and given quantitative expression in terms of the bond and atomic properties determined within the quantum theory of atoms-in-molecules (QTAIM) that defines atoms and bonds in terms of the observable charge density. The properties so defined are demonstrated to be remarkably transferable, a reflection of the underlying transferability of the charge distributions of the main chain and other groups common to the AA. The use of the atomic properties in obtaining an understanding of the biological functions of the AA, whether free or bound in a polypeptide, is demonstrated by the excellent statistical correlations they yield with experimental physicochemical properties. A property of the AA side chains of particular importance is the charge separation index (CSI), a quantity previously defined as the sum of the magnitudes of the atomic charges and which measures the degree of separation of positive and negative charges in the side chain of interest. The CSI values provide a correlation with the measured free energies of transfer of capped side chain analogues, from the vapor phase to aqueous solution, yielding a linear regression equation with r2 = 0.94. The atomic volume is defined by the van der Waals isodensity surface and it, together with the CSI, which accounts for the electrostriction of the solvent, yield a linear regression (r2 = 0.98) with the measured partial molar volumes of the AAs. The changes in free energies of transfer from octanol to water upon interchanging 153 pairs of AAs and from cyclohexane to water upon interchanging 190 pairs of AAs, were modeled using only three calculated parameters (representing electrostatic and volume contributions) yielding linear regressions with r2 values of 0.78 and 0.89, respectively. These results are a prelude to the single-site mutation-induced changes in the stabilities of two typical proteins: ubiquitin and staphylococcal nuclease. Strong quadratic correlations (r2 approximately 0.9) were obtained between DeltaCSI upon mutation and each of the two terms DeltaDeltaH and TDeltaDeltaS taken from recent and accurate differential scanning calorimetry experiments on ubiquitin. When the two terms are summed to yield DeltaDeltaG, the quadratic terms nearly cancel, and the result is a simple linear fit between DeltaDeltaG and DeltaCSI with r2 = 0.88. As another example, the change in the stability of staphylococcal nuclease upon mutation has been fitted linearly (r2 = 0.83) to the sum of a DeltaCSI term and a term representing the change in the van der Waals volume of the side chains upon mutation. The suggested correlation of the polarity of the side chain with the second letter of the AA triplet genetic codon is given concrete expression in a classification of the side chains in terms of their CSI values and their group dipole moments. For example, all amino acids with a pyrimidine base as their second letter in mRNA possess side-chain CSI < or = 2.8 (with the exception of Cys), whereas all those with CSI > 2.8 possess an purine base. The article concludes with two proposals for measuring and predicting molecular complementarity: van der Waals complementarity expressed in terms of the van der Waals isodensity surface and Lewis complementarity expressed in terms of the local charge concentrations and depletions defined by the topology of the Laplacian of the electron density. A display of the experimentally accessible Laplacian distribution for a folded protein would offer a clear picture of the operation of the "stereochemical code" proposed as the determinant in the folding process. Copyright 2003 Wiley-Liss, Inc.

Stability analysis and stabilization strategies for linear supply chains

NASA Astrophysics Data System (ADS)

Nagatani, Takashi; Helbing, Dirk

2004-04-01

Due to delays in the adaptation of production or delivery rates, supply chains can be dynamically unstable with respect to perturbations in the consumption rate, which is known as “bull-whip effect”. Here, we study several conceivable production strategies to stabilize supply chains, which is expressed by different specifications of the management function controlling the production speed in dependence of the stock levels. In particular, we will investigate, whether the reaction to stock levels of other producers or suppliers has a stabilizing effect. We will also demonstrate that the anticipation of future stock levels can stabilize the supply system, given the forecast horizon τ is long enough. To show this, we derive linear stability conditions and carry out simulations for different control strategies. The results indicate that the linear stability analysis is a helpful tool for the judgement of the stabilization effect, although unexpected deviations can occur in the non-linear regime. There are also signs of phase transitions and chaotic behavior, but this remains to be investigated more thoroughly in the future.

Synthesis and antimalarial activity of new chloroquine analogues carrying a multifunctional linear side chain

PubMed Central

Iwaniuk, Daniel P.; Whetmore, Eric D.; Rosa, Nicholas; Ekoue-Kovi, Kekeli; Alumasa, John; de Dios, Angel C.; Roepe, Paul D.; Wolf, Christian

2009-01-01

We report the synthesis and in vitro antimalarial activity of several new 4-amino-and 4-alkoxy-7-chloroquinolines carrying a linear dibasic side chain. Many of these chloroquine analogues have submicromolar antimalarial activity versus HB3 (chloroquine sensitive) and Dd2 (chloroquine resistant strain of P. falciparum) and low resistance indices were obtained in most cases. Importantly, compounds 11–15 and 24 proved to be more potent against Dd2 than chloroquine. Branching of the side chain structure proved detrimental to the activity against the CQR strain. PMID:19703776

GRAVITY DATA OBTAINED DURING CHAIN CRUISE NO. 70.

DTIC Science & Technology

Profiles, tabulations, and charts are presented of principal gravity facts, free-air gravity anomalies, and simple Bouguer gravity anomalies obtained in the western North Atlantic Ocean during R/V CHAIN cruise 70. (Author)

Simple taper: Taper equations for the field forester

Treesearch

David R. Larsen

2017-01-01

"Simple taper" is set of linear equations that are based on stem taper rates; the intent is to provide taper equation functionality to field foresters. The equation parameters are two taper rates based on differences in diameter outside bark at two points on a tree. The simple taper equations are statistically equivalent to more complex equations. The linear...

Using Simple Linear Regression to Assess the Success of the Montreal Protocol in Reducing Atmospheric Chlorofluorocarbons

ERIC Educational Resources Information Center

Nelson, Dean

2009-01-01

Following the Guidelines for Assessment and Instruction in Statistics Education (GAISE) recommendation to use real data, an example is presented in which simple linear regression is used to evaluate the effect of the Montreal Protocol on atmospheric concentration of chlorofluorocarbons. This simple set of data, obtained from a public archive, can…

Non-Linear Dependence of the Height of a Chain Fountain on Drop Height

ERIC Educational Resources Information Center

Andrew, Y.; Kearns, F.; Mustafa, T.; Salih, R.; Ioratim-Uba, A.; Udall, I.; Usama, M.

2015-01-01

If the end of a long chain, which is contained in an elevated beaker, is dropped over the edge of the beaker and falls, it is observed that as the speed of the chain increases the chain rises to form a loop well above the top of the beaker. The name "chain fountain" has been applied to this phenomenon. In this study the dependence of the…

Prediction of Solution Properties of Flexible-Chain Polymers: A Computer Simulation Undergraduate Experiment

ERIC Educational Resources Information Center

de la Torre, Jose Garcia; Cifre, Jose G. Hernandez; Martinez, M. Carmen Lopez

2008-01-01

This paper describes a computational exercise at undergraduate level that demonstrates the employment of Monte Carlo simulation to study the conformational statistics of flexible polymer chains, and to predict solution properties. Three simple chain models, including excluded volume interactions, have been implemented in a public-domain computer…

Synthesis, Crystal Structure, and Magnetic Properties of the Linear-Chain Cobalt Oxide Sr 5Pb 3CoO 12

NASA Astrophysics Data System (ADS)

Yamaura, K.; Huang, Q.; Takayama-Muromachi, E.

2002-02-01

The novel spin-chain cobalt oxide Sr5Pb3CoO12 [Poverline6×2m, a=10.1093(2) Å and c=3.562 51(9) Å at 295 K] is reported. A polycrystalline sample of the compound was studied by neutron diffraction (at 6 and 295 K) and magnetic susceptibility measurements (5 to 390 K). The cobalt oxide was found to be analogous to the copper oxide Sr5Pb3CuO12, which is comprised of magnetic-linear chains at an interchain distance of 10 Å. Although the cobalt oxide chains (μeff of 3.64 μB per Co) are substantially antiferromagnetic (θW=-38.8 K), neither low-dimensional magnetism nor long-range ordering has been found; a local-structure disorder in the chains might have an impact on the magnetism. This compound is highly electrically insulating.

Reinforcement learning in supply chains.

PubMed

Valluri, Annapurna; North, Michael J; Macal, Charles M

2009-10-01

Effective management of supply chains creates value and can strategically position companies. In practice, human beings have been found to be both surprisingly successful and disappointingly inept at managing supply chains. The related fields of cognitive psychology and artificial intelligence have postulated a variety of potential mechanisms to explain this behavior. One of the leading candidates is reinforcement learning. This paper applies agent-based modeling to investigate the comparative behavioral consequences of three simple reinforcement learning algorithms in a multi-stage supply chain. For the first time, our findings show that the specific algorithm that is employed can have dramatic effects on the results obtained. Reinforcement learning is found to be valuable in multi-stage supply chains with several learning agents, as independent agents can learn to coordinate their behavior. However, learning in multi-stage supply chains using these postulated approaches from cognitive psychology and artificial intelligence take extremely long time periods to achieve stability which raises questions about their ability to explain behavior in real supply chains. The fact that it takes thousands of periods for agents to learn in this simple multi-agent setting provides new evidence that real world decision makers are unlikely to be using strict reinforcement learning in practice.

Posttranslational Modification of HOIP Blocks Toll-Like Receptor 4-Mediated Linear-Ubiquitin-Chain Formation

PubMed Central

Bowman, James; Rodgers, Mary A.; Shi, Mude; Amatya, Rina; Hostager, Bruce; Iwai, Kazuhiro; Gao, Shou-Jiang

2015-01-01

ABSTRACT Linear ubiquitination is an atypical posttranslational modification catalyzed by the linear-ubiquitin-chain assembly complex (LUBAC), containing HOIP, HOIL-1L, and Sharpin. LUBAC facilitates NF-κB activation and inflammation upon receptor stimulation by ligating linear ubiquitin chains to critical signaling molecules. Indeed, linear-ubiquitination-dependent signaling is essential to prevent pyogenic bacterial infections that can lead to death. While linear ubiquitination is essential for intracellular receptor signaling upon microbial infection, this response must be measured and stopped to avoid tissue damage and autoimmunity. While LUBAC is activated upon bacterial stimulation, the mechanisms regulating LUBAC activity in response to bacterial stimuli have remained elusive. We demonstrate that LUBAC activity itself is downregulated through ubiquitination, specifically, ubiquitination of the catalytic subunit HOIP at the carboxyl-terminal lysine 1056. Ubiquitination of Lys1056 dynamically altered HOIP conformation, resulting in the suppression of its catalytic activity. Consequently, HOIP Lys1056-to-Arg mutation led not only to persistent LUBAC activity but also to prolonged NF-κB activation induced by bacterial lipopolysaccharide-mediated Toll-like receptor 4 (TLR4) stimulation, whereas it showed no effect on NF-κB activation induced by CD40 stimulation. This study describes a novel posttranslational regulation of LUBAC-mediated linear ubiquitination that is critical for specifically directing TLR4-mediated NF-κB activation. PMID:26578682

A multichain polymer slip-spring model with fluctuating number of entanglements for linear and nonlinear rheology

DOE PAGES

Ramírez-Hernández, Abelardo; Peters, Brandon L.; Andreev, Marat; ...

2015-12-15

A theoretically informed entangled polymer simulation approach is presented for description of the linear and non-linear rheology of entangled polymer melts. The approach relies on a many-chain representation and introduces the topological effects that arise from the non-crossability of molecules through effective fluctuating interactions, mediated by slip-springs, between neighboring pairs of macromolecules. The total number of slip-springs is not preserved but, instead, it is controlled through a chemical potential that determines the average molecular weight between entanglements. The behavior of the model is discussed in the context of a recent theory for description of homogeneous materials, and its relevance ismore » established by comparing its predictions to experimental linear and non-linear rheology data for a series of well-characterized linear polyisoprene melts. Furthermore, the results are shown to be in quantitative agreement with experiment and suggest that the proposed formalism may also be used to describe the dynamics of inhomogeneous systems, such as composites and copolymers. Importantly, the fundamental connection made here between our many-chain model and the well-established, thermodynamically consistent single-chain mean-field models provides a path to systematic coarse-graining for prediction of polymer rheology in structurally homogeneous and heterogeneous materials.« less

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

Relationships for electron-vibrational coupling in conjugated π organic systems

NASA Astrophysics Data System (ADS)

O'Neill, L.; Lynch, P.; McNamara, M.; Byrne, H. J.

2005-06-01

A series of π conjugated systems were studied by absorption, photoluminescence and vibrational spectroscopy. As is common for these systems, a linear relationship between the positioning of the absorption and photoluminescence maxima plotted against inverse conjugation length is observed. The relationships are in good agreement with the simple particle in a box method, one of the earliest descriptions of the properties of one-dimensional organic molecules. In addition to the electronic transition energies, it was observed that the Stokes shift also exhibited a well-defined relationship with increasing conjugation length, implying a correlation between the electron-vibrational coupling and chain length. This correlation is further examined using Raman spectroscopy, whereby the integrated Raman scattering is seen to behave superlinearly with chain length. There is a clear indication that the vibrational activity and thus nonradiative decay processes are controllable through molecular structure. The correlations between the Stokes energies and the vibrational structure are also observed in a selection of PPV based polymers and a clear trend of increasing luminescence efficiency with decreasing vibrational activity and Stokes shift is observable. The implications of such structure property relationships in terms of materials design are discussed.

Free flowing and cohesive powders agitation in a cylindrical convective blender- kinetics experiments and Markov chain modelling

NASA Astrophysics Data System (ADS)

Legoix, Léonard; Milhé, Mathieu; Gatumel, Cendrine; Berthiaux, Henri

2017-06-01

An original methodology for studying powder flow in a cylindrical convective blender has been developed. A free-flowing and a cohesive powder were studied, at a fixed stirring speed, in rolling regime. For both powders, three apparent flow mechanisms were evidenced: convection in the volume swept by the blades, diffusion/shearing between the agitated zone and the stagnant one, as well as in the stagnant zone itself, and avalanches at the powder bed surface between agitated and stagnant zones. After defining six zones in the blender, tracing experiments were carried out by placing appropriate tracers in different starting zones and sampling the whole bed at different stirring times, which lead to mixing kinetics of the powders into themselves. A Markov chains model of the blender allowed the quantification of the three mechanisms respective magnitude by fitting the experimental data. This simple model has a good agreement with the free-flowing powder data, but is not able to represent well the observations for the cohesive powder. Bed consolidation should probably be taken into account for this kind of powders and thus a linear Markov model is not sufficient.

Chained versus Post-Stratification Equating in a Linear Context: An Evaluation Using Empirical Data. Research Report. ETS RR-10-06

ERIC Educational Resources Information Center

Puhan, Gautam

2010-01-01

This study used real data to construct testing conditions for comparing results of chained linear, Tucker, and Levine-observed score equatings. The comparisons were made under conditions where the new- and old-form samples were similar in ability and when they differed in ability. The length of the anchor test was also varied to enable examination…

Numerical methods in Markov chain modeling

NASA Technical Reports Server (NTRS)

Philippe, Bernard; Saad, Youcef; Stewart, William J.

1989-01-01

Several methods for computing stationary probability distributions of Markov chains are described and compared. The main linear algebra problem consists of computing an eigenvector of a sparse, usually nonsymmetric, matrix associated with a known eigenvalue. It can also be cast as a problem of solving a homogeneous singular linear system. Several methods based on combinations of Krylov subspace techniques are presented. The performance of these methods on some realistic problems are compared.

Analytical Studies on the Synchronization of a Network of Linearly-Coupled Simple Chaotic Systems

NASA Astrophysics Data System (ADS)

Sivaganesh, G.; Arulgnanam, A.; Seethalakshmi, A. N.; Selvaraj, S.

2018-05-01

We present explicit generalized analytical solutions for a network of linearly-coupled simple chaotic systems. Analytical solutions are obtained for the normalized state equations of a network of linearly-coupled systems driven by a common chaotic drive system. Two parameter bifurcation diagrams revealing the various hidden synchronization regions, such as complete, phase and phase-lag synchronization are identified using the analytical results. The synchronization dynamics and their stability are studied using phase portraits and the master stability function, respectively. Further, experimental results for linearly-coupled simple chaotic systems are presented to confirm the analytical results. The synchronization dynamics of a network of chaotic systems studied analytically is reported for the first time.

Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. I. An efficient and simple linear scaling local MP2 method that uses an intermediate basis of pair natural orbitals

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

Pinski, Peter; Riplinger, Christoph; Neese, Frank, E-mail: evaleev@vt.edu, E-mail: frank.neese@cec.mpg.de

2015-07-21

In this work, a systematic infrastructure is described that formalizes concepts implicit in previous work and greatly simplifies computer implementation of reduced-scaling electronic structure methods. The key concept is sparse representation of tensors using chains of sparse maps between two index sets. Sparse map representation can be viewed as a generalization of compressed sparse row, a common representation of a sparse matrix, to tensor data. By combining few elementary operations on sparse maps (inversion, chaining, intersection, etc.), complex algorithms can be developed, illustrated here by a linear-scaling transformation of three-center Coulomb integrals based on our compact code library that implementsmore » sparse maps and operations on them. The sparsity of the three-center integrals arises from spatial locality of the basis functions and domain density fitting approximation. A novel feature of our approach is the use of differential overlap integrals computed in linear-scaling fashion for screening products of basis functions. Finally, a robust linear scaling domain based local pair natural orbital second-order Möller-Plesset (DLPNO-MP2) method is described based on the sparse map infrastructure that only depends on a minimal number of cutoff parameters that can be systematically tightened to approach 100% of the canonical MP2 correlation energy. With default truncation thresholds, DLPNO-MP2 recovers more than 99.9% of the canonical resolution of the identity MP2 (RI-MP2) energy while still showing a very early crossover with respect to the computational effort. Based on extensive benchmark calculations, relative energies are reproduced with an error of typically <0.2 kcal/mol. The efficiency of the local MP2 (LMP2) method can be drastically improved by carrying out the LMP2 iterations in a basis of pair natural orbitals. While the present work focuses on local electron correlation, it is of much broader applicability to computation with sparse tensors in quantum chemistry and beyond.« less

Non-Linear Dynamics of Saturn's Rings

NASA Astrophysics Data System (ADS)

Esposito, L. W.

2015-12-01

Non-linear processes can explain why Saturn's rings are so active and dynamic. Some of this non-linearity is captured in a simple Predator-Prey Model: Periodic forcing from the moon causes streamline crowding; This damps the relative velocity, and allows aggregates to grow. About a quarter phase later, the aggregates stir the system to higher relative velocity and the limit cycle repeats each orbit, with relative velocity ranging from nearly zero to a multiple of the orbit average: 2-10x is possible. Summary of Halo Results: A predator-prey model for ring dynamics produces transient structures like 'straw' that can explain the halo structure and spectroscopy: Cyclic velocity changes cause perturbed regions to reach higher collision speeds at some orbital phases, which preferentially removes small regolith particles; Surrounding particles diffuse back too slowly to erase the effect: this gives the halo morphology; This requires energetic collisions (v ≈ 10m/sec, with throw distances about 200km, implying objects of scale R ≈ 20km); We propose 'straw', as observed ny Cassini cameras. Transform to Duffing Eqn : With the coordinate transformation, z = M2/3, the Predator-Prey equations can be combined to form a single second-order differential equation with harmonic resonance forcing. Ring dynamics and history implications: Moon-triggered clumping at perturbed regions in Saturn's rings creates both high velocity dispersion and large aggregates at these distances, explaining both small and large particles observed there. This confirms the triple architecture of ring particles: a broad size distribution of particles; these aggregate into temporary rubble piles; coated by a regolith of dust. We calculate the stationary size distribution using a cell-to-cell mapping procedure that converts the phase-plane trajectories to a Markov chain. Approximating the Markov chain as an asymmetric random walk with reflecting boundaries allows us to determine the power law index from results of numerical simulations in the tidal environment surrounding Saturn. Aggregates can explain many dynamic aspects of the rings and can renew rings by shielding and recycling the material within them, depending on how long the mass is sequestered. We can ask: Are Saturn's rings a chaotic non-linear driven system?

Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. I. An efficient and simple linear scaling local MP2 method that uses an intermediate basis of pair natural orbitals.

PubMed

Pinski, Peter; Riplinger, Christoph; Valeev, Edward F; Neese, Frank

2015-07-21

In this work, a systematic infrastructure is described that formalizes concepts implicit in previous work and greatly simplifies computer implementation of reduced-scaling electronic structure methods. The key concept is sparse representation of tensors using chains of sparse maps between two index sets. Sparse map representation can be viewed as a generalization of compressed sparse row, a common representation of a sparse matrix, to tensor data. By combining few elementary operations on sparse maps (inversion, chaining, intersection, etc.), complex algorithms can be developed, illustrated here by a linear-scaling transformation of three-center Coulomb integrals based on our compact code library that implements sparse maps and operations on them. The sparsity of the three-center integrals arises from spatial locality of the basis functions and domain density fitting approximation. A novel feature of our approach is the use of differential overlap integrals computed in linear-scaling fashion for screening products of basis functions. Finally, a robust linear scaling domain based local pair natural orbital second-order Möller-Plesset (DLPNO-MP2) method is described based on the sparse map infrastructure that only depends on a minimal number of cutoff parameters that can be systematically tightened to approach 100% of the canonical MP2 correlation energy. With default truncation thresholds, DLPNO-MP2 recovers more than 99.9% of the canonical resolution of the identity MP2 (RI-MP2) energy while still showing a very early crossover with respect to the computational effort. Based on extensive benchmark calculations, relative energies are reproduced with an error of typically <0.2 kcal/mol. The efficiency of the local MP2 (LMP2) method can be drastically improved by carrying out the LMP2 iterations in a basis of pair natural orbitals. While the present work focuses on local electron correlation, it is of much broader applicability to computation with sparse tensors in quantum chemistry and beyond.

Cuticular hydrocarbons as a tool for the identification of insect species: Puparial cases from Sarcophagidae

PubMed Central

Braga, Marina Vianna; Pinto, Zeneida Teixeira; de Carvalho Queiroz, Margareth Maria; Matsumoto, Nana; Blomquist, Gary James

2013-01-01

The external surface of all insects is covered by a species-specific complex mixture of highly stable, very long chain cuticular hydrocarbons (CHCs). Gas chromatography coupled to mass spectrometry was used to identify CHCs from four species of Sarcophagidae, Peckia (Peckia) chrysostoma, Peckia (Pattonella) intermutans, Sarcophaga (Liopygia) ruficornis and Sarcodexia lambens. The identified CHCs were mostly a mixture of n-alkanes, monomethylalkanes and dimethylalkanes with linear chain lengths varying from 23 to 33 carbons. Only two alkenes were found in all four species. S. lambens had a composition of CHCs with linear chain lengths varying from C23 to C33, while the other three species linear chain lengths from 24 to 31 carbons. n-Heptacosane, n-nonacosane and 3-methylnonacosane, n-triacontane and n-hentriacontane occurred in all four species. The results show that these hydrocarbon profiles may be used for the taxonomic differentiation of insect species and are a useful additional tool for taxonomic classification, especially when only parts of the insect specimen are available. PMID:23932943

Biodiesel production from triolein and short chain alcohols through biocatalysis.

PubMed

Salis, Andrea; Pinna, Marcella; Monduzzi, Maura; Solinas, Vincenzo

2005-09-29

Oleic acid alkyl esters (biodiesel) were synthesised by biocatalysis in solvent-free conditions. Different commercial immobilised lipases, namely Candida antarctica B, Rizhomucor miehei, and Pseudomonas cepacia, were tested towards the reaction between triolein and butanol to produce butyl oleate. Pseudomonas cepacia lipase resulted to be the most active enzyme reaching 100% of conversion after 6h. Different operative conditions such as reaction temperature, water activity, and reagent stoichiometric ratio were investigated and optimised. These conditions were then used to investigate the effect of linear and branched short chain alcohols. Methanol and 2-butanol were the worst alcohols: the former, probably, due to its low miscibility with the oil and the latter because secondary alcohols usually are less reactive than primary alcohols. Conversely, linear and branched primary alcohols with short alkyl chains (C(2)--C(4)) showed high reaction rate and conversion. A mixture of linear and branched short chain alcohols that mimics the residual of ethanol distillation (fusel oil) was successfully used for oleic acid ester synthesis. These compounds are important in biodiesel mixtures since they improve low temperature properties.

Correlation and simple linear regression.

PubMed

Eberly, Lynn E

2007-01-01

This chapter highlights important steps in using correlation and simple linear regression to address scientific questions about the association of two continuous variables with each other. These steps include estimation and inference, assessing model fit, the connection between regression and ANOVA, and study design. Examples in microbiology are used throughout. This chapter provides a framework that is helpful in understanding more complex statistical techniques, such as multiple linear regression, linear mixed effects models, logistic regression, and proportional hazards regression.

High sensitivity of positrons to oxygen vacancies and to copper-oxygen chain disorder in YBa2Cu3O(7-x)

NASA Astrophysics Data System (ADS)

von Stetten, E. C.; Berko, S.; Li, X. S.; Lee, R. R.; Brynestad, J.

1988-05-01

Temperature-dependent positron-electron momentum densities have been studied by two-dimensional angular correlation of annihilation radiation from 10 to 320 K in YBa2Cu3O(7-x) samples. The positron ground-state charge density, computed by the linearized augmented-plane-wave method, indicates that in YBa2Cu3O7 delocalized positrons sample preferentially the linear copper-oxygen chains. Positron localization due to disorder in these chains is invoked to explain the striking differences observed between superconducting (x = about 0.02) and nonsuperconducting (x = about 0.70) samples.

Estimating linear temporal trends from aggregated environmental monitoring data

USGS Publications Warehouse

Erickson, Richard A.; Gray, Brian R.; Eager, Eric A.

2017-01-01

Trend estimates are often used as part of environmental monitoring programs. These trends inform managers (e.g., are desired species increasing or undesired species decreasing?). Data collected from environmental monitoring programs is often aggregated (i.e., averaged), which confounds sampling and process variation. State-space models allow sampling variation and process variations to be separated. We used simulated time-series to compare linear trend estimations from three state-space models, a simple linear regression model, and an auto-regressive model. We also compared the performance of these five models to estimate trends from a long term monitoring program. We specifically estimated trends for two species of fish and four species of aquatic vegetation from the Upper Mississippi River system. We found that the simple linear regression had the best performance of all the given models because it was best able to recover parameters and had consistent numerical convergence. Conversely, the simple linear regression did the worst job estimating populations in a given year. The state-space models did not estimate trends well, but estimated population sizes best when the models converged. We found that a simple linear regression performed better than more complex autoregression and state-space models when used to analyze aggregated environmental monitoring data.

Rare-event statistics and modular invariance

NASA Astrophysics Data System (ADS)

Nechaev, S. K.; Polovnikov, K.

2018-01-01

Simple geometric arguments based on constructing the Euclid orchard are presented, which explain the equivalence of various types of distributions that result from rare-event statistics. In particular, the spectral density of the exponentially weighted ensemble of linear polymer chains is examined for its number-theoretic properties. It can be shown that the eigenvalue statistics of the corresponding adjacency matrices in the sparse regime show a peculiar hierarchical structure and are described by the popcorn (Thomae) function discontinuous in the dense set of rational numbers. Moreover, the spectral edge density distribution exhibits Lifshitz tails, reminiscent of 1D Anderson localization. Finally, a continuous approximation for the popcorn function is suggested based on the Dedekind η-function, and the hierarchical ultrametric structure of the popcorn-like distributions is demonstrated to be related to hidden SL(2,Z) modular symmetry.

Comparison of estimation methods for creating small area rates of acute myocardial infarction among Medicare beneficiaries in California.

PubMed

Yasaitis, Laura C; Arcaya, Mariana C; Subramanian, S V

2015-09-01

Creating local population health measures from administrative data would be useful for health policy and public health monitoring purposes. While a wide range of options--from simple spatial smoothers to model-based methods--for estimating such rates exists, there are relatively few side-by-side comparisons, especially not with real-world data. In this paper, we compare methods for creating local estimates of acute myocardial infarction rates from Medicare claims data. A Bayesian Monte Carlo Markov Chain estimator that incorporated spatial and local random effects performed best, followed by a method-of-moments spatial Empirical Bayes estimator. As the former is more complicated and time-consuming, spatial linear Empirical Bayes methods may represent a good alternative for non-specialist investigators. Copyright © 2015 Elsevier Ltd. All rights reserved.

Spectrophotometric determination of protein concentration.

PubMed

Grimsley, Gerald R; Pace, C Nick

2004-11-01

The concentration of a purified protein in solution is most conveniently and accurately measured using absorbance spectroscopy. The absorbance, A, is a linear function of the molar concentration, C, according to the Beer-Lambert law: A = epsilon x l x c, where e is the molar absorption coefficient and l is the cell path length. This unit provides protocols for calculation of epsilon for a folded or unfolded protein, making use of the average epsilon values for the three contributing chromophores in proteins (the side chains of Trp, Tyr, and Cys). A basic protocol describes how to measure the concentration of a protein using the calculated epsilon and the Beer-Lambert law. A sensitive method is provided for measuring the concentration of proteins that contain few if any tryptophan or tyrosine residues, and a simple method is provided for estimating total protein concentration in crude extracts.

Effect of Molecular Architecture on Polymer Melt Surface Dynamics

NASA Astrophysics Data System (ADS)

Foster, Mark

The dynamics of the thermally stimulated surface height fluctuations in a polymer melt dictate wetting, adhesion, and tribology at that surface. These surface fluctuations can be profoundly altered by tethering of the chains. One type of tethering is the tethering of one part of a molecule to another part of the same molecule. This tethering is found in both long chain branched polymers and in macrocycles. We have studied the surface fluctuations with X-ray Photon Correlation Spectroscopy for melts of well-defined, anionically polymerized polystyrenes of various architectures, including linear, 6 arm star, pom-pom, comb and cyclic architectures. For linear chains, the variation of surface relaxation time with in-plane scattering vector can be fit using a hydrodynamic continuum theory (HCT) of thermally stimulated capillary waves that knows nothing of the chain architecture. Assuming the theory is applicable, apparent viscosities of the films may then be inferred from the XPCS data. For unentangled linear chains, the viscosity inferred from XPCS data in this manner is the same as that measured by conventional bulk rheometry. The HCT does a reasonable job of describing the variation of relaxation time with scattering vector for long branched chains also, but only if a viscosity much larger than that of the bulk is assumed. The discrepancy between the viscosity inferred from surface relaxation times using the HCT and that derived from conventional rheometry grows larger as the bulk Tg is approached and is different for each long chain branched architecture. However, for densely branched combs and cyclic chains different behaviors are found. Acknowledgement: Thanks to NSF (CBET 0730692) and the Advanced Photon Source, supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Science, under Contract No. W-31-109-ENG-38.

Energy level alignment of self-assembled linear chains of benzenediamine on Au(111) from first principles

DOE PAGES

Li, Guo; Rangel, Tonatiuh; Liu, Zhen -Fei; ...

2016-03-24

Using density functional theory (DFT) with van der Waals functionals, we calculate the adsorption energetics and geometry of benzenediamine (BDA) molecules on Au(111) surfaces. Our results demonstrate that the reported self-assembled linear chain structure of BDA, stabilized via hydrogen bonds between amine groups, is energetically favored over previously-studied monomeric phases. Moreover, using a model based on many-body perturbation theory within the GW approximation, we obtain approximate self-energy corrections to the DFT highest occupied molecular orbital (HOMO) energy associated with BDA adsorbate phases. As a result, we find that, independent of coverage, the HOMO energy of the linear chain phase ismore » lower relative to the Fermi energy than that of the monomer phase, and in good agreement with values measured with ultraviolet photoelectron spectroscopy and X-ray photoelectron spectroscopy.« less

Energy level alignment of self-assembled linear chains of benzenediamine on Au(111) from first principles

NASA Astrophysics Data System (ADS)

Li, Guo; Rangel, Tonatiuh; Liu, Zhen-Fei; Cooper, Valentino R.; Neaton, Jeffrey B.

2016-03-01

Using density functional theory (DFT) with a van der Waals density functional, we calculate the adsorption energetics and geometry of benzenediamine (BDA) molecules on Au(111) surfaces. Our results demonstrate that the reported self-assembled linear chain structure of BDA, stabilized via hydrogen bonds between amine groups, is energetically favored over previously studied monomeric phases. Moreover, using a model, which includes nonlocal polarization effects from the substrate and the neighboring molecules and incorporates many-body perturbation theory calculations within the GW approximation, we obtain approximate self-energy corrections to the DFT highest occupied molecular orbital (HOMO) energy associated with BDA adsorbate phases. We find that, independent of coverage, the HOMO energy of the linear chain phase is lower relative to the Fermi energy than that of the monomer phase, and in good agreement with values measured with ultraviolet photoelectron spectroscopy and x-ray photoelectron spectroscopy.

Searching for a 4 α linear-chain structure in excited states of 16O with covariant density functional theory

NASA Astrophysics Data System (ADS)

Yao, J. M.; Itagaki, N.; Meng, J.

2014-11-01

A study of the 4 α linear-chain structure in high-lying collective excitation states of 16O with covariant density functional theory is presented. The low-spin states are obtained by configuration mixing of particle-number and angular-momentum projected quadrupole deformed mean-field states with the generator coordinate method. The high-spin states are determined by cranking calculations. These two calculations are based on the same energy density functional PC-PK1. We have found a rotational band at low spin with the dominant intrinsic configuration considered to be the one whereby 4 α clusters stay along a common axis. The strongly deformed rod shape also appears in the high-spin region with the angular momentum 13 ℏ to18 ℏ ; however, whether the state is a pure 4 α linear chain is less obvious than for the low-spin states.

The Linear ubiquitin chain assembly complex acts as a liver tumor suppressor and inhibits hepatocyte apoptosis and hepatitis.

PubMed

Shimizu, Yutaka; Peltzer, Nieves; Sevko, Alexandra; Lafont, Elodie; Sarr, Aida; Draberova, Helena; Walczak, Henning

2017-06-01

Linear ubiquitination is a key posttranslational modification that regulates immune signaling and cell death pathways, notably tumor necrosis factor receptor 1 (TNFR1) signaling. The only known enzyme complex capable of forming linear ubiquitin chains under native conditions to date is the linear ubiquitin chain assembly complex, of which the catalytic core component is heme-oxidized iron regulatory protein 2 ubiquitin ligase-1-interacting protein (HOIP). To understand the underlying mechanisms of maintenance of liver homeostasis and the role of linear ubiquitination specifically in liver parenchymal cells, we investigated the physiological role of HOIP in the liver parenchyma. To do so, we created mice harboring liver parenchymal cell-specific deletion of HOIP (Hoip Δhep mice) by crossing Hoip-floxed mice with albumin-Cre mice. HOIP deficiency in liver parenchymal cells triggered tumorigenesis at 18 months of age preceded by spontaneous hepatocyte apoptosis and liver inflammation within the first month of life. In line with the emergence of inflammation, Hoip Δhep mice displayed enhanced liver regeneration and DNA damage. In addition, consistent with increased apoptosis, HOIP-deficient hepatocytes showed enhanced caspase activation and endogenous formation of a death-inducing signaling complex which activated caspase-8. Unexpectedly, exacerbated caspase activation and apoptosis were not dependent on TNFR1, whereas ensuing liver inflammation and tumorigenesis were promoted by TNFR1 signaling. The linear ubiquitin chain assembly complex serves as a previously undescribed tumor suppressor in the liver, restraining TNFR1-independent apoptosis in hepatocytes which, in its absence, is causative of TNFR1-mediated inflammation, resulting in hepatocarcinogenesis. (Hepatology 2017;65:1963-1978). © 2017 The Authors. Hepatology published by Wiley Periodicals, Inc., on behalf of the American Association for the Study of Liver Diseases.

Efficient dynamic simulation for multiple chain robotic mechanisms

NASA Technical Reports Server (NTRS)

Lilly, Kathryn W.; Orin, David E.

1989-01-01

An efficient O(mN) algorithm for dynamic simulation of simple closed-chain robotic mechanisms is presented, where m is the number of chains, and N is the number of degrees of freedom for each chain. It is based on computation of the operational space inertia matrix (6 x 6) for each chain as seen by the body, load, or object. Also, computation of the chain dynamics, when opened at one end, is required, and the most efficient algorithm is used for this purpose. Parallel implementation of the dynamics for each chain results in an O(N) + O(log sub 2 m+1) algorithm.

Simple Test Functions in Meshless Local Petrov-Galerkin Methods

NASA Technical Reports Server (NTRS)

Raju, Ivatury S.

2016-01-01

Two meshless local Petrov-Galerkin (MLPG) methods based on two different trial functions but that use a simple linear test function were developed for beam and column problems. These methods used generalized moving least squares (GMLS) and radial basis (RB) interpolation functions as trial functions. These two methods were tested on various patch test problems. Both methods passed the patch tests successfully. Then the methods were applied to various beam vibration problems and problems involving Euler and Beck's columns. Both methods yielded accurate solutions for all problems studied. The simple linear test function offers considerable savings in computing efforts as the domain integrals involved in the weak form are avoided. The two methods based on this simple linear test function method produced accurate results for frequencies and buckling loads. Of the two methods studied, the method with radial basis trial functions is very attractive as the method is simple, accurate, and robust.

Glass transition of polymers in bulk, confined geometries, and near interfaces

NASA Astrophysics Data System (ADS)

Napolitano, Simone; Glynos, Emmanouil; Tito, Nicholas B.

2017-03-01

When cooled or pressurized, polymer melts exhibit a tremendous reduction in molecular mobility. If the process is performed at a constant rate, the structural relaxation time of the liquid eventually exceeds the time allowed for equilibration. This brings the system out of equilibrium, and the liquid is operationally defined as a glass—a solid lacking long-range order. Despite almost 100 years of research on the (liquid/)glass transition, it is not yet clear which molecular mechanisms are responsible for the unique slow-down in molecular dynamics. In this review, we first introduce the reader to experimental methodologies, theories, and simulations of glassy polymer dynamics and vitrification. We then analyse the impact of connectivity, structure, and chain environment on molecular motion at the length scale of a few monomers, as well as how macromolecular architecture affects the glass transition of non-linear polymers. We then discuss a revised picture of nanoconfinement, going beyond a simple picture based on interfacial interactions and surface/volume ratio. Analysis of a large body of experimental evidence, results from molecular simulations, and predictions from theory supports, instead, a more complex framework where other parameters are relevant. We focus discussion specifically on local order, free volume, irreversible chain adsorption, the Debye-Waller factor of confined and confining media, chain rigidity, and the absolute value of the vitrification temperature. We end by highlighting the molecular origin of distributions in relaxation times and glass transition temperatures which exceed, by far, the size of a chain. Fast relaxation modes, almost universally present at the free surface between polymer and air, are also remarked upon. These modes relax at rates far larger than those characteristic of glassy dynamics in bulk. We speculate on how these may be a signature of unique relaxation processes occurring in confined or heterogeneous polymeric systems.

Degradation of 4-n-nonylphenol under nitrate reducing conditions

PubMed Central

Viñas, Marc; Grotenhuis, Tim; Rijnaarts, Huub H. M.; Langenhoff, Alette A. M.

2010-01-01

Nonylphenol (NP) is an endocrine disruptor present as a pollutant in river sediment. Biodegradation of NP can reduce its toxicological risk. As sediments are mainly anaerobic, degradation of linear (4-n-NP) and branched nonylphenol (tNP) was studied under methanogenic, sulphate reducing and denitrifying conditions in NP polluted river sediment. Anaerobic bioconversion was observed only for linear NP under denitrifying conditions. The microbial population involved herein was further studied by enrichment and molecular characterization. The largest change in diversity was observed between the enrichments of the third and fourth generation, and further enrichment did not affect the diversity. This implies that different microorganisms are involved in the degradation of 4-n-NP in the sediment. The major degrading bacteria were most closely related to denitrifying hexadecane degraders and linear alkyl benzene sulphonate (LAS) degraders. The molecular structures of alkanes and LAS are similar to the linear chain of 4-n-NP, this might indicate that the biodegradation of linear NP under denitrifying conditions starts at the nonyl chain. Initiation of anaerobic NP degradation was further tested using phenol as a structure analogue. Phenol was chosen instead of an aliphatic analogue, because phenol is the common structure present in all NP isomers while the structure of the aliphatic chain differs per isomer. Phenol was degraded in all cases, but did not affect the linear NP degradation under denitrifying conditions and did not initiate the degradation of tNP and linear NP under the other tested conditions. PMID:20640878

Circuit topology of self-interacting chains: implications for folding and unfolding dynamics.

PubMed

Mugler, Andrew; Tans, Sander J; Mashaghi, Alireza

2014-11-07

Understanding the relationship between molecular structure and folding is a central problem in disciplines ranging from biology to polymer physics and DNA origami. Topology can be a powerful tool to address this question. For a folded linear chain, the arrangement of intra-chain contacts is a topological property because rearranging the contacts requires discontinuous deformations. Conversely, the topology is preserved when continuously stretching the chain while maintaining the contact arrangement. Here we investigate how the folding and unfolding of linear chains with binary contacts is guided by the topology of contact arrangements. We formalize the topology by describing the relations between any two contacts in the structure, which for a linear chain can either be in parallel, in series, or crossing each other. We show that even when other determinants of folding rate such as contact order and size are kept constant, this 'circuit' topology determines folding kinetics. In particular, we find that the folding rate increases with the fractions of parallel and crossed relations. Moreover, we show how circuit topology constrains the conformational phase space explored during folding and unfolding: the number of forbidden unfolding transitions is found to increase with the fraction of parallel relations and to decrease with the fraction of series relations. Finally, we find that circuit topology influences whether distinct intermediate states are present, with crossed contacts being the key factor. The approach presented here can be more generally applied to questions on molecular dynamics, evolutionary biology, molecular engineering, and single-molecule biophysics.

Application of Nearly Linear Solvers to Electric Power System Computation

NASA Astrophysics Data System (ADS)

Grant, Lisa L.

To meet the future needs of the electric power system, improvements need to be made in the areas of power system algorithms, simulation, and modeling, specifically to achieve a time frame that is useful to industry. If power system time-domain simulations could run in real-time, then system operators would have situational awareness to implement online control and avoid cascading failures, significantly improving power system reliability. Several power system applications rely on the solution of a very large linear system. As the demands on power systems continue to grow, there is a greater computational complexity involved in solving these large linear systems within reasonable time. This project expands on the current work in fast linear solvers, developed for solving symmetric and diagonally dominant linear systems, in order to produce power system specific methods that can be solved in nearly-linear run times. The work explores a new theoretical method that is based on ideas in graph theory and combinatorics. The technique builds a chain of progressively smaller approximate systems with preconditioners based on the system's low stretch spanning tree. The method is compared to traditional linear solvers and shown to reduce the time and iterations required for an accurate solution, especially as the system size increases. A simulation validation is performed, comparing the solution capabilities of the chain method to LU factorization, which is the standard linear solver for power flow. The chain method was successfully demonstrated to produce accurate solutions for power flow simulation on a number of IEEE test cases, and a discussion on how to further improve the method's speed and accuracy is included.

Combinations of Aromatic and Aliphatic Radiolysis.

PubMed

LaVerne, Jay A; Dowling-Medley, Jennifer

2015-10-08

The production of H(2) in the radiolysis of benzene, methylbenzene (toluene), ethylbenzene, butylbenzene, and hexylbenzene with γ-rays, 2-10 MeV protons, 5-20 MeV helium ions, and 10-30 MeV carbon ions is used as a probe of the overall radiation sensitivity and to determine the relative contributions of aromatic and aliphatic entities in mixed hydrocarbons. The addition of an aliphatic side chain with progressively from one to six carbon lengths to benzene increases the H(2) yield with γ-rays, but the yield seems to reach a plateau far below that found from a simple aliphatic such as cyclohexane. There is a large increase in H(2) with LET (linear energy transfer) for all of the substituted benzenes, which indicates that the main process for H(2) formation is a second-order process and dominated by the aromatic entity. The addition of a small amount of benzene to cyclohexane can lower the H(2) yield from the value expected from a simple mixture law. A 50:50% volume mixture of benzene-cyclohexane has essentially the same H(2) yield as cyclohexylbenzene at a wide variation in LET, suggesting that intermolecular energy transfer is as efficient as intramolecular energy transfer.

Stick-slip nanofriction in cold-ion traps

NASA Astrophysics Data System (ADS)

Mandelli, Davide; Vanossi, Andrea; Tosatti, Erio

2013-03-01

Trapped cold ions are known to form linear or planar zigzag chains, helices or clusters depending on trapping conditions. They may be forced to slide over a laser induced corrugated potential, a mimick of sliding friction. We present MD simulations of an incommensurate 101 ions chain sliding subject to an external electric field. As expected with increasing corrugation, we observe the transition from a smooth-sliding, highly lubric regime to a strongly dissipative stick-slip regime. Owing to inhomogeneity the dynamics shows features reminiscent of macroscopic frictional behaviors. While the chain extremities are pinned, the incommensurate central part is initially free to slide. The onset of global sliding is preceded by precursor events consisting of partial slips of chain portions further from the center. We also look for frictional anomalies expected for the chain sliding across the linear-zigzag structural phase transition. Although the chain is too short for a proper critical behavior, the sliding friction displays a frank rise near the transition, due to opening of a new dissipative channel via excitations of transverse modes. Research partly sponsored by Sinergia Project CRSII2 136287/1.

Exploring Alkyl Chains in Benzobisthiazole-Naphthobisthiadiazole Polymers: Impact on Solar-Cell Performance, Crystalline Structures, and Optoelectronics.

PubMed

Al-Naamani, Eman; Gopal, Anesh; Ide, Marina; Osaka, Itaru; Saeki, Akinori

2017-11-01

The shapes and lengths of the alkyl chains of conjugated polymers greatly affect the efficiencies of organic photovoltaic devices. This often results in a trade-off between solubility and self-organizing behavior; however, each material has specific optimal chains. Here we report on the effect of alkyl side chains on the film morphologies, crystallinities, and optoelectronic properties of new benzobisthiazole-naphthobisthiadiazole (PBBT-NTz) polymers. The power conversion efficiencies (PCEs) of linear-branched and all-branched polymers range from 2.5% to 6.6%; the variations in these PCEs are investigated by atomic force microscopy, two-dimensional X-ray diffraction (2D-GIXRD), and transient photoconductivity techniques. The best-performing linear-branched polymer, bearing dodecyl and decyltetradecyl chains (C12-DT), exhibits nanometer-scale fibers along with the highest crystallinity, comprising predominant edge-on and partial face-on orientations. This morphology leads to the highest photoconductivity and the longest carrier lifetime. These results highlight the importance of long alkyl chains for inducing intermolecular stacking, which is in contrast to observations made for analogous previously reported polymers.

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.

Single-polymer dynamics under constraints: scaling theory and computer experiment.

PubMed

Milchev, Andrey

2011-03-16

The relaxation, diffusion and translocation dynamics of single linear polymer chains in confinement is briefly reviewed with emphasis on the comparison between theoretical scaling predictions and observations from experiment or, most frequently, from computer simulations. Besides cylindrical, spherical and slit-like constraints, related problems such as the chain dynamics in a random medium and the translocation dynamics through a nanopore are also considered. Another particular kind of confinement is imposed by polymer adsorption on attractive surfaces or selective interfaces--a short overview of single-chain dynamics is also contained in this survey. While both theory and numerical experiments consider predominantly coarse-grained models of self-avoiding linear chain molecules with typically Rouse dynamics, we also note some recent studies which examine the impact of hydrodynamic interactions on polymer dynamics in confinement. In all of the aforementioned cases we focus mainly on the consequences of imposed geometric restrictions on single-chain dynamics and try to check our degree of understanding by assessing the agreement between theoretical predictions and observations.

Small Angle Neutron Scattering Observation of Chain Retraction after a Large Step Deformation

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

Blanchard, A.; Heinrich, M.; Pyckhout-Hintzen, W.

The process of retraction in entangled linear chains after a fast nonlinear stretch was detected from time-resolved but quenched small angle neutron scattering (SANS) experiments on long, well-entangled polyisoprene chains. The statically obtained SANS data cover the relevant time regime for retraction, and they provide a direct, microscopic verification of this nonlinear process as predicted by the tube model. Clear, quantitative agreement is found with recent theories of contour length fluctuations and convective constraint release, using parameters obtained mainly from linear rheology. The theory captures the full range of scattering vectors once the crossover to fluctuations on length scales belowmore » the tube diameter is accounted for.« less

A correlated ab initio study of linear carbon-chain radicals CnH (n = 2-7)

NASA Technical Reports Server (NTRS)

Woon, D. E.; Loew, G. H. (Principal Investigator)

1995-01-01

Linear carbon-chain radicals CnH for n = 2-7 have been studied with correlation consistent valence and core-valence basis sets and the coupled cluster method RCCSD(T). Equilibrium structures, rotational constants, and dipole moments are reported and compared with available experimental data. The ground state of the even-n series changes from 2 sigma+ to 2 pi as the chain is extended. For C4H, the 2 sigma+ state was found to lie only 72 cm-1 below the 2 pi state in the estimated complete basis set limit for valence correlation. The C2H- and C3H- anions have also been characterized.

Morse Code, Scrabble, and the Alphabet

ERIC Educational Resources Information Center

Richardson, Mary; Gabrosek, John; Reischman, Diann; Curtiss, Phyliss

2004-01-01

In this paper we describe an interactive activity that illustrates simple linear regression. Students collect data and analyze it using simple linear regression techniques taught in an introductory applied statistics course. The activity is extended to illustrate checks for regression assumptions and regression diagnostics taught in an…

A simple protocol for combinatorial cyclic depsipeptide libraries sequencing by matrix-assisted laser desorption/ionisation mass spectrometry.

PubMed

Gurevich-Messina, Juan M; Giudicessi, Silvana L; Martínez-Ceron, María C; Acosta, Gerardo; Erra-Balsells, Rosa; Cascone, Osvaldo; Albericio, Fernando; Camperi, Silvia A

2015-01-01

Short cyclic peptides have a great interest in therapeutic, diagnostic and affinity chromatography applications. The screening of 'one-bead-one-peptide' combinatorial libraries combined with mass spectrometry (MS) is an excellent tool to find peptides with affinity for any target protein. The fragmentation patterns of cyclic peptides are quite more complex than those of their linear counterparts, and the elucidation of the resulting tandem mass spectra is rather more difficult. Here, we propose a simple protocol for combinatorial cyclic libraries synthesis and ring opening before MS analysis. In this strategy, 4-hydroxymethylbenzoic acid, which forms a benzyl ester with the first amino acid, was used as the linker. A glycolamidic ester group was incorporated after the combinatorial positions by adding glycolic acid. The library synthesis protocol consisted in the following: (i) incorporation of Fmoc-Asp[2-phenylisopropyl (OPp)]-OH to Ala-Gly-oxymethylbenzamide-ChemMatrix, (ii) synthesis of the combinatorial library, (iii) assembly of a glycolic acid, (iv) couple of an Ala residue in the N-terminal, (v) removal of OPp, (vi) peptide cyclisation through side chain Asp and N-Ala amino terminus and (vii) removal of side chain protecting groups. In order to simultaneously open the ring and release each peptide, benzyl and glycolamidic esters were cleaved with ammonia. Peptide sequences could be deduced from the tandem mass spectra of each single bead evaluated. The strategy herein proposed is suitable for the preparation of one-bead-one-cyclic depsipeptide libraries that can be easily open for its sequencing by matrix-assisted laser desorption/ionisation MS. It employs techniques and reagents frequently used in a broad range of laboratories without special expertise in organic synthesis. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.

Theoretical study of the self-assembly of Janus Bottlebrush Polymers from A-Branch-B Diblock Macromonomers

NASA Astrophysics Data System (ADS)

Gadelrab, Karim; Alexander-Katz, Alfredo; LaboratoryTheoretical Soft Materials Team

The self-assembly of block copolymers BCP has provided an impressive control over the nanoscale structure of soft matter. While the main focus of the research in the field has been directed towards simple linear diblocks, the development of advanced polymer architecture provided improved performance and access to new structures. In particular, bottlebrush BCPs (BBCPs) have interesting characteristics due to their dense functionality, high molecular weight, low levels of entanglement, and tendency to efficiently undergo rapid bulk phase separation. In this work, we are interested in theoretically studying the self-assembly of Janus-type ``A-branch-B'' BBCPs where A and B blocks can phase separate with the bottlebrush polymer backbone serving as the interface between the two blocks. Hence, the polymer backbone adds an extra constraint on the equilibrium spacing between neighboring linear diblock chains. In this regard, the segment length of the backbone separating the AB junctions has a direct effect of the observed domain spacing and effective segregation strength of the AB blocks. We employ self-consistent field theoretic SCFT simulations to capture the effect of volume fraction of different constituents and construct a phase diagram of the accessible morphologies of these BBCPs.

Phi-value analysis of a linear, sequential reaction mechanism: theory and application to ion channel gating.

PubMed

Zhou, Yu; Pearson, John E; Auerbach, Anthony

2005-12-01

We derive the analytical form of a rate-equilibrium free-energy relationship (with slope Phi) for a bounded, linear chain of coupled reactions having arbitrary connecting rate constants. The results confirm previous simulation studies showing that Phi-values reflect the position of the perturbed reaction within the chain, with reactions occurring earlier in the sequence producing higher Phi-values than those occurring later in the sequence. The derivation includes an expression for the transmission coefficients of the overall reaction based on the rate constants of an arbitrary, discrete, finite Markov chain. The results indicate that experimental Phi-values can be used to calculate the relative heights of the energy barriers between intermediate states of the chain but provide no information about the energies of the wells along the reaction path. Application of the equations to the case of diliganded acetylcholine receptor channel gating suggests that the transition-state ensemble for this reaction is nearly flat. Although this mechanism accounts for many of the basic features of diliganded and unliganded acetylcholine receptor channel gating, the experimental rate-equilibrium free-energy relationships appear to be more linear than those predicted by the theory.

Activated-Sludge Nitrification in the Presence of Linear and Branched-Chain Alkyl Benzene Sulfonates

PubMed Central

Baillod, Charles R.; Boyle, W. C.

1968-01-01

The effects of biodegradable linear alkyl benzene sulfonate and branched-chain alkyl benzene sulfonate detergents on activated-sludge nitrification were investigated by administering a synthetic waste containing up to 23 mg of each detergent per liter to eight bench-scale, batch, activated-sludge units. It was found that both detergents tended to promote complete oxidation of ammonia to nitrate, whereas control units produced approximately equal amounts of nitrite and nitrate. Various hypotheses are offered to explain the phenomenon. PMID:5636474

Linear viscoelasticity of a single semiflexible polymer with internal friction.

PubMed

Hiraiwa, Tetsuya; Ohta, Takao

2010-07-28

The linear viscoelastic behaviors of single semiflexible chains with internal friction are studied based on the wormlike-chain model. It is shown that the frequency dependence of the complex compliance in the high frequency limit is the same as that of the Voigt model. This asymptotic behavior appears also for the Rouse model with internal friction. We derive the characteristic times for both the high frequency limit and the low frequency limit and compare the results with those obtained by Khatri et al.

Operational Evaluation of Tug/Barge Systems.

DTIC Science & Technology

1979-07-01

it would be expected that push-towing on the oceans would have developed long ago. However, the simple pin and wire/ chain lashings used on the rivers...better maneuverability available with push-towing. Thus, they began deepening the notches and using sophisticated cable/ chain linking and chafing...denied. But since mechanical linkages would result in increased manning rd capital costs, they instead began to develop improved cable/ chain linkages

Determination of real-time polymerase chain reaction uncertainty of measurement using replicate analysis and a graphical user interface with Fieller’s theorem

PubMed Central

Stuart, James Ian; Delport, Johan; Lannigan, Robert; Zahariadis, George

2014-01-01

BACKGROUND: Disease monitoring of viruses using real-time polymerase chain reaction (PCR) requires knowledge of the precision of the test to determine what constitutes a significant change. Calculation of quantitative PCR confidence limits requires bivariate statistical methods. OBJECTIVE: To develop a simple-to-use graphical user interface to determine the uncertainty of measurement (UOM) of BK virus, cytomegalovirus (CMV) and Epstein-Barr virus (EBV) real-time PCR assays. METHODS: Thirty positive clinical samples for each of the three viral assays were repeated once. A graphical user interface was developed using a spreadsheet (Excel, Microsoft Corporation, USA) to enable data entry and calculation of the UOM (according to Fieller’s theorem) and PCR efficiency. RESULTS: The confidence limits for the BK virus, CMV and EBV tests were ∼0.5 log, 0.5 log to 1.0 log, and 0.5 log to 1.0 log, respectively. The efficiencies of these assays, in the same order were 105%, 119% and 90%. The confidence limits remained stable over the linear range of all three tests. DISCUSSION: A >5 fold (0.7 log) and a >3-fold (0.5 log) change in viral load were significant for CMV and EBV when the results were ≤1000 copies/mL and >1000 copies/mL, respectively. A >3-fold (0.5 log) change in viral load was significant for BK virus over its entire linear range. PCR efficiency was ideal for BK virus and EBV but not CMV. Standardized international reference materials and shared reporting of UOM among laboratories are required for the development of treatment guidelines for BK virus, CMV and EBV in the context of changes in viral load. PMID:25285125

Determination of real-time polymerase chain reaction uncertainty of measurement using replicate analysis and a graphical user interface with Fieller's theorem.

PubMed

Stuart, James Ian; Delport, Johan; Lannigan, Robert; Zahariadis, George

2014-07-01

Disease monitoring of viruses using real-time polymerase chain reaction (PCR) requires knowledge of the precision of the test to determine what constitutes a significant change. Calculation of quantitative PCR confidence limits requires bivariate statistical methods. To develop a simple-to-use graphical user interface to determine the uncertainty of measurement (UOM) of BK virus, cytomegalovirus (CMV) and Epstein-Barr virus (EBV) real-time PCR assays. Thirty positive clinical samples for each of the three viral assays were repeated once. A graphical user interface was developed using a spreadsheet (Excel, Microsoft Corporation, USA) to enable data entry and calculation of the UOM (according to Fieller's theorem) and PCR efficiency. The confidence limits for the BK virus, CMV and EBV tests were ∼0.5 log, 0.5 log to 1.0 log, and 0.5 log to 1.0 log, respectively. The efficiencies of these assays, in the same order were 105%, 119% and 90%. The confidence limits remained stable over the linear range of all three tests. A >5 fold (0.7 log) and a >3-fold (0.5 log) change in viral load were significant for CMV and EBV when the results were ≤1000 copies/mL and >1000 copies/mL, respectively. A >3-fold (0.5 log) change in viral load was significant for BK virus over its entire linear range. PCR efficiency was ideal for BK virus and EBV but not CMV. Standardized international reference materials and shared reporting of UOM among laboratories are required for the development of treatment guidelines for BK virus, CMV and EBV in the context of changes in viral load.

Evaluation of certain food additives.

PubMed

2012-01-01

This report represents the conclusions of a Joint FAO/WHO Expert Committee convened to evaluate the safety of various food additives, including flavouring agents, with a view to concluding as to safety concerns and to preparing specifications for identity and purity. The first part of the report contains a general discussion of the principles governing the toxicological evaluation of and assessment of dietary exposure to food additives, including flavouring agents. A summary follows of the Committee's evaluations of technical, toxicological and dietary exposure data for five food additives (magnesium dihydrogen diphosphate; mineral oil (medium and low viscosity) classes II and III; 3-phytase from Aspergillus niger expressed in Aspergillus niger; serine protease (chymotrypsin) from Nocardiopsis prasina expressed in Bacillus licheniformis; and serine protease (trypsin) from Fusarium oxysporum expressed in Fusarium venenatum) and 16 groups of flavouring agents (aliphatic and aromatic amines and amides; aliphatic and aromatic ethers; aliphatic hydrocarbons, alcohols, aldehydes, ketones, carboxylic acids and related esters, sulfides, disulfides and ethers containing furan substitution; aliphatic linear alpha,beta-unsaturated aldehydes, acids and related alcohols, acetals and esters; amino acids and related substances; epoxides; furfuryl alcohol and related substances; linear and branched-chain aliphatic, unsaturated, unconjugated alcohols, aldehydes, acids and related esters; miscellaneous nitrogen-containing substances; phenol and phenol derivatives; pyrazine derivatives; pyridine, pyrrole and quinoline derivatives; saturated aliphatic acyclic branched-chain primary alcohols, aldehydes and acids; simple aliphatic and aromatic sulfides and thiols; sulfur-containing heterocyclic compounds; and sulfur-substituted furan derivatives). Specifications for the following food additives were revised: ethyl cellulose, mineral oil (medium viscosity), modified starches and titanium dioxide. Annexed to the report are tables summarizing the Committee's recommendations for dietary exposures to and toxicological evaluations of the food additives and flavouring agents considered.

S-SPatt: simple statistics for patterns on Markov chains.

PubMed

Nuel, Grégory

2005-07-01

S-SPatt allows the counting of patterns occurrences in text files and, assuming these texts are generated from a random Markovian source, the computation of the P-value of a given observation using a simple binomial approximation.

Linear and nonlinear susceptibilities from diffusion quantum Monte Carlo: application to periodic hydrogen chains.

PubMed

Umari, P; Marzari, Nicola

2009-09-07

We calculate the linear and nonlinear susceptibilities of periodic longitudinal chains of hydrogen dimers with different bond-length alternations using a diffusion quantum Monte Carlo approach. These quantities are derived from the changes in electronic polarization as a function of applied finite electric field--an approach we recently introduced and made possible by the use of a Berry-phase, many-body electric-enthalpy functional. Calculated susceptibilities and hypersusceptibilities are found to be in excellent agreement with the best estimates available from quantum chemistry--usually extrapolations to the infinite-chain limit of calculations for chains of finite length. It is found that while exchange effects dominate the proper description of the susceptibilities, second hypersusceptibilities are greatly affected by electronic correlations. We also assess how different approximations to the nodal surface of the many-body wave function affect the accuracy of the calculated susceptibilities.

Lithium/organosulfur redox cell having protective solid electrolyte barrier formed on anode and method of making same

DOEpatents

De Jonghe, Lutgard C.; Visco, Steven J.; Liu, Meilin; Mailhe, Catherine C.

1990-01-01

A lithium/organosulfur redox cell is disclosed which comprises a solid lium anode, a liquid organosulfur cathode, and a barrier layer formed adjacent a surface of the solid lithium anode facing the liquid organosulfur cathode consisting of a reaction product of the lithium anode with the organosulfur cathode. The organosulfur cathode comprises a material having the formula (R(S).sub.y).sub.N where y=1 to 6, n=2 to 20 and R is one or more different aliphatic or aromatic organic moieties having 1 to 20 carbon atoms, which may include one or more oxygen, sulfur, nitrogen, or fluorine atoms associated with the chain when R comprises an aliphatic chain, wherein the linear chain may be linear or branched, saturated or unsaturated, and wherein either the aliphatic chain or the aromatic ring may have substituted groups thereon.

Single-molecule Protein Unfolding in Solid State Nanopores

PubMed Central

Talaga, David S.; Li, Jiali

2009-01-01

We use single silicon nitride nanopores to study folded, partially folded and unfolded single proteins by measuring their excluded volumes. The DNA-calibrated translocation signals of β-lactoglobulin and histidine-containing phosphocarrier protein match quantitatively with that predicted by a simple sum of the partial volumes of the amino acids in the polypeptide segment inside the pore when translocation stalls due to the primary charge sequence. Our analysis suggests that the majority of the protein molecules were linear or looped during translocation and that the electrical forces present under physiologically relevant potentials can unfold proteins. Our results show that the nanopore translocation signals are sensitive enough to distinguish the folding state of a protein and distinguish between proteins based on the excluded volume of a local segment of the polypeptide chain that transiently stalls in the nanopore due to the primary sequence of charges. PMID:19530678

Coin state properties in quantum walks

PubMed Central

Andrade, R. F. S.

2013-01-01

Recent experimental advances have measured individual coin components in discrete time quantum walks, which have not received the due attention in most theoretical studies on the theme. Here is presented a detailed investigation of the properties of M, the difference between square modulus of coin states of discrete quantum walks on a linear chain. Local expectation values are obtained in terms of real and imaginary parts of the Fourier transformed wave function. A simple expression is found for the average difference between coin states in terms of an angle θ gauging the coin operator and its initial state. These results are corroborated by numerical integration of dynamical equations in real space. The local dependence is characterized both by large and short period modulations. The richness of revealed patterns suggests that the amount of information stored and retrieved from quantum walks is significantly enhanced if M is taken into account. PMID:23756358

Network-induced oscillatory behavior in material flow networks and irregular business cycles

NASA Astrophysics Data System (ADS)

Helbing, Dirk; Lämmer, Stefen; Witt, Ulrich; Brenner, Thomas

2004-11-01

Network theory is rapidly changing our understanding of complex systems, but the relevance of topological features for the dynamic behavior of metabolic networks, food webs, production systems, information networks, or cascade failures of power grids remains to be explored. Based on a simple model of supply networks, we offer an interpretation of instabilities and oscillations observed in biological, ecological, economic, and engineering systems. We find that most supply networks display damped oscillations, even when their units—and linear chains of these units—behave in a nonoscillatory way. Moreover, networks of damped oscillators tend to produce growing oscillations. This surprising behavior offers, for example, a different interpretation of business cycles and of oscillating or pulsating processes. The network structure of material flows itself turns out to be a source of instability, and cyclical variations are an inherent feature of decentralized adjustments.

Characterization of non-endcapped polymeric ODS column for the separation of triacylglycerol positional isomers.

PubMed

Gotoh, Naohiro; Matsumoto, Yumiko; Yuji, Hiromi; Nagai, Toshiharu; Mizobe, Hoyo; Ichioka, Kenji; Kuroda, Ikuma; Noguchi, Noriko; Wada, Shun

2010-01-01

The characteristics of a non-endcapped polymeric ODS column for the resolution of triacylglycerol positional isomers (TAG-PI) were examined using a recycle HPLC-atmospheric pressure chemical ionization/mass spectrometry system. A pair of TAG-PI containing saturated fatty acids at least 12 carbons was separated. Except for TAG-PI containing elaidic acid, pairs of TAG-PI containing three unsaturated fatty acids were not separated, even by recycle runs. These results indicate that the resolution of TAG-PI on a non-endcapped polymeric ODS stationary phase is realized by the recognition of the linear structure of the fatty acid and the binding position of the saturated fatty acid in TAG-PI. Chain length was also an important factor for resolution. This method may be a useful and simple for measuring the abundance ratio of TAG-PI containing saturated fatty acids in natural oils.

Locomotive and reptation motion induced by internal force and friction.

PubMed

Sakaguchi, Hidetsugu; Ishihara, Taisuke

2011-06-01

We propose a simple mechanical model of locomotion induced by internal force and friction. We first construct a system of two elements as an analog of the bipedal motion. The internal force does not induce a directional motion by itself because of the action-reaction law, but a directional motion becomes possible by the control of the frictional force. The efficiency of these model systems is studied using an analogy to the heat engine. As a modified version of the two-element model, we construct a model that exhibits a bipedal motion similar to kinesin's motion of molecular motor. Next, we propose a linear chain model and a ladder model as an extension of the original two-element model. We find a transition from a straight to a snake-like motion in a ladder model by changing the strength of the internal force.

Seismic anisotropy and large-scale deformation of the Eastern Alps

NASA Astrophysics Data System (ADS)

Bokelmann, Götz; Qorbani, Ehsan; Bianchi, Irene

2013-12-01

Mountain chains at the Earth's surface result from deformation processes within the Earth. Such deformation processes can be observed by seismic anisotropy, via the preferred alignment of elastically anisotropic minerals. The Alps show complex deformation at the Earth's surface. In contrast, we show here that observations of seismic anisotropy suggest a relatively simple pattern of internal deformation. Together with earlier observations from the Western Alps, the SKS shear-wave splitting observations presented here show one of the clearest examples yet of mountain chain-parallel fast orientations worldwide, with a simple pattern nearly parallel to the trend of the mountain chain. In the Eastern Alps, the fast orientations do not connect with neighboring mountain chains, neither the present-day Carpathians, nor the present-day Dinarides. In that region, the lithosphere is thin and the observed anisotropy thus resides within the asthenosphere. The deformation is consistent with the eastward extrusion toward the Pannonian basin that was previously suggested based on seismicity and surface geology.

Gushing metal chain

NASA Astrophysics Data System (ADS)

Belyaev, Alexander; Sukhanov, Alexander; Tsvetkov, Alexander

2016-03-01

This article addresses the problem in which a chain falls from a glass from some height. This phenomenon demonstrates a paradoxical rise of the chain over the glass. To explain this effect, an initial hypothesis and an appropriate theory are proposed for calculating the steady fall parameters of the chain. For this purpose, the modified Cayley's problem of falling chain given its rise due to the centrifugal force of upward inertia is solved. Results show that the lift caused by an increase in linear density at the part of chain where it is being bent (the upper part) is due to the convergence of the chain balls to one another. The experiments confirm the obtained estimates of the lifting chain.

Principles of protein folding--a perspective from simple exact models.

PubMed Central

Dill, K. A.; Bromberg, S.; Yue, K.; Fiebig, K. M.; Yee, D. P.; Thomas, P. D.; Chan, H. S.

1995-01-01

General principles of protein structure, stability, and folding kinetics have recently been explored in computer simulations of simple exact lattice models. These models represent protein chains at a rudimentary level, but they involve few parameters, approximations, or implicit biases, and they allow complete explorations of conformational and sequence spaces. Such simulations have resulted in testable predictions that are sometimes unanticipated: The folding code is mainly binary and delocalized throughout the amino acid sequence. The secondary and tertiary structures of a protein are specified mainly by the sequence of polar and nonpolar monomers. More specific interactions may refine the structure, rather than dominate the folding code. Simple exact models can account for the properties that characterize protein folding: two-state cooperativity, secondary and tertiary structures, and multistage folding kinetics--fast hydrophobic collapse followed by slower annealing. These studies suggest the possibility of creating "foldable" chain molecules other than proteins. The encoding of a unique compact chain conformation may not require amino acids; it may require only the ability to synthesize specific monomer sequences in which at least one monomer type is solvent-averse. PMID:7613459

A Novel Algorithm for the Generation of Distinct Kinematic Chain

NASA Astrophysics Data System (ADS)

Medapati, Sreenivasa Reddy; Kuchibhotla, Mallikarjuna Rao; Annambhotla, Balaji Srinivasa Rao

2016-07-01

Generation of distinct kinematic chains is an important topic in the design of mechanisms for various industrial applications i.e., robotic manipulator, tractor, crane etc. Many researchers have intently focused on this area and explained various processes of generating distinct kinematic chains which are laborious and complex. It is desirable to enumerate the kinematic chains systematically to know the inherent characteristics of a chain related to its structure so that all the distinct chains can be analyzed in depth, prior to the selection of a chain for a purpose. This paper proposes a novel and simple method with set of rules defined to eliminate isomorphic kinematic chains generating distinct kinematic chains. Also, this method simplifies the process of generating distinct kinematic chains even at higher levels i.e., 10-link, 11-link with single and multiple degree of freedom.

A Novel Algorithm for the Generation of Distinct Kinematic Chain

NASA Astrophysics Data System (ADS)

Medapati, Sreenivasa Reddy; Kuchibhotla, Mallikarjuna Rao; Annambhotla, Balaji Srinivasa Rao

2018-06-01

Generation of distinct kinematic chains is an important topic in the design of mechanisms for various industrial applications i.e., robotic manipulator, tractor, crane etc. Many researchers have intently focused on this area and explained various processes of generating distinct kinematic chains which are laborious and complex. It is desirable to enumerate the kinematic chains systematically to know the inherent characteristics of a chain related to its structure so that all the distinct chains can be analyzed in depth, prior to the selection of a chain for a purpose. This paper proposes a novel and simple method with set of rules defined to eliminate isomorphic kinematic chains generating distinct kinematic chains. Also, this method simplifies the process of generating distinct kinematic chains even at higher levels i.e., 10-link, 11-link with single and multiple degree of freedom.

Multivalency of Sonic hedgehog conjugated to linear polymer chains modulates protein potency.

PubMed

Wall, Samuel T; Saha, Krishanu; Ashton, Randolph S; Kam, Kimberly R; Schaffer, David V; Healy, Kevin E

2008-04-01

A potently active multivalent form of the protein Sonic hedgehog (Shh) was produced by bioconjugation of a modified recombinant form of Shh to the linear polymers poly(acrylic acid) (pAAc) and hyaluronic acid (HyA) via a two-step reaction exploiting carboimiide and maleimide chemistry. Efficiency of the conjugation was approximately 75% even at stoichiometric ratios of 30 Shh molecules per linear HyA chain (i.e., 30:1 Shh/HyA). Bioactivity of the conjugates was tested via a cellular assay across a range of stoichiometric ratios of Shh molecules to HyA linear chains, which was varied from 0.6:1 Shh/HyA to 22:1 Shh/HyA. Results indicate that low conjugation ratios decrease Shh bioactivity and high ratios increase this activity beyond the potency of monomeric Shh, with approximately equal activity between monomeric soluble Shh and conjugated Shh at 7:1 Shh/HyA. In addition, high-ratio constructs increased angiogenesis determined by the in vivo chick chorioallantoic membrane (CAM) assay. These results are captured by a kinetic model of multiple interactions between the Shh/HyA conjugates and cell surface receptors resulting in higher cell signaling at lower bulk Shh concentrations.

Structure of gel phase saturated lecithin bilayers: temperature and chain length dependence.

PubMed Central

Sun, W J; Tristram-Nagle, S; Suter, R M; Nagle, J F

1996-01-01

Systematic low-angle and wide-angle x-ray scattering studies have been performed on fully hydrated unoriented multilamamellar vesicles of saturated lecithins with even chain lengths N = 16, 18, 20, 22, and 24 as a function of temperature T in the normal gel (L beta') phase. For all N, the area per chain Ac increases linearly with T with an average slope dAc/dT = 0.027 A2/degree C, and the lamellar D-spacings also increase linearly with an average slope dD/dT = 0.040 A/degree C. At the same T, longer chain length lecithins have more densely packed chains, i.e., smaller Ac's, than shorter chain lengths. The chain packing of longer chain lengths is found to be more distorted from hexagonal packing than that of smaller N, and the distortion epsilon of all N approaches the same value at the respective transition temperatures. The thermal volume expansion of these lipids is accounted for by the expansion in the hydrocarbon chain region. Electron density profiles are constructed using four orders of low-angle lamellar peaks. These show that most of the increase in D with increasing T is due to thickening of the bilayers that is consistent with a decrease in tilt angle theta and with little change in water spacing with either T or N. Because of the opposing effects of temperature on area per chain Ac and tilt angle 0, the area expansivity alpha A is quite small. A qualitative theoretical model based on competing head and chain interactions accounts for our results. PMID:8842227

Associative Algebraic Approach to Logarithmic CFT in the Bulk: The Continuum Limit of the {gl(1|1)} Periodic Spin Chain, Howe Duality and the Interchiral Algebra

NASA Astrophysics Data System (ADS)

Gainutdinov, A. M.; Read, N.; Saleur, H.

2016-01-01

We develop in this paper the principles of an associative algebraic approach to bulk logarithmic conformal field theories (LCFTs). We concentrate on the closed {gl(1|1)} spin-chain and its continuum limit—the {c=-2} symplectic fermions theory—and rely on two technical companion papers, Gainutdinov et al. (Nucl Phys B 871:245-288, 2013) and Gainutdinov et al. (Nucl Phys B 871:289-329, 2013). Our main result is that the algebra of local Hamiltonians, the Jones-Temperley-Lieb algebra JTL N , goes over in the continuum limit to a bigger algebra than {V}, the product of the left and right Virasoro algebras. This algebra, {S}—which we call interchiral, mixes the left and right moving sectors, and is generated, in the symplectic fermions case, by the additional field {S(z,bar{z})≡ S_{αβ} ψ^α(z)bar{ψ}^β(bar{z})}, with a symmetric form {S_{αβ}} and conformal weights (1,1). We discuss in detail how the space of states of the LCFT (technically, a Krein space) decomposes onto representations of this algebra, and how this decomposition is related with properties of the finite spin-chain. We show that there is a complete correspondence between algebraic properties of finite periodic spin chains and the continuum limit. An important technical aspect of our analysis involves the fundamental new observation that the action of JTL N in the {gl(1|1)} spin chain is in fact isomorphic to an enveloping algebra of a certain Lie algebra, itself a non semi-simple version of {sp_{N-2}}. The semi-simple part of JTL N is represented by {U sp_{N-2}}, providing a beautiful example of a classical Howe duality, for which we have a non semi-simple version in the full JTL N image represented in the spin-chain. On the continuum side, simple modules over {S} are identified with "fundamental" representations of {sp_∞}.

Doubly self-consistent field theory of grafted polymers under simple shear in steady state.

PubMed

Suo, Tongchuan; Whitmore, Mark D

2014-03-21

We present a generalization of the numerical self-consistent mean-field theory of polymers to the case of grafted polymers under simple shear. The general theoretical framework is presented, and then applied to three different chain models: rods, Gaussian chains, and finitely extensible nonlinear elastic (FENE) chains. The approach is self-consistent at two levels. First, for any flow field, the polymer density profile and effective potential are calculated self-consistently in a manner similar to the usual self-consistent field theory of polymers, except that the calculation is inherently two-dimensional even for a laterally homogeneous system. Second, through the use of a modified Brinkman equation, the flow field and the polymer profile are made self-consistent with respect to each other. For all chain models, we find that reasonable levels of shear cause the chains to tilt, but it has very little effect on the overall thickness of the polymer layer, causing a small decrease for rods, and an increase of no more than a few percent for the Gaussian and FENE chains. Using the FENE model, we also probe the individual bond lengths, bond correlations, and bond angles along the chains, the effects of the shear on them, and the solvent and bonded stress profiles. We find that the approximations needed within the theory for the Brinkman equation affect the bonded stress, but none of the other quantities.

Graphite grain-size spectrum and molecules from core-collapse supernovae

NASA Astrophysics Data System (ADS)

Clayton, Donald D.; Meyer, Bradley S.

2018-01-01

Our goal is to compute the abundances of carbon atomic complexes that emerge from the C + O cores of core-collapse supernovae. We utilize our chemical reaction network in which every atomic step of growth employs a quantum-mechanically guided reaction rate. This tool follows step-by-step the growth of linear carbon chain molecules from C atoms in the oxygen-rich C + O cores. We postulate that once linear chain molecules reach a sufficiently large size, they isomerize to ringed molecules, which serve as seeds for graphite grain growth. We demonstrate our technique for merging the molecular reaction network with a parallel program that can follow 1017 steps of C addition onto the rare seed species. Due to radioactivity within the C + O core, abundant ambient oxygen is unable to convert C to CO, except to a limited degree that actually facilitates carbon molecular ejecta. But oxygen severely minimizes the linear-carbon-chain abundances. Despite the tiny abundances of these linear-carbon-chain molecules, they can give rise to a small abundance of ringed-carbon molecules that serve as the nucleations on which graphite grain growth builds. We expand the C + O-core gas adiabatically from 6000 K for 109 s when reactions have essentially stopped. These adiabatic tracks emulate the actual expansions of the supernova cores. Using a standard model of 1056 atoms of C + O core ejecta having O/C = 3, we calculate standard ejection yields of graphite grains of all sizes produced, of the CO molecular abundance, of the abundances of linear-carbon molecules, and of Buckminsterfullerene. None of these except CO was expected from the C + O cores just a few years past.

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.

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.

Aqueous solubilities, vapor pressures, and 1-octanol-water partition coefficients for C9-C14 linear alkylbenzenes

USGS Publications Warehouse

Sherblom, P.M.; Gschwend, P.M.; Eganhouse, R.P.

1992-01-01

Measurements and estimates of aqueous solubilities, 1-octanol-water partition coefficients (Kow), and vapor pressures were made for 29 linear alkylbenzenes having alkyl chain lengths of 9-14 carbons. The ranges of values observed were vapor pressures from 0.002 to 0.418 Pa, log Kow, from 6.83 to 9.95, and aqueous solubilities from 4 to 38 nmol??L-1. Measured values exhibited a relationship to both the alkyl chain length and the position of phenyl substitution on the alkyl chain. Measurement of the aqueous concentrations resulting from equilibration of a mixture of alkylbenzenes yielded higher than expected values, indicating cosolute or other interactive effects caused enhanced aqueous concentrations of these compounds. ?? 1992 American Chemical Society.

A Correlated Ab Initio Study of Linear Carbon-Chain Radicals C(sub n)H (n=2-7)

NASA Technical Reports Server (NTRS)

Woon, David E.

1995-01-01

Linear carbon-chain radicals C(sub n) H for n = 2-7 have been studied with correlation consistent valence and core-valence basis sets and the coupled cluster method RCCSD(T). Equilibrium structures, rotational constants, and dipole moments are reported and compared with available experimental data. The ground state of the even-n series changes from 2Sigma(+) to 2Pi as the chain is extended. For C4H, the 2Sigma(+) state was found to lie only 72 cm(exp -1) below the 2Pi state in the estimated complete basis set limit for valence correlation. The C2H(-) and C3H(-) anions have also been characterized.

Motion of spin label side chains in cellular retinol-binding protein: correlation with structure and nearest-neighbor interactions in an antiparallel beta-sheet.

PubMed

Lietzow, Michael A; Hubbell, Wayne L

2004-03-23

A goal in the development of site-directed spin labeling in proteins is to correlate the motion of a nitroxide side chain with local structure, interactions, and dynamics. Significant progress toward this goal has been made using alpha-helical proteins of known structure, and the present study is the first step in a similar exploration of a beta-sheet protein, cellular retinol-binding protein (CRBP). Nitroxide side chains were introduced along both interior and edge strands. At sites in interior strands, the side-chain motion is strongly influenced by interactions with side chains of neighboring strands, giving rise to a rich variety of dynamic modes (weakly ordered, strongly ordered, immobilized) and complex electron paramagnetic resonance spectra that are modulated by strand twist. The interactions giving rise to the dynamic modes are explored using mutagenesis, and the results demonstrate the particular importance of the non-hydrogen-bonded neighbor residue in giving rise to highly ordered states. Along edge strands of the beta-sheet, the motion of the side chain is simple and weakly ordered, resembling that at solvent-exposed surfaces of an alpha-helix. A simple working model is proposed that can account for the wide variety of dynamic modes encountered. Collectively, the results suggest that the nitroxide side chain is an effective probe of side-chain interactions, and that site-directed spin labeling should be a powerful means of monitoring conformational changes that involve changes in beta-sheet topology.

Untying a nanoscale knotted polymer structure to linear chains for efficient gene delivery in vitro and to the brain

NASA Astrophysics Data System (ADS)

Newland, B.; Aied, A.; Pinoncely, A. V.; Zheng, Y.; Zhao, T.; Zhang, H.; Niemeier, R.; Dowd, E.; Pandit, A.; Wang, W.

2014-06-01

The purpose of this study was to develop a platform transfection technology, for applications in the brain, which could transfect astrocytes without requiring cell specific functionalization and without the common cause of toxicity through high charge density. Here we show that a simple and scalable preparation technique can be used to produce a ``knot'' structured cationic polymer, where single growing chains can crosslink together via disulphide intramolecular crosslinks (internal cyclizations). This well-defined knot structure can thus ``untie'' under reducing conditions, showing a more favorable transfection profile for astrocytes compared to 25 kDa-PEI (48-fold), SuperFect® (39-fold) and Lipofectamine®2000 (18-fold) whilst maintaining neural cell viability at over 80% after four days of culture. The high transfection/lack of toxicity of this knot structured polymer in vitro, combined with its ability to mediate luciferase transgene expression in the adult rat brain, demonstrates its use as a platform transfection technology which should be investigated further for neurodegenerative disease therapies.The purpose of this study was to develop a platform transfection technology, for applications in the brain, which could transfect astrocytes without requiring cell specific functionalization and without the common cause of toxicity through high charge density. Here we show that a simple and scalable preparation technique can be used to produce a ``knot'' structured cationic polymer, where single growing chains can crosslink together via disulphide intramolecular crosslinks (internal cyclizations). This well-defined knot structure can thus ``untie'' under reducing conditions, showing a more favorable transfection profile for astrocytes compared to 25 kDa-PEI (48-fold), SuperFect® (39-fold) and Lipofectamine®2000 (18-fold) whilst maintaining neural cell viability at over 80% after four days of culture. The high transfection/lack of toxicity of this knot structured polymer in vitro, combined with its ability to mediate luciferase transgene expression in the adult rat brain, demonstrates its use as a platform transfection technology which should be investigated further for neurodegenerative disease therapies. Electronic supplementary information (ESI) available: 1H NMR spectroscopy data and gel permeation chromatography data. See DOI: 10.1039/c3nr06737h

A simple smoothness indicator for the WENO scheme with adaptive order

NASA Astrophysics Data System (ADS)

Huang, Cong; Chen, Li Li

2018-01-01

The fifth order WENO scheme with adaptive order is competent for solving hyperbolic conservation laws, its reconstruction is a convex combination of a fifth order linear reconstruction and three third order linear reconstructions. Note that, on uniform mesh, the computational cost of smoothness indicator for fifth order linear reconstruction is comparable with the sum of ones for three third order linear reconstructions, thus it is too heavy; on non-uniform mesh, the explicit form of smoothness indicator for fifth order linear reconstruction is difficult to be obtained, and its computational cost is much heavier than the one on uniform mesh. In order to overcome these problems, a simple smoothness indicator for fifth order linear reconstruction is proposed in this paper.

Hybridization chain reaction-based instantaneous derivatization technology for chemiluminescence detection of specific DNA sequences.

PubMed

Wang, Xin; Lau, Choiwan; Kai, Masaaki; Lu, Jianzhong

2013-05-07

We propose here a new amplifying strategy that uses hybridization chain reaction (HCR) to detect specific sequences of DNA, where stable DNA monomers assemble on the magnetic beads only upon exposure to a target DNA. Briefly, in the HCR process, two complementary stable species of hairpins coexist in solution until the introduction of initiator reporter strands triggers a cascade of hybridization events that yield nicked double helices analogous to alternating copolymers. Moreover, a "sandwich-type" detection strategy is employed in our design. Magnetic beads, which are functionalized with capture DNA, are reacted with the target, and sandwiched with the above nicked double helices. Then, chemiluminescence (CL) detection proceeds via an instantaneous derivatization reaction between a specific CL reagent, 3,4,5-trimethoxylphenylglyoxal (TMPG), and the guanine nucleotides within the target DNA, reporter strands and DNA monomers for the generation of light. Our results clearly show that the amplification detection of specific sequences of DNA achieves a better performance (e.g. wide linear response range, low detection limit, and high specificity) as compared to the traditional sandwich type (capture/target/reporter) assays. Upon modification, the approach presented could be extended to detect other types of targets. We believe that this simple technique is promising for improving medical diagnosis and treatment.

Sequence and Temperature Dependence of the End-to-End Collision Dynamics of Single-Stranded DNA

PubMed Central

Uzawa, Takanori; Isoshima, Takashi; Ito, Yoshihiro; Ishimori, Koichiro; Makarov, Dmitrii E.; Plaxco, Kevin W.

2013-01-01

Intramolecular collision dynamics play an essential role in biomolecular folding and function and, increasingly, in the performance of biomimetic technologies. To date, however, the quantitative studies of dynamics of single-stranded nucleic acids have been limited. Thus motivated, here we investigate the sequence composition, chain-length, viscosity, and temperature dependencies of the end-to-end collision dynamics of single-stranded DNAs. We find that both the absolute collision rate and the temperature dependencies of these dynamics are base-composition dependent, suggesting that base stacking interactions are a significant contributor. For example, whereas the end-to-end collision dynamics of poly-thymine exhibit simple, linear Arrhenius behavior, the behavior of longer poly-adenine constructs is more complicated. Specifically, 20- and 25-adenine constructs exhibit biphasic temperature dependencies, with their temperature dependences becoming effectively indistinguishable from that of poly-thymine above 335 K for 20-adenines and 328 K for 25-adenines. The differing Arrhenius behaviors of poly-thymine and poly-adenine and the chain-length dependence of the temperature at which poly-adenine crosses over to behave like poly-thymine can be explained by a barrier friction mechanism in which, at low temperatures, the energy barrier for the local rearrangement of poly-adenine becomes the dominant contributor to its end-to-end collision dynamics. PMID:23746521

Surface segregation and surface tension of polydisperse polymer melts.

PubMed

Minnikanti, Venkatachala S; Qian, Zhenyu; Archer, Lynden A

2007-04-14

The effect of polydispersity on surface segregation of a lower molecular weight polymer component in a higher molecular weight linear polymer melt host is investigated theoretically. We show that the integrated surface excess zM of a polymer component of molecular weight M satisfies a simple relation zM=2Ue(M/Mw-1)phiM, where Mw is the weight averaged molecular weight, phiM is the polymer volume fraction, and Ue is the attraction of polymer chain ends to the surface. Ue is principally of entropic origin, but also reflects any energetic preference of chain ends to the surface. We further show that the surface tension gammaM of a polydisperse melt of high molar mass components depends on the number average degree of polymerization Mn as, gammaM=gammainfinity+2UerhobRT/Mn. The parameter gammainfinity is the asymptotic surface tension of an infinitely long polymer of the same chemistry, rhob is the bulk density of the polymer, R is the universal gas constant, and T is the temperature. The predicted gammaM compare favorably with surface tension values obtained from self-consistent field theory simulations that include equation of state effects, which account for changes in polymer density with molecular weight. We also compare the predicted surface tension with available experimental data.

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.

Correlation and simple linear regression.

PubMed

Zou, Kelly H; Tuncali, Kemal; Silverman, Stuart G

2003-06-01

In this tutorial article, the concepts of correlation and regression are reviewed and demonstrated. The authors review and compare two correlation coefficients, the Pearson correlation coefficient and the Spearman rho, for measuring linear and nonlinear relationships between two continuous variables. In the case of measuring the linear relationship between a predictor and an outcome variable, simple linear regression analysis is conducted. These statistical concepts are illustrated by using a data set from published literature to assess a computed tomography-guided interventional technique. These statistical methods are important for exploring the relationships between variables and can be applied to many radiologic studies.

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.

Teaching the Concept of Breakdown Point in Simple Linear Regression.

ERIC Educational Resources Information Center

Chan, Wai-Sum

2001-01-01

Most introductory textbooks on simple linear regression analysis mention the fact that extreme data points have a great influence on ordinary least-squares regression estimation; however, not many textbooks provide a rigorous mathematical explanation of this phenomenon. Suggests a way to fill this gap by teaching students the concept of breakdown…

Polymerase chain reaction system

DOEpatents

Benett, William J.; Richards, James B.; Stratton, Paul L.; Hadley, Dean R.; Milanovich, Fred P.; Belgrader, Phil; Meyer, Peter L.

2004-03-02

A portable polymerase chain reaction DNA amplification and detection system includes one or more chamber modules. Each module supports a duplex assay of a biological sample. Each module has two parallel interrogation ports with a linear optical system. The system is capable of being handheld.

Linear analysis of auto-organization in Hebbian neural networks.

PubMed

Carlos Letelier, J; Mpodozis, J

1995-01-01

The self-organization of neurotopies where neural connections follow Hebbian dynamics is framed in terms of linear operator theory. A general and exact equation describing the time evolution of the overall synaptic strength connecting two neural laminae is derived. This linear matricial equation, which is similar to the equations used to describe oscillating systems in physics, is modified by the introduction of non-linear terms, in order to capture self-organizing (or auto-organizing) processes. The behavior of a simple and small system, that contains a non-linearity that mimics a metabolic constraint, is analyzed by computer simulations. The emergence of a simple "order" (or degree of organization) in this low-dimensionality model system is discussed.

Evaluation of Two Statistical Methods Provides Insights into the Complex Patterns of Alternative Polyadenylation Site Switching

PubMed Central

Li, Jie; Li, Rui; You, Leiming; Xu, Anlong; Fu, Yonggui; Huang, Shengfeng

2015-01-01

Switching between different alternative polyadenylation (APA) sites plays an important role in the fine tuning of gene expression. New technologies for the execution of 3’-end enriched RNA-seq allow genome-wide detection of the genes that exhibit significant APA site switching between different samples. Here, we show that the independence test gives better results than the linear trend test in detecting APA site-switching events. Further examination suggests that the discrepancy between these two statistical methods arises from complex APA site-switching events that cannot be represented by a simple change of average 3’-UTR length. In theory, the linear trend test is only effective in detecting these simple changes. We classify the switching events into four switching patterns: two simple patterns (3’-UTR shortening and lengthening) and two complex patterns. By comparing the results of the two statistical methods, we show that complex patterns account for 1/4 of all observed switching events that happen between normal and cancerous human breast cell lines. Because simple and complex switching patterns may convey different biological meanings, they merit separate study. We therefore propose to combine both the independence test and the linear trend test in practice. First, the independence test should be used to detect APA site switching; second, the linear trend test should be invoked to identify simple switching events; and third, those complex switching events that pass independence testing but fail linear trend testing can be identified. PMID:25875641

Valid statistical approaches for analyzing sholl data: Mixed effects versus simple linear models.

PubMed

Wilson, Machelle D; Sethi, Sunjay; Lein, Pamela J; Keil, Kimberly P

2017-03-01

The Sholl technique is widely used to quantify dendritic morphology. Data from such studies, which typically sample multiple neurons per animal, are often analyzed using simple linear models. However, simple linear models fail to account for intra-class correlation that occurs with clustered data, which can lead to faulty inferences. Mixed effects models account for intra-class correlation that occurs with clustered data; thus, these models more accurately estimate the standard deviation of the parameter estimate, which produces more accurate p-values. While mixed models are not new, their use in neuroscience has lagged behind their use in other disciplines. A review of the published literature illustrates common mistakes in analyses of Sholl data. Analysis of Sholl data collected from Golgi-stained pyramidal neurons in the hippocampus of male and female mice using both simple linear and mixed effects models demonstrates that the p-values and standard deviations obtained using the simple linear models are biased downwards and lead to erroneous rejection of the null hypothesis in some analyses. The mixed effects approach more accurately models the true variability in the data set, which leads to correct inference. Mixed effects models avoid faulty inference in Sholl analysis of data sampled from multiple neurons per animal by accounting for intra-class correlation. Given the widespread practice in neuroscience of obtaining multiple measurements per subject, there is a critical need to apply mixed effects models more widely. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

Persistence in Food Webs. I. Lotka-Volterra Food Chains,

DTIC Science & Technology

1978-07-01

0256 UNCLASSIFIED N i EE’hEZE *1 Al 1,1 IqI 0 - r ~PERSISTENCE IN FOOD WEBS.A I. LOTKA - VOLTERRA FOOD CHAINS Thomas C./Gard en9 Mt aisFEB 2 7 1980...2260n80 PERSISTENCE IN FOOD WEBS: \\’ ,.’ ’,-’ - 1. LOTKA - VOLTERRA FOOD CHAINS Thomas C. Gard and Thomas G. Hallam \\\\ . ’ \\7 INTRODUCTION bf numerous...modelled by Lotka - Volterra dynamics are determined. Here a simple food chain has a single species composing each trophic level with its dynamics

Surgery for left ventricular aneurysm: early and late survival after simple linear repair and endoventricular patch plasty.

PubMed

Lundblad, Runar; Abdelnoor, Michel; Svennevig, Jan Ludvig

2004-09-01

Simple linear resection and endoventricular patch plasty are alternative techniques to repair postinfarction left ventricular aneurysm. The aim of the study was to compare these 2 methods with regard to early mortality and long-term survival. We retrospectively reviewed 159 patients undergoing operations between 1989 and 2003. The epidemiologic design was of an exposed (simple linear repair, n = 74) versus nonexposed (endoventricular patch plasty, n = 85) cohort with 2 endpoints: early mortality and long-term survival. The crude effect of aneurysm repair technique versus endpoint was estimated by odds ratio, rate ratio, or relative risk and their 95% confidence intervals. Stratification analysis by using the Mantel-Haenszel method was done to quantify confounders and pinpoint effect modifiers. Adjustment for multiconfounders was performed by using logistic regression and Cox regression analysis. Survival curves were analyzed with the Breslow test and the log-rank test. Early mortality was 8.2% for all patients, 13.5% after linear repair and 3.5% after endoventricular patch plasty. When adjusted for multiconfounders, the risk of early mortality was significantly higher after simple linear repair than after endoventricular patch plasty (odds ratio, 4.4; 95% confidence interval, 1.1-17.8). Mean follow-up was 5.8 +/- 3.8 years (range, 0-14.0 years). Overall 5-year cumulative survival was 78%, 70.1% after linear repair and 91.4% after endoventricular patch plasty. The risk of total mortality was significantly higher after linear repair than after endoventricular patch plasty when controlled for multiconfounders (relative risk, 4.5; 95% confidence interval, 2.0-9.7). Linear repair dominated early in the series and patch plasty dominated later, giving a possible learning-curve bias in favor of patch plasty that could not be adjusted for in the regression analysis. Postinfarction left ventricular aneurysm can be repaired with satisfactory early and late results. Surgical risk was lower and long-term survival was higher after endoventricular patch plasty than simple linear repair. Differences in outcome should be interpreted with care because of the retrospective study design and the chronology of the 2 repair methods.

Targeted energy transfers and passive acoustic wave redirection in a two-dimensional granular network under periodic excitation

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

Zhang, Yijing, E-mail: yzhng123@illinois.edu; Moore, Keegan J.; Vakakis, Alexander F.

2015-12-21

We study passive pulse redirection and nonlinear targeted energy transfer in a granular network composed of two semi-infinite, ordered homogeneous granular chains mounted on linear elastic foundations and coupled by weak linear stiffnesses. Periodic excitation in the form of repetitive half-sine pulses is applied to one of the chains, designated as the “excited chain,” whereas the other chain is initially at rest and is regarded as the “absorbing chain.” We show that passive pulse redirection and targeted energy transfer from the excited to the absorbing chain can be achieved by macro-scale realization of the spatial analog of the Landau-Zener quantummore » tunneling effect. This is realized by finite stratification of the elastic foundation of the excited chain and depends on the system parameters (e.g., the percentage of stratification) and on the parameters of the periodic excitation. Utilizing empirical mode decomposition and numerical Hilbert transforms, we detect the existence of two distinct nonlinear phenomena in the periodically forced network; namely, (i) energy localization in the absorbing chain due to sustained 1:1 resonance capture leading to irreversible pulse redirection from the excited chain, and (ii) continuous energy exchanges in the form of nonlinear beats between the two chains in the absence of resonance capture. Our results extend previous findings of transient passive energy redirection in impulsively excited granular networks and demonstrate that steady state passive pulse redirection in these networks can be robustly achieved under periodic excitation.« less

ORGANIC CONTAMINANT DISTRIBUTION IN SEDIMENTS, POLYCHAETES (NEREIS VIRENS) AND THE AMERICAN LOBSTER, HOMARUS AMERICANUS IN A LABORATORY FOOD CHAIN EXPERIMENT

EPA Science Inventory

A laboratory experiment was conducted to investigate the transfer of organic contaminants from an environmentally contaminated marine sediment through a simple marine food chain. The infaunal polychaete, Nereis virens, was exposed to contaminated sediment collected from the Passa...

The Electron Transport Chain: An Interactive Simulation

ERIC Educational Resources Information Center

Romero, Chris; Choun, James

2014-01-01

This activity provides students an interactive demonstration of the electron transport chain and chemiosmosis during aerobic respiration. Students use simple, everyday objects as hydrogen ions and electrons and play the roles of the various proteins embedded in the inner mitochondrial membrane to show how this specific process in cellular…

Turbulent drag reduction and degradation of DNA.

PubMed

Choi, H J; Lim, S T; Lai, Pik-Yin; Chan, C K

2002-08-19

Turbulent drag reduction induced by lambda-DNA is studied. The double-stranded DNA is found to be a good drag reducer when compared with the other normal linear polymers. However, this drag reducing power disappears when the DNA denatures to form two single-strand molecules. Mechanical degradation of DNA is also different from that of the normal linear-chain polymers: DNA is always cut in half by the turbulence. Our results suggest that the mechanism for turbulent degradation of DNA is different from that of the normal flexible long-chain polymers.

Typed Linear Chain Conditional Random Fields and Their Application to Intrusion Detection

NASA Astrophysics Data System (ADS)

Elfers, Carsten; Horstmann, Mirko; Sohr, Karsten; Herzog, Otthein

Intrusion detection in computer networks faces the problem of a large number of both false alarms and unrecognized attacks. To improve the precision of detection, various machine learning techniques have been proposed. However, one critical issue is that the amount of reference data that contains serious intrusions is very sparse. In this paper we present an inference process with linear chain conditional random fields that aims to solve this problem by using domain knowledge about the alerts of different intrusion sensors represented in an ontology.

The possibility of a new resonance of three-body linear chain structure in the reaction 12C+16O at Ec.mapprox-33.5MeV

NASA Astrophysics Data System (ADS)

Kong, Xiangjing; P, L. Li; J, J. Kolata; A, Morsad; L, Goetting; R, A. Kryger; S, Dixit; R, Tighe; W, Chune

1990-05-01

There is a peak in the excitation function of total cross section of low energy α-particles in the reaction 12C+16O at Ec.m approx33.5MeV. The experimental distribution of α-particle emitted event has been obtained. The result of theoretical calculation roughly agrees with experimental data, gives an orientation where three-body resonances can be expected, and the information on internal structure of three-body linear chain molecule.

Structure and dynamics of solvated polyethylenimine chains

NASA Astrophysics Data System (ADS)

Beu, Titus A.; Farcaş, Alexandra

2017-12-01

Polimeric gene-delivery carriers have attracted great interest in recent years, owing to their applicability in gene therapy. In particular, cationic polymers represent the most promising delivery vectors for nucleic acids into the cells. This study presents extensive atomistic molecular dynamics simulations of linear polyethylenimine chains. The simulations show that the variation of the chain size and protonation fraction causes a substantial change of the diffusion coefficient. Examination of the solvated chains suggests the possibility of controlling the polymer diffusion mobility in solution.

Single molecule studies of flexible polymers under shear and mixed flows

NASA Astrophysics Data System (ADS)

Teixeira, Rodrigo Esquivel

We combine manipulation and single molecule visualization of flexible DNA polymers with the generation of controlled simple shear and planar mixed flows for the investigation of polymer flow physics. With the ability to observe polymer conformation directly and follow its evolution in both dilute and entangled regimes we provide a direct test for molecular models. The coil-stretch transition of polymer extension was investigated in planar mixed flows approaching simple shear. Visualization of individual molecules revealed a sharp coil-stretch transition in the steady-state length of the polymer with increasing strain rate in flows slightly more straining than rotational. In slightly more rotational flows significant transient polymer deformation was observed. Next, dilute polymers were visualized in the flow-gradient plane of a steady shear flow. By exploiting the linear proportionality between polymer mass and image intensity, the radius of gyration tensor elements ( Gij) were measured over time. Then, the Giesekus stress tensor was used to obtain the bulk shear viscosity and first normal stress coefficient, thus performing rheology measurements from single molecule conformations. End-over-end tumbling was discovered for the first time, confirming a long-standing prediction and numerous single-chain computer simulation studies. The tumbling frequency followed Wi0.62, and an equation derived from simple advection and diffusion arguments was able to reproduce these observations. Power spectral densities of chain orientation trajectories were found to be single-peaked around the tumbling frequency, thus suggesting a periodic character for polymer dynamics. Finally, we investigated well-entangled polymer solutions. Identical preparations were used in both rheological characterizations and single molecule observations under a variety of shear flow histories. Polymer extension relaxations after the cessation of a fast shear flow revealed two intrinsic characteristic times. The fast one was insensitive to concentration and at least an order of magnitude larger than the Rouse time presupposed by theoretical treatments. The slow timescale grew steeply with concentration, in qualitative agreement with theory. Transient and steady shear flows showed vastly different conformations even among identical molecules subjected to identical flow histories. This "molecular individualism" of well-entangled solutions and its broad conformational distributions calls into question the validity of preaveraging approximations made in molecular-level theories.

Viscoelastic properties of dendrimers in the melt from nonequlibrium molecular dynamics

NASA Astrophysics Data System (ADS)

Bosko, Jaroslaw T.; Todd, B. D.; Sadus, Richard J.

2004-12-01

The viscoelastic properties of dendrimers of generation 1-4 are studied using nonequilibrium molecular dynamics. Flow properties of dendrimer melts under shear are compared to systems composed of linear chain polymers of the same molecular weight, and the influence of molecular architecture is discussed. Rheological material properties, such as the shear viscosity and normal stress coefficients, are calculated and compared for both systems. We also calculate and compare the microscopic properties of both linear chain and dendrimer molecules, such as their molecular alignment, order parameters and rotational velocities. We find that the highly symmetric shape of dendrimers and their highly constrained geometry allows for substantial differences in their material properties compared to traditional linear polymers of equivalent molecular weight.

Novel odd/even effect of alkylene chain length on the photopolymerizability of organogelators.

PubMed

Aoki, Ken'ichi; Kudo, Masabumi; Tamaoki, Nobuyuki

2004-10-28

[reaction: see text] Starting from diactylene diacarboxylic acids, we have synthesized a series of photopolymerizable organogelators that possess simple amide structures, different alkylene chain lengths, and either optically active or racemic 3,7-dimethyl-1-octylamine units. The alkylene chain length of these compounds exhibits a prominent odd/even effect with respect to the photopolymerization in the gel state and is accompanied by a stereostructural effect on the gelation ability.

Ranking Forestry Investments With Parametric Linear Programming

Treesearch

Paul A. Murphy

1976-01-01

Parametric linear programming is introduced as a technique for ranking forestry investments under multiple constraints; it combines the advantages of simple tanking and linear programming as capital budgeting tools.

Fitting mechanistic epidemic models to data: A comparison of simple Markov chain Monte Carlo approaches.

PubMed

Li, Michael; Dushoff, Jonathan; Bolker, Benjamin M

2018-07-01

Simple mechanistic epidemic models are widely used for forecasting and parameter estimation of infectious diseases based on noisy case reporting data. Despite the widespread application of models to emerging infectious diseases, we know little about the comparative performance of standard computational-statistical frameworks in these contexts. Here we build a simple stochastic, discrete-time, discrete-state epidemic model with both process and observation error and use it to characterize the effectiveness of different flavours of Bayesian Markov chain Monte Carlo (MCMC) techniques. We use fits to simulated data, where parameters (and future behaviour) are known, to explore the limitations of different platforms and quantify parameter estimation accuracy, forecasting accuracy, and computational efficiency across combinations of modeling decisions (e.g. discrete vs. continuous latent states, levels of stochasticity) and computational platforms (JAGS, NIMBLE, Stan).

On the formation of suspended noble-metal monatomic chains

NASA Astrophysics Data System (ADS)

Hasmy, A.; Rincón, L.; Hernández, R.; Mujica, V.; Márquez, M.; González, C.

2008-09-01

We present a tight-binding molecular-dynamics investigation of the geometrical and the electronic structure of suspended monatomic noble-metal chains. We show that linear monatomic chains are formed at temperatures equal to or smaller than 500 K for Au, 200 K for Ag, and 4 K for Cu and that they are stable for at least 10 ns. We also evidence that such stability is associated with the persisting sd orbital hybridization along the chains. The study highlights fundamental limitations of conductance measurement experiments to detect these chains in the breaking process of nanowires.

Time Evolving Fission Chain Theory and Fast Neutron and Gamma-Ray Counting Distributions

DOE PAGES

Kim, K. S.; Nakae, L. F.; Prasad, M. K.; ...

2015-11-01

Here, we solve a simple theoretical model of time evolving fission chains due to Feynman that generalizes and asymptotically approaches the point model theory. The point model theory has been used to analyze thermal neutron counting data. This extension of the theory underlies fast counting data for both neutrons and gamma rays from metal systems. Fast neutron and gamma-ray counting is now possible using liquid scintillator arrays with nanosecond time resolution. For individual fission chains, the differential equations describing three correlated probability distributions are solved: the time-dependent internal neutron population, accumulation of fissions in time, and accumulation of leaked neutronsmore » in time. Explicit analytic formulas are given for correlated moments of the time evolving chain populations. The equations for random time gate fast neutron and gamma-ray counting distributions, due to randomly initiated chains, are presented. Correlated moment equations are given for both random time gate and triggered time gate counting. There are explicit formulas for all correlated moments are given up to triple order, for all combinations of correlated fast neutrons and gamma rays. The nonlinear differential equations for probabilities for time dependent fission chain populations have a remarkably simple Monte Carlo realization. A Monte Carlo code was developed for this theory and is shown to statistically realize the solutions to the fission chain theory probability distributions. Combined with random initiation of chains and detection of external quanta, the Monte Carlo code generates time tagged data for neutron and gamma-ray counting and from these data the counting distributions.« less

Doubly self-consistent field theory of grafted polymers under simple shear in steady state

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

Suo, Tongchuan; Whitmore, Mark D., E-mail: mark-whitmore@umanitoba.ca

2014-03-21

We present a generalization of the numerical self-consistent mean-field theory of polymers to the case of grafted polymers under simple shear. The general theoretical framework is presented, and then applied to three different chain models: rods, Gaussian chains, and finitely extensible nonlinear elastic (FENE) chains. The approach is self-consistent at two levels. First, for any flow field, the polymer density profile and effective potential are calculated self-consistently in a manner similar to the usual self-consistent field theory of polymers, except that the calculation is inherently two-dimensional even for a laterally homogeneous system. Second, through the use of a modified Brinkmanmore » equation, the flow field and the polymer profile are made self-consistent with respect to each other. For all chain models, we find that reasonable levels of shear cause the chains to tilt, but it has very little effect on the overall thickness of the polymer layer, causing a small decrease for rods, and an increase of no more than a few percent for the Gaussian and FENE chains. Using the FENE model, we also probe the individual bond lengths, bond correlations, and bond angles along the chains, the effects of the shear on them, and the solvent and bonded stress profiles. We find that the approximations needed within the theory for the Brinkman equation affect the bonded stress, but none of the other quantities.« less

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

Kim, K. S.; Nakae, L. F.; Prasad, M. K.

Here, we solve a simple theoretical model of time evolving fission chains due to Feynman that generalizes and asymptotically approaches the point model theory. The point model theory has been used to analyze thermal neutron counting data. This extension of the theory underlies fast counting data for both neutrons and gamma rays from metal systems. Fast neutron and gamma-ray counting is now possible using liquid scintillator arrays with nanosecond time resolution. For individual fission chains, the differential equations describing three correlated probability distributions are solved: the time-dependent internal neutron population, accumulation of fissions in time, and accumulation of leaked neutronsmore » in time. Explicit analytic formulas are given for correlated moments of the time evolving chain populations. The equations for random time gate fast neutron and gamma-ray counting distributions, due to randomly initiated chains, are presented. Correlated moment equations are given for both random time gate and triggered time gate counting. There are explicit formulas for all correlated moments are given up to triple order, for all combinations of correlated fast neutrons and gamma rays. The nonlinear differential equations for probabilities for time dependent fission chain populations have a remarkably simple Monte Carlo realization. A Monte Carlo code was developed for this theory and is shown to statistically realize the solutions to the fission chain theory probability distributions. Combined with random initiation of chains and detection of external quanta, the Monte Carlo code generates time tagged data for neutron and gamma-ray counting and from these data the counting distributions.« less

Complete structural characterization of ceramides as [M – H]− ions by multiple-stage linear ion trap mass spectrometry

PubMed Central

Hsu, Fong-Fu

2016-01-01

Ceramide is a huge lipid family consisting of diversified structures including various modifications in the fatty acyl chain and the long chain base (LCB). In this contribution, negative-ion ESI linear ion-trap multiple-stage mass spectrometric method (LIT MSn) towards complete structural determination of ceramides in ten major families characterized as the [M – H]− ions is described. Multiple sets of fragment ions reflecting the fatty acyl chain and LCB were observed in the CID MS2 spectrum, while the sequential MS3 and MS4 spectra contain structural information for locating the double bond and the functional groups, permitting realization of the fragmentation processes. Thereby, differentiation of ceramide molecules varied by chain length, the LCB (sphingosine, phytosphigosine, 6-hydroxy-sphingosine), and by the modification (α-hydroxy-, β-hydroxy-, ω-hydroxy-FA) can be achieved; and many isomeric structures in the biological specimen can be revealed in detail. PMID:27523779

Simulating the performance of a distance-3 surface code in a linear ion trap

NASA Astrophysics Data System (ADS)

Trout, Colin J.; Li, Muyuan; Gutiérrez, Mauricio; Wu, Yukai; Wang, Sheng-Tao; Duan, Luming; Brown, Kenneth R.

2018-04-01

We explore the feasibility of implementing a small surface code with 9 data qubits and 8 ancilla qubits, commonly referred to as surface-17, using a linear chain of 171Yb+ ions. Two-qubit gates can be performed between any two ions in the chain with gate time increasing linearly with ion distance. Measurement of the ion state by fluorescence requires that the ancilla qubits be physically separated from the data qubits to avoid errors on the data due to scattered photons. We minimize the time required to measure one round of stabilizers by optimizing the mapping of the two-dimensional surface code to the linear chain of ions. We develop a physically motivated Pauli error model that allows for fast simulation and captures the key sources of noise in an ion trap quantum computer including gate imperfections and ion heating. Our simulations showed a consistent requirement of a two-qubit gate fidelity of ≥99.9% for the logical memory to have a better fidelity than physical two-qubit operations. Finally, we perform an analysis of the error subsets from the importance sampling method used to bound the logical error rates to gain insight into which error sources are particularly detrimental to error correction.

Theory of polyelectrolytes in solvents.

PubMed

Chitanvis, Shirish M

2003-12-01

Using a continuum description, we account for fluctuations in the ionic solvent surrounding a Gaussian, charged chain and derive an effective short-ranged potential between the charges on the chain. This potential is repulsive at short separations and attractive at longer distances. The chemical potential can be derived from this potential. When the chemical potential is positive, it leads to a meltlike state. For a vanishingly low concentration of segments, this state exhibits scaling behavior for long chains. The Flory exponent characterizing the radius of gyration for long chains is calculated to be approximately 0.63, close to the classical value obtained for second order phase transitions. For short chains, the radius of gyration varies linearly with N, the chain length, and is sensitive to the parameters in the interaction potential. The linear dependence on the chain length N indicates a stiff behavior. The chemical potential associated with this interaction changes sign, when the screening length in the ionic solvent exceeds a critical value. This leads to condensation when the chemical potential is negative. In this state, it is shown using the mean-field approximation that spherical and toroidal condensed shapes can be obtained. The thickness of the toroidal polyelectrolyte is studied as a function of the parameters of the model, such as the ionic screening length. The predictions of this theory should be amenable to experimental verification.

A simple next-best alternative to seasonal predictions in Europe

NASA Astrophysics Data System (ADS)

Buontempo, Carlo; De Felice, Matteo

2016-04-01

In order to build a climate proof society, we need to learn how to best use the climate information we have. Having spent time and resources in developing complex numerical models has often blinded us on the value some of this information really has in the eyes of a decision maker. An effective way to assess this is to check the quality of the forecast (and its cost) to the quality of the forecast from a prediction system based on simpler assumption (and thus cheaper to run). Such a practice is common in marketing analysis where it is often referred to as the next-best alternative. As a way to facilitate such an analysis, climate service providers should always provide alongside the predictions a set of skill scores. These are usually based on climatological means, anomaly persistence or more recently multiple linear regressions. We here present an equally simple benchmark based on a Markov chain process locally trained at a monthly or seasonal time-scale. We demonstrate that in spite of its simplicity the model easily outperforms not only the standard benchmark but also most of the seasonal predictions system at least in EUROPE. We suggest that a benchmark of this kind could represent a useful next-best alternative for a number of users.

Colloidal nanocrystals as LEGO® bricks for building electronic band structure models.

PubMed

Tadjine, Athmane; Delerue, Christophe

2018-03-28

The synthesis of self-assembled semiconductor nanocrystal (NC) superlattices using oriented attachment recently became a flourishing research topic. This technique already produced remarkable forms of NC superlattices, such as linear chains, mono and multilayer square lattices, and silicene-like honeycomb lattices. In the case of lead chalcogenide semiconductors where NCs are in the form of truncated nanocubes, the attachment mostly occurs via (100) facets. In this work, we show that all these structures can be seen as sub-structures of a simple cubic lattice. From this, we investigate a rich variety of one-dimensional or two-dimensional superlattices that could be built as few lines or few layers taken from the same cubic system following different crystallographic orientations. Each NC can be therefore considered as a LEGO® brick, and any superlattice can be obtained from another one by rearranging the bricks. Moreover, we show that this concept of LEGO® bricks can be extended to the calculation of the electronic band structure of the superlattices. This leads to a simple yet powerful way to build analytical Hamiltonians that present band structures in excellent agreement with more elaborate atomistic tight-binding calculations. This LEGO® concept could guide the synthesis of superlattices and LEGO® Hamiltonians should greatly simplify further studies on the (opto-)electronic properties of such structures.

Characterization of single chain antibody targets through yeast two hybrid

PubMed Central

2010-01-01

Background Due to their unique ability to bind their targets with high fidelity, antibodies are used widely not only in biomedical research, but also in many clinical applications. Recombinant antibodies, including single chain variable fragments (scFv), are gaining momentum because they allow powerful in vitro selection and manipulation without loss of function. Regardless of the ultimate application or type of antibody used, precise understanding of the interaction between the antibody's binding site and its specific target epitope(s) is of great importance. However, such data is frequently difficult to obtain. Results We describe an approach that allows detailed characterization of a given antibody's target(s) using the yeast two-hybrid system. Several recombinant scFv were used as bait and screened against highly complex cDNA libraries. Systematic sequencing of all retained clones and statistical analysis allowed efficient ranking of the prey fragments. Multiple alignment of the obtained cDNA fragments provided a selected interacting domain (SID), efficiently narrowing the epitope-containing region. Interactions between antibodies and their respective targets were characterized for several scFv. For AA2 and ROF7, two conformation-specific sensors that exclusively bind the activated forms of the small GTPases Rab6 and Rab1 respectively, only fragments expressing the entire target protein's core region were retained. This strongly suggested interaction with a non-linear epitope. For two other scFv, TA10 and SF9, which recognize the large proteins giantin and non-muscle myosin IIA, respectively, precise antibody-binding regions within the target were defined. Finally, for some antibodies, secondary targets within and across species could be revealed. Conclusions Our method, utilizing the yeast two-hybrid technology and scFv as bait, is a simple yet powerful approach for the detailed characterization of antibody targets. It allows precise domain mapping for linear epitopes, confirmation of non-linear epitopes for conformational sensors, and detection of secondary binding partners. This approach may thus prove to be an elegant and rapid method for the target characterization of newly obtained scFv antibodies. It may be considered prior to any research application and particularly before any use of such recombinant antibodies in clinical medicine. PMID:20727208

Linear Equating for the NEAT Design: Parameter Substitution Models and Chained Linear Relationship Models

ERIC Educational Resources Information Center

Kane, Michael T.; Mroch, Andrew A.; Suh, Youngsuk; Ripkey, Douglas R.

2009-01-01

This paper analyzes five linear equating models for the "nonequivalent groups with anchor test" (NEAT) design with internal anchors (i.e., the anchor test is part of the full test). The analysis employs a two-dimensional framework. The first dimension contrasts two general approaches to developing the equating relationship. Under a "parameter…

Models for Models: An Introduction to Polymer Models Employing Simple Analogies

NASA Astrophysics Data System (ADS)

Tarazona, M. Pilar; Saiz, Enrique

1998-11-01

An introduction to the most common models used in the calculations of conformational properties of polymers, ranging from the freely jointed chain approximation to Monte Carlo or molecular dynamics methods, is presented. Mathematical formalism is avoided and simple analogies, such as human chains, gases, opinion polls, or marketing strategies, are used to explain the different models presented. A second goal of the paper is to teach students how models required for the interpretation of a system can be elaborated, starting with the simplest model and introducing successive improvements until the refinements become so sophisticated that it is much better to use an alternative approach.

Psychological Distance to Reward: Effects of S+ Duration and the Delay Reduction It Signals

ERIC Educational Resources Information Center

Alessandri, Jerome; Stolarz-Fantino, Stephanie; Fantino, Edmund

2011-01-01

A concurrent-chains procedure was used to examine choice between segmented (two-component chained schedules) and unsegmented schedules (simple schedules) in terminal links with equal inter-reinforcement intervals. Previous studies using this kind of experimental procedure showed preference for unsegmented schedules for both pigeons and humans. In…

Atwood's Heavy Chain

ERIC Educational Resources Information Center

Beeken, Paul

2011-01-01

While perusing various websites in search of a more challenging lab for my students, I came across a number of ideas where replacing the string in an Atwood's machine with a simple ball chain like the kind found in lamp pulls created an interesting system to investigate. The replacement of the string produced a nice nonuniform acceleration, but…

Action Centered Contextual Bandits.

PubMed

Greenewald, Kristjan; Tewari, Ambuj; Klasnja, Predrag; Murphy, Susan

2017-12-01

Contextual bandits have become popular as they offer a middle ground between very simple approaches based on multi-armed bandits and very complex approaches using the full power of reinforcement learning. They have demonstrated success in web applications and have a rich body of associated theoretical guarantees. Linear models are well understood theoretically and preferred by practitioners because they are not only easily interpretable but also simple to implement and debug. Furthermore, if the linear model is true, we get very strong performance guarantees. Unfortunately, in emerging applications in mobile health, the time-invariant linear model assumption is untenable. We provide an extension of the linear model for contextual bandits that has two parts: baseline reward and treatment effect. We allow the former to be complex but keep the latter simple. We argue that this model is plausible for mobile health applications. At the same time, it leads to algorithms with strong performance guarantees as in the linear model setting, while still allowing for complex nonlinear baseline modeling. Our theory is supported by experiments on data gathered in a recently concluded mobile health study.

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.

Building Simple Hidden Markov Models. Classroom Notes

ERIC Educational Resources Information Center

Ching, Wai-Ki; Ng, Michael K.

2004-01-01

Hidden Markov models (HMMs) are widely used in bioinformatics, speech recognition and many other areas. This note presents HMMs via the framework of classical Markov chain models. A simple example is given to illustrate the model. An estimation method for the transition probabilities of the hidden states is also discussed.

A Practical Workshop for Generating Simple DNA Fingerprints of Plants

ERIC Educational Resources Information Center

Rouziere, A.-S.; Redman, J. E.

2011-01-01

Gel electrophoresis DNA fingerprints offer a graphical and visually appealing illumination of the similarities and differences between DNA sequences of different species and individuals. A polymerase chain reaction (PCR) and restriction digest protocol was designed to give high-school students the opportunity to generate simple fingerprints of…

New Paenibacillus strain produces a family of linear and cyclic antimicrobial lipopeptides: cyclization is not essential for their antimicrobial activity.

PubMed

Huang, En; Yang, Xu; Zhang, Liwen; Moon, Sun Hee; Yousef, Ahmed E

2017-04-01

A new bacterial isolate, Paenibacillus sp. OSY-N, showed potent antimicrobial activity against Gram-negative and Gram-positive bacteria. Antimicrobials produced by this strain were purified by reverse-phase high-performance liquid chromatography. Structural analysis, using mass spectrometry, of a single active HPLC fraction revealed two known cyclic lipopeptides (BMY-28160 and permetin A), a new cyclic lipopeptide, and the linear counterparts of these cyclic compounds. The latter were designated as paenipeptins A, B and C, respectively. The paenipeptins have not been reported before as naturally occurring products. Paenipeptins B and C differ at the acyl side chain; paenipeptin C contains a C8-, instead of C7-fatty acyl side chain. To demonstrate unequivocally the antimicrobial activity of the linear forms of this family of cyclic lipopeptides, analogs of the paenipeptins were synthesized chemically and their antimicrobial activity was tested individually. The synthetic linear lipopeptide with an octanoic acid side chain (designated as paenipeptin C΄) showed potent antimicrobial activity with minimum inhibitory concentrations of 0.5-4.0 μg/mL for Gram-negative and 0.5-32 μg/mL for Gram-positive bacteria. Findings demonstrated that peptide cyclization in this lipopeptide family is not essential for their antimicrobial activity. Most importantly, linear lipopeptides are more accessible than their cyclic counterparts through chemical synthesis. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Kinetics of DSB rejoining and formation of simple chromosome exchange aberrations

NASA Technical Reports Server (NTRS)

Cucinotta, F. A.; Nikjoo, H.; O'Neill, P.; Goodhead, D. T.

2000-01-01

PURPOSE: To investigate the role of kinetics in the processing of DNA double strand breaks (DSB), and the formation of simple chromosome exchange aberrations following X-ray exposures to mammalian cells based on an enzymatic approach. METHODS: Using computer simulations based on a biochemical approach, rate-equations that describe the processing of DSB through the formation of a DNA-enzyme complex were formulated. A second model that allows for competition between two processing pathways was also formulated. The formation of simple exchange aberrations was modelled as misrepair during the recombination of single DSB with undamaged DNA. Non-linear coupled differential equations corresponding to biochemical pathways were solved numerically by fitting to experimental data. RESULTS: When mediated by a DSB repair enzyme complex, the processing of single DSB showed a complex behaviour that gives the appearance of fast and slow components of rejoining. This is due to the time-delay caused by the action time of enzymes in biomolecular reactions. It is shown that the kinetic- and dose-responses of simple chromosome exchange aberrations are well described by a recombination model of DSB interacting with undamaged DNA when aberration formation increases with linear dose-dependence. Competition between two or more recombination processes is shown to lead to the formation of simple exchange aberrations with a dose-dependence similar to that of a linear quadratic model. CONCLUSIONS: Using a minimal number of assumptions, the kinetics and dose response observed experimentally for DSB rejoining and the formation of simple chromosome exchange aberrations are shown to be consistent with kinetic models based on enzymatic reaction approaches. A non-linear dose response for simple exchange aberrations is possible in a model of recombination of DNA containing a DSB with undamaged DNA when two or more pathways compete for DSB repair.

Constructing and decoding unconventional ubiquitin chains.

PubMed

Behrends, Christian; Harper, J Wade

2011-05-01

One of the most notable discoveries in the ubiquitin system during the past decade is the extensive use of diverse chain linkages to control signaling networks. Although the utility of Lys48- and Lys63-linked chains in protein turnover and molecular assembly, respectively, are well known, we are only beginning to understand how unconventional chain linkages are formed on target proteins and how such linkages are decoded by specific binding proteins. In this review, we summarize recent efforts to elucidate the machinery and mechanisms controlling assembly of Lys11-linked and linear (or Met1-linked) ubiquitin chains, and describe current models for how these chain types function in immune signaling and cell-cycle control.

Polarizable polymer chain under external electric field: Effects of many-body electrostatic dipole correlations.

PubMed

Budkov, Yu A; Kolesnikov, A L

2016-11-01

We present a new simple self-consistent field theory of a polarizable flexible polymer chain under an external constant electric field with account for the many-body electrostatic dipole correlations. We show the effects of electrostatic dipole correlations on the electric-field-induced globule-coil transition. We demonstrate that only when the polymer chain is in the coil conformation, the electrostatic dipole correlations of monomers can be considered as pairwise. However, when the polymer chain is in a collapsed state, the dipole correlations have to be considered at the many-body level.

Simple quasi-analytical holonomic homogenization model for the non-linear analysis of in-plane loaded masonry panels: Part 1, meso-scale

NASA Astrophysics Data System (ADS)

Milani, G.; Bertolesi, E.

2017-07-01

A simple quasi analytical holonomic homogenization approach for the non-linear analysis of masonry walls in-plane loaded is presented. The elementary cell (REV) is discretized with 24 triangular elastic constant stress elements (bricks) and non-linear interfaces (mortar). A holonomic behavior with softening is assumed for mortar. It is shown how the mechanical problem in the unit cell is characterized by very few displacement variables and how homogenized stress-strain behavior can be evaluated semi-analytically.

Seeing the order in a mess: optical signature of periodicity in a cloud of plasmonic nanowires.

PubMed

Natarov, Denys M; Marciniak, Marian; Sauleau, Ronan; Nosich, Alexander I

2014-11-17

We consider the two-dimensional (2-D) problem of the H-polarized plane wave scattering by a linear chain of silver nanowires in a cloud of similar pseudo-randomly located wires, in the visible range. Numerical solution uses the field expansions in local coordinates and addition theorems for cylindrical functions and has a guaranteed convergence. The total scattering cross-sections and near- and far-zone field patterns are presented. The observed resonance effects are studied and compared with their counterparts in the scattering by the same linear chain of wires in free space.

Linear and Non-Linear Visual Feature Learning in Rat and Humans

PubMed Central

Bossens, Christophe; Op de Beeck, Hans P.

2016-01-01

The visual system processes visual input in a hierarchical manner in order to extract relevant features that can be used in tasks such as invariant object recognition. Although typically investigated in primates, recent work has shown that rats can be trained in a variety of visual object and shape recognition tasks. These studies did not pinpoint the complexity of the features used by these animals. Many tasks might be solved by using a combination of relatively simple features which tend to be correlated. Alternatively, rats might extract complex features or feature combinations which are nonlinear with respect to those simple features. In the present study, we address this question by starting from a small stimulus set for which one stimulus-response mapping involves a simple linear feature to solve the task while another mapping needs a well-defined nonlinear combination of simpler features related to shape symmetry. We verified computationally that the nonlinear task cannot be trivially solved by a simple V1-model. We show how rats are able to solve the linear feature task but are unable to acquire the nonlinear feature. In contrast, humans are able to use the nonlinear feature and are even faster in uncovering this solution as compared to the linear feature. The implications for the computational capabilities of the rat visual system are discussed. PMID:28066201

Collision of Identical Solitary Waves in Hertzian Chains

NASA Astrophysics Data System (ADS)

Sen, Surajit; Manciu, Marian; Hurd, Alan J.

2000-03-01

We consider a chain of elastic beads, which repel upon contact according to the non-linear Hertz potential. We further assume that the chain is under zero loading, i.e., the grains have zero initial overlap. We show via careful numerical solution of the equations of motion that an impulse propagates as a solitary wave and that the collision of identical solitary waves propagating in opposite directions along the chain spawns a hierarchy of multiple weak solitary waves [1]. [1] M. Manciu, S. Sen and A.J. Hurd, Phys Lett A (submitted).

Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression

PubMed Central

Polka, Jessica K.

2014-01-01

Bacteria from several taxa, including Kurthia zopfii, Myxococcus xanthus, and Bacillus mycoides, have been reported to align growth of their colonies to small features on the surface of solid media, including anisotropies created by compression. While the function of this phenomenon is unclear, it may help organisms navigate on solid phases, such as soil. The origin of this behavior is also unknown: it may be biological (that is, dependent on components that sense the environment and regulate growth accordingly) or merely physical. Here we show that B. subtilis, an organism that typically does not respond to media compression, can be induced to do so with two simple and synergistic perturbations: a mutation that maintains cells in the swarming (chained) state, and the addition of EDTA to the growth media, which further increases chain length. EDTA apparently increases chain length by inducing defects in cell separation, as the treatment has only marginal effects on the length of individual cells. These results lead us to three conclusions. First, the wealth of genetic tools available to B. subtilis will provide a new, tractable chassis for engineering compression sensitive organisms. Second, the sensitivity of colony morphology to media compression in Bacillus can be modulated by altering a simple physical property of rod-shaped cells. And third, colony morphology under compression holds promise as a rapid, simple, and low-cost way to screen for changes in the length of rod-shaped cells or chains thereof. PMID:25289183

The influence of polymer architectures on the dewetting behavior of thin polymer films: from linear chains to ring chains.

PubMed

Wang, Lina; Xu, Lin; Liu, Binyuan; Shi, Tongfei; Jiang, Shichun; An, Lijia

2017-05-03

The dewetting behavior of ring polystyrene (RPS) film and linear polystyrene (LPS) film on silanized Si substrates with different grafting densities and PDMS substrate was investigated. Results showed that polymer architectures greatly influenced the dewetting behavior of the thin polymer film. On the silanized Si substrate with 69% grafting density, RPS chains exhibited stronger adsorption compared with LPS chains, and as a result the wetting layer formed more easily. For LPS films, with a decreased annealing temperature, the stability of the polymer film changed from non-slip dewetting via apparent slip dewetting to apparently stable. However, for RPS films, the polymer film stability switched from apparent slip dewetting to apparently stable. On the silanized Si substrate with 94% grafting density, the chain adsorption became weaker and the dewetting processes were faster than that on the substrate with 69% grafting density at the same experimental temperature for both the LPS and RPS films. Moreover, on the PDMS substrate, LPS films always showed non-slip dewetting, while the dewetting kinetics of RPS films switched from non-slip dewetting to slip dewetting behaviour. Forming the wetting layer strongly influenced the stability and dewetting behavior of the thin polymer films.

Endocrine disrupting alkylphenols: structural requirements for their adverse effects on Ca2+ pumps, Ca2+ homeostasis & Sertoli TM4 cell viability.

PubMed

Michelangeli, Francesco; Ogunbayo, Oluseye A; Wootton, Laura L; Lai, Pei F; Al-Mousa, Fawaz; Harris, Robert M; Waring, Rosemary H; Kirk, Christopher J

2008-11-25

Alkylphenols such as nonylphenol are pollutants that are widely dispersed within our environment. They bio-accumulate within man, with levels in the muM concentration range reported in human tissues. These chemicals act as endocrine disruptors, having xenoestrogenic activity. More recently alkylphenols have also been shown to affect Ca2+ signalling pathways. Here we show that alkylphenols are potent inhibitors of sarcoplasmic-endoplasmic reticulum Ca2+-ATPase (SERCA) activity. For linear chain alkylphenols the potency of inhibition is related to chain length, with the IC50 values for inhibition ranging from 8 microM for 4-n-nonylphenol (C9) to 1.3 mM for 4-n-propylphenol (C3). Branched chain alkylphenols generally had lower potencies than their linear chain counterparts, however, good correlations for all alkylphenols were observed between their Ca2+ pump inhibition and hydrophobicity, molecular volume and flexibility, indicating that these parameters are all important factors. Alkylphenols cause abnormal elevations of intracellular [Ca2+] within TM4 Sertoli cells (cells involved in sperm maturation) depolarise their mitochondria and induce cell death in these cells, in an alkyl chain size-dependent manner.

First principles study of hydrogen adsorption on carbon nanowires.

NASA Astrophysics Data System (ADS)

Tapia, Alejandro; Aguilera, Luis; Murrieta, Gabriel; de Coss, Romeo

2007-03-01

Recently has been reported a new type of one-dimensional carbon structures. Carbon nanowires formed by a linear carbon-atom chain inside an armchair (5,5) carbon nanotube has been observed using high-resolution transmission electron microscopy. In the present work we have studied the changes in the electronic structure of a carbon nanowires and (5,5) single-walled carbon nanotubes (SWCN) when a hydrogen atom is adsorbed. We used the Density Functional Theory and the calculations where performed by the pseudopotentials LCAO method (SIESTA code) and the Generalized Gradient Approximation (GGA) for the exchange-correlation potential. We have analyzed the changes in the atomic structure, density of states (LDOS), and the local orbital population. We found charge transfer from the nanotube to the linear chain and the hydrogen atom, the electronic character of the chain and nanotube sub-systems in chain@SWCN is the same that in the corresponding isolated systems, chain or SWCN. But the hydrogen adsorption produced changes in the atomic estructure and the electronic properties. This research was supported by PRIORI-UADY under Grant No. FING-05-004 and Consejo Nacional de Ciencia y Tecnolog'ia (Conacyt) under Grants No. 43830-F and 49985-J.

Circuit topology of proteins and nucleic acids.

PubMed

Mashaghi, Alireza; van Wijk, Roeland J; Tans, Sander J

2014-09-02

Folded biomolecules display a bewildering structural complexity and diversity. They have therefore been analyzed in terms of generic topological features. For instance, folded proteins may be knotted, have beta-strands arranged into a Greek-key motif, or display high contact order. In this perspective, we present a method to formally describe the topology of all folded linear chains and hence provide a general classification and analysis framework for a range of biomolecules. Moreover, by identifying the fundamental rules that intrachain contacts must obey, the method establishes the topological constraints of folded linear chains. We also briefly illustrate how this circuit topology notion can be applied to study the equivalence of folded chains, the engineering of artificial RNA structures and DNA origami, the topological structure of genomes, and the role of topology in protein folding. Copyright © 2014 Elsevier Ltd. All rights reserved.

The weight hierarchies and chain condition of a class of codes from varieties over finite fields

NASA Technical Reports Server (NTRS)

Wu, Xinen; Feng, Gui-Liang; Rao, T. R. N.

1996-01-01

The generalized Hamming weights of linear codes were first introduced by Wei. These are fundamental parameters related to the minimal overlap structures of the subcodes and very useful in several fields. It was found that the chain condition of a linear code is convenient in studying the generalized Hamming weights of the product codes. In this paper we consider a class of codes defined over some varieties in projective spaces over finite fields, whose generalized Hamming weights can be determined by studying the orbits of subspaces of the projective spaces under the actions of classical groups over finite fields, i.e., the symplectic groups, the unitary groups and orthogonal groups. We give the weight hierarchies and generalized weight spectra of the codes from Hermitian varieties and prove that the codes satisfy the chain condition.

Less can be more: How to make operations more flexible and robust with fewer resources

NASA Astrophysics Data System (ADS)

Haksöz, ćaǧrı; Katsikopoulos, Konstantinos; Gigerenzer, Gerd

2018-06-01

We review empirical evidence from practice and general theoretical conditions, under which simple rules of thumb can help to make operations flexible and robust. An operation is flexible when it responds adaptively to adverse events such as natural disasters; an operation is robust when it is less affected by adverse events in the first place. We illustrate the relationship between flexibility and robustness in the context of supply chain risk. In addition to increasing flexibility and robustness, simple rules simultaneously reduce the need for resources such as time, money, information, and computation. We illustrate the simple-rules approach with an easy-to-use graphical aid for diagnosing and managing supply chain risk. More generally, we recommend a four-step process for determining the amount of resources that decision makers should invest in so as to increase flexibility and robustness.

Mycobacterium avium restriction fragment length polymorphism-IS IS1245 and the simple double repetitive element polymerase chain reaction typing method to screen genetic diversity in Brazilian strains.

PubMed

Sequeira, Patrícia Carvalho de; Fonseca, Leila de Souza; Silva, Marlei Gomes da; Saad, Maria Helena Féres

2005-11-01

Simple double repetitive element polymerase chain reaction (MaDRE-PCR) and Pvu II-IS1245 restriction fragment length polymorphism (RFLP) typing methods were used to type 41 Mycobacterium avium isolates obtained from 14 AIDS inpatients and 10 environment and animals specimens identified among 53 mycobacteria isolated from 237 food, chicken, and pig. All environmental and animals strains showed orphan patterns by both methods. By MaDRE-PCR four patients, with multiple isolates, showed different patterns, suggesting polyclonal infection that was confirmed by RFLP in two of them. This first evaluation of MaDRE-PCR on Brazilian M. avium strains demonstrated that the method seems to be useful as simple and less expensive typing method for screening genetic diversity in M. avium strains on selected epidemiological studies, although with limitation on analysis identical patterns except for one band.

Organometallic macromolecules with piano stool coordination repeating units: chain configuration and stimulated solution behaviour.

PubMed

Cao, Kai; Ward, Jonathan; Amos, Ryan C; Jeong, Moon Gon; Kim, Kyoung Taek; Gauthier, Mario; Foucher, Daniel; Wang, Xiaosong

2014-09-11

Theoretical calculations illustrate that organometallic macromolecules with piano stool coordination repeating units (Fe-acyl complex) adopt linear chain configuration with a P-Fe-C backbone surrounded by aromatic groups. The macromolecules show molecular weight-dependent and temperature stimulated solution behaviour in DMSO.

A comparison of the solvation structure and dynamics of the lithium ion in linear organic carbonates with different alkyl chain lengths.

PubMed

Fulfer, K D; Kuroda, D G

2017-09-20

The structure and dynamics of electrolytes composed of lithium hexafluorophosphate (LiPF 6 ) in dimethyl carbonate, ethyl methyl carbonate, and diethyl carbonate were investigated using a combination of linear and two-dimensional infrared spectroscopies. The solutions studied here have a LiPF 6 concentration of X(LiPF 6 ) = 0.09, which is typically found in commercial lithium ion batteries. This study focuses on comparing the differences in the solvation shell structure and dynamics produced by linear organic carbonates of different alkyl chain lengths. The IR experiments show that either linear carbonate forms a tetrahedral solvation shell (coordination number of 4) around the lithium ion irrespective of whether the solvation shell has anions in close proximity to the carbonates. Moreover, analysis of the absorption cross sections via FTIR and DFT computations reveals a distortion in the angle formed by Li + -O[double bond, length as m-dash]C which decreases from the expected 180° when the alkyl chains of the carbonate are lengthened. In addition, our findings also reveal that, likely due to its asymmetric structure, ethyl methyl carbonate has a significantly more distorted tetrahedral lithium ion solvation shell than either of the other two investigated carbonates. IR photon echo studies further demonstrate that the motions of the solvation shell have a time scale of a few picoseconds for all three linear carbonates. Interestingly, a slowdown of the in place-motions of the first solvation shell is observed when the carbonate has a longer alkyl chain length irrespective of the symmetry. In addition, vibrational energy transfer with a time scale of tens of picoseconds is observed between strongly coupled modes arising from the solvation shell structure of the Li + which corroborates the modeling of these solvation shells in terms of highly coupled vibrational states. Results of this study provide new insights into the molecular structure and dynamics of the lithium ion electrolyte components as a function of solvent structure.

Multi-scale modeling of biophysical phenomena: ionic transport, biomineralization, and force spectroscopy

NASA Astrophysics Data System (ADS)

Kelly, Mark A.

2011-07-01

Biophysics is the study of the complex physical processes occurring in biological systems that are responsible for life. This dissertation addresses three important topics in biophysics: ionic transport, biomineralization, and force spectroscopy. Ionic transport involves the passage of ions through a special class of hollow, transmembrane proteins called ion channels which regulate the movement of charged species across nearly all biological membranes with varying degrees of specificity. Despite the fundamental importance of these channels to many physiological processes little is known about how channel structure and composition couple to determine its function. Deriving inspiration from these systems, a simple computational platform is developed to study the salient features of these channels in order to better understand the fundamental physics of these systems. The results of this work indicate that a converging-diverging region formed within the pore to create a single constriction is the most effective method to regulate the passage of ions through the pore. By controlling the geometry of the constriction the local potential and chemical gradients can be manipulated to tailor the channel for specific applications. The process of selective extraction and incorporation of local elements from the surrounding environment into functional structures under strict biological control is known as biomineralization. As an initial step to gain a more fundamental understanding of directed crystallization of zinc oxide molecular dynamics simulations were performed to study the conformational behavior of two experimentally derived biomimetic peptides in a precursor solution. Substantial differences in the conformational properties and affinity for zinc and hydroxide ions in solution were observed. These findings are in qualitative agreement with experimental observations. The mechanical response of biopolymers such as RNA and DNA to externally applied forces is a topic that has received wide interest both experimentally and theoretically. In the first of two separate force spectroscopy studies, the mechanical response of linear uncharged polymer chains of variable molecular weight subjected to repeated pulling-retraction cycles in poor solvent was investigated. It was found that the observed hysteresis in this system is highly dependent on the speed at which the chain is perturbed. In the second study, the force-induced globule-coil transition of a linear polyelectrolyte chain in poor solvent was examined. It was observed that the magnitude of the change in the degree of ionization of the chain at the transition is a strong function of counterion size and Coulombic strength.

Early Understandings of Simple Food Chains: A Learning Progression for the Preschool Years

ERIC Educational Resources Information Center

Allen, Michael

2017-01-01

Aspects of preschoolers' ecological understandings were explored in a cross-age, quantitative study that utilised a sample of seventy-five 3- to 5-year-old children. Specifically, their concepts of feeding relationships were determined by presenting physical models of three-step food chains during structured interviews. A majority of children,…

Multi-Mode Analysis of Dual Ridged Waveguide Systems for Material Characterization

DTIC Science & Technology

2015-09-17

characterization is the process of determining the dielectric, magnetic, and magnetoelectric properties of a material. For simple (i.e., linear ...field expressions in terms of elementary functions (sines, cosines, exponentials and Bessel functions) and corresponding propagation constants of the...with material parameters 0 and µ0. • The MUT is simple ( linear , isotropic, homogeneous), and the sample has a uniform thickness. • The waveguide

Microbial synthesis of medium-chain chemicals from renewables.

PubMed

Sarria, Stephen; Kruyer, Nicholas S; Peralta-Yahya, Pamela

2017-12-01

Linear, medium-chain (C8-C12) hydrocarbons are important components of fuels as well as commodity and specialty chemicals. As industrial microbes do not contain pathways to produce medium-chain chemicals, approaches such as overexpression of endogenous enzymes or deletion of competing pathways are not available to the metabolic engineer; instead, fatty acid synthesis and reversed β-oxidation are manipulated to synthesize medium-chain chemical precursors. Even so, chain lengths remain difficult to control, which means that purification must be used to obtain the desired products, titers of which are typically low and rarely exceed milligrams per liter. By engineering the substrate specificity and activity of the pathway enzymes that generate the fatty acyl intermediates and chain-tailoring enzymes, researchers can boost the type and yield of medium-chain chemicals. Development of technologies to both manipulate chain-tailoring enzymes and to assay for products promises to enable the generation of g/L yields of medium-chain chemicals.

A reversible-jump Markov chain Monte Carlo algorithm for 1D inversion of magnetotelluric data

NASA Astrophysics Data System (ADS)

Mandolesi, Eric; Ogaya, Xenia; Campanyà, Joan; Piana Agostinetti, Nicola

2018-04-01

This paper presents a new computer code developed to solve the 1D magnetotelluric (MT) inverse problem using a Bayesian trans-dimensional Markov chain Monte Carlo algorithm. MT data are sensitive to the depth-distribution of rock electric conductivity (or its reciprocal, resistivity). The solution provided is a probability distribution - the so-called posterior probability distribution (PPD) for the conductivity at depth, together with the PPD of the interface depths. The PPD is sampled via a reversible-jump Markov Chain Monte Carlo (rjMcMC) algorithm, using a modified Metropolis-Hastings (MH) rule to accept or discard candidate models along the chains. As the optimal parameterization for the inversion process is generally unknown a trans-dimensional approach is used to allow the dataset itself to indicate the most probable number of parameters needed to sample the PPD. The algorithm is tested against two simulated datasets and a set of MT data acquired in the Clare Basin (County Clare, Ireland). For the simulated datasets the correct number of conductive layers at depth and the associated electrical conductivity values is retrieved, together with reasonable estimates of the uncertainties on the investigated parameters. Results from the inversion of field measurements are compared with results obtained using a deterministic method and with well-log data from a nearby borehole. The PPD is in good agreement with the well-log data, showing as a main structure a high conductive layer associated with the Clare Shale formation. In this study, we demonstrate that our new code go beyond algorithms developend using a linear inversion scheme, as it can be used: (1) to by-pass the subjective choices in the 1D parameterizations, i.e. the number of horizontal layers in the 1D parameterization, and (2) to estimate realistic uncertainties on the retrieved parameters. The algorithm is implemented using a simple MPI approach, where independent chains run on isolated CPU, to take full advantage of parallel computer architectures. In case of a large number of data, a master/slave appoach can be used, where the master CPU samples the parameter space and the slave CPUs compute forward solutions.

Self-organization and stability of magnetosome chains—A simulation study

PubMed Central

Faivre, Damien; Klumpp, Stefan

2018-01-01

Magnetotactic bacteria orient in magnetic fields with the help of their magnetosome chain, a linear structure of membrane enclosed magnetic nanoparticles (magnetosomes) anchored to a cytoskeletal filament. Here, we use simulations to study the assembly and the stability of magnetosome chains. We introduce a computational model describing the attachment of the magnetosomes to the filament and their magnetic interactions. We show that the filamentous backbone is crucial for the robust assembly of the magnetic particles into a linear chain, which in turn is key for the functionality of the chain in cellular orientation and magnetically directed swimming. In addition, we simulate the response to an external magnetic field that is rotated away from the axis of the filament, an experimental method used to probe the mechanical stability of the chain. The competition between alignment along the filament and alignment with the external fields leads to the rupture of a chain if the applied field exceeeds a threshold value. These observations are in agreement with previous experiments at the population level. Beyond that, our simulations provide a detailed picture of chain rupture at the single cell level, which is found to happen through two abrupt events, which both depend on the field strength and orientation. The re-formation of the chain structure after such rupture is found to be strongly sped up in the presence of a magnetic field parallel to the filament, an observation that may also be of interest for the design of self-healing materials. Our simulations underline the dynamic nature of the magnetosome chain. More generally, they show the rich complexity of self-assembly in systems with competing driving forces for alignment. PMID:29315342

Modeling fructose-load-induced hepatic de-novo lipogenesis by model simplification.

PubMed

Allen, Richard J; Musante, Cynthia J

2017-01-01

Hepatic de-novo lipogenesis is a metabolic process implemented in the pathogenesis of type 2 diabetes. Clinically, the rate of this process can be ascertained by use of labeled acetate and stimulation by fructose administration. A systems pharmacology model of this process is desirable because it facilitates the description, analysis, and prediction of this experiment. Due to the multiple enzymes involved in de-novo lipogenesis, and the limited data, it is desirable to use single functional expressions to encapsulate the flux between multiple enzymes. To accomplish this we developed a novel simplification technique which uses the available information about the properties of the individual enzymes to bound the parameters of a single governing 'transfer function'. This method should be applicable to any model with linear chains of enzymes that are well stimulated. We validated this approach with computational simulations and analytical justification in a limiting case. Using this technique we generated a simple model of hepatic de-novo lipogenesis in these experimental conditions that matched prior data. This model can be used to assess pharmacological intervention at specific points on this pathway. We have demonstrated this with prospective simulation of acetyl-CoA carboxylase inhibition. This simplification technique suggests how the constituent properties of an enzymatic chain of reactions gives rise to the sensitivity (to substrate) of the pathway as a whole.

Modeling fructose-load-induced hepatic de-novo lipogenesis by model simplification

PubMed Central

Allen, Richard J; Musante, Cynthia J

2017-01-01

Hepatic de-novo lipogenesis is a metabolic process implemented in the pathogenesis of type 2 diabetes. Clinically, the rate of this process can be ascertained by use of labeled acetate and stimulation by fructose administration. A systems pharmacology model of this process is desirable because it facilitates the description, analysis, and prediction of this experiment. Due to the multiple enzymes involved in de-novo lipogenesis, and the limited data, it is desirable to use single functional expressions to encapsulate the flux between multiple enzymes. To accomplish this we developed a novel simplification technique which uses the available information about the properties of the individual enzymes to bound the parameters of a single governing ‘transfer function’. This method should be applicable to any model with linear chains of enzymes that are well stimulated. We validated this approach with computational simulations and analytical justification in a limiting case. Using this technique we generated a simple model of hepatic de-novo lipogenesis in these experimental conditions that matched prior data. This model can be used to assess pharmacological intervention at specific points on this pathway. We have demonstrated this with prospective simulation of acetyl-CoA carboxylase inhibition. This simplification technique suggests how the constituent properties of an enzymatic chain of reactions gives rise to the sensitivity (to substrate) of the pathway as a whole. PMID:28469410

Quantification and characterization of enzymatically produced hyaluronan with fluorophore-assisted carbohydrate electrophoresis.

PubMed

Kooy, Floor K; Ma, Muyuan; Beeftink, Hendrik H; Eggink, Gerrit; Tramper, Johannes; Boeriu, Carmen G

2009-01-15

Hyaluronan (HA) is a polysaccharide with high-potential medical applications, depending on the chain length and the chain length distribution. Special interest goes to homogeneous HA oligosaccharides, which can be enzymatically produced using Pasteurella multocida hyaluronan synthase (PmHAS). We have developed a sensitive, simple, and fast method, based on fluorophore-assisted carbohydrate electrophoresis (FACE), for characterization and quantification of polymerization products. A chromatographic pure fluorescent template was synthesized from HA tetrasaccharide (HA4) and 2-aminobenzoic acid. HA4-fluor and HA4 were used as template for PmHAS-mediated polymerization of nucleotide sugars. All products, fluorescent and nonfluorescent, were analyzed with gel electrophoresis and quantified using lane densitometry. Comparison of HA4- and HA4-fluor-derived polymers showed that the fluorophore did not negatively influence the PmHAS-mediated polymerization. Only even-numbered oligosaccharide products were observed using HA4-fluor or HA4 as template. The fluorophore intensity was linearly related to its concentration, and the limit of detection was determined to be 7.4pmol per product band. With this assay, we can now differentiate oligosaccharides of size range DP2 (degree of polymerization 2) to approximately DP400, monitor the progress of polymerization reactions, and measure subtle differences in polymerization rate. Quantifying polymerization products enables us to study the influence of experimental conditions on HA synthesis.

Determination of linear short chain aliphatic aldehyde and ketone vapors in air using a polystyrene-coated quartz crystal nanobalance sensor.

PubMed

Mirmohseni, Abdolreza; Olad, Ali

2010-01-01

A polystyrene coated quartz crystal nanobalance (QCN) sensor was developed for use in the determination of a number of linear short-chain aliphatic aldehyde and ketone vapors contained in air. The quartz crystal was modified by a thin-layer coating of a commercial grade general purpose polystyrene (GPPS) from Tabriz petrochemical company using a solution casting method. Determination was based on frequency shifts of the modified quartz crystal due to the adsorption of analytes at the surface of modified electrode in exposure to various concentrations of analytes. The frequency shift was found to have a linear relation to the concentration of analytes. Linear calibration curves were obtained for 7-70 mg l(-1) of analytes with correlation coefficients in the range of 0.9935-0.9989 and sensitivity factors in the range of 2.07-6.74 Hz/mg l(-1). A storage period of over three months showed no loss in the sensitivity and performance of the sensor.

Comments on the variational modified-hypernetted-chain theory for simple fluids

NASA Astrophysics Data System (ADS)

Rosenfeld, Yaakov

1986-02-01

The variational modified-hypernetted-chain (VMHNC) theory, based on the approximation of universality of the bridge functions, is reformulated. The new formulation includes recent calculations by Lado and by Lado, Foiles, and Ashcroft, as two stages in a systematic approach which is analyzed. A variational iterative procedure for solving the exact (diagrammatic) equations for the fluid structure which is formally identical to the VMHNC is described, featuring the theory of simple classical fluids as a one-iteration theory. An accurate method for calculating the pair structure for a given potential and for inverting structure factor data in order to obtain the potential and the thermodynamic functions, follows from our analysis.

Algebraic Bethe ansatz for the XXX chain with triangular boundaries and Gaudin model

NASA Astrophysics Data System (ADS)

Cirilo António, N.; Manojlović, N.; Salom, I.

2014-12-01

We implement fully the algebraic Bethe ansatz for the XXX Heisenberg spin chain in the case when both boundary matrices can be brought to the upper-triangular form. We define the Bethe vectors which yield the strikingly simple expression for the off shell action of the transfer matrix, deriving the spectrum and the relevant Bethe equations. We explore further these results by obtaining the off shell action of the generating function of the Gaudin Hamiltonians on the corresponding Bethe vectors through the so-called quasi-classical limit. Moreover, this action is as simple as it could possibly be, yielding the spectrum and the Bethe equations of the Gaudin model.

Dewetting Kinetics in Polymer Grafted Nanoparticle Thin Films: Impact of Architecture and Viscosity on Thermal Stability

NASA Astrophysics Data System (ADS)

Che, Justin; Jawaid, Ali; Grabowski, Christopher; Yi, Yoon-Jae; Vaia, Richard; AFRL Collaboration

Rapid formation of ordered monolayers of polymer grafted nanoparticles (PGN) directly onto solid surfaces has spurred interest in using these materials for additive manufacturing of optical devices and energy storage. Herein, we discuss dewetting of polystyrene grafted Au nanoparticles (PS@Au) with an increased thermal (10-25oC) and energetic (5-15 mN/m) stability relative to linear polymer films of comparable thickness. Analogous to star macromolecules, the enhanced stability is related to the conformations of chains in the grafted canopy. Mechanistically, dewetting of PS@Au is similar to linear PS, however, the thickness transition from spinodal to heterogeneous nucleation is at least 5-6x larger. Time resolved optical microscopy during dewetting at 160oC revealed that the zero shear viscosity for linear PS scaled as η0 Mn3. 3 , consistent with reptation of entangled polymers. In contrast, PS@Au showed η0 Mn2. 2 where Mn reflects the molecular weight of the grafted chains. Overall, PS@Au exhibited significantly slower dewetting rates, consistent with a 100x increase in viscosity relative to the linear chain analogues. Quantification of the relationship between PGN architecture (e.g. nanoparticle size, graft density, polymer molecular weight) and dewetting processes is crucial to optimize the order of these assemblies via post-processing, as well as design the PGN canopy to maximize stability for devices.

Mining Distance Based Outliers in Near Linear Time with Randomization and a Simple Pruning Rule

NASA Technical Reports Server (NTRS)

Bay, Stephen D.; Schwabacher, Mark

2003-01-01

Defining outliers by their distance to neighboring examples is a popular approach to finding unusual examples in a data set. Recently, much work has been conducted with the goal of finding fast algorithms for this task. We show that a simple nested loop algorithm that in the worst case is quadratic can give near linear time performance when the data is in random order and a simple pruning rule is used. We test our algorithm on real high-dimensional data sets with millions of examples and show that the near linear scaling holds over several orders of magnitude. Our average case analysis suggests that much of the efficiency is because the time to process non-outliers, which are the majority of examples, does not depend on the size of the data set.

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.

Nanoscopic dynamics in hybrid hydroxyapatite-CTAB composite

NASA Astrophysics Data System (ADS)

Dubey, P. S.; Sharma, V. K.; Mitra, S.; Verma, G.; Hassan, P. A.; Dutta, B.; Johnson, M.; Mukhopadhyay, R.

2017-06-01

Synthetic hydroxyapatite (HAp) is an important material in biomedical engineering due to its excellent biocompatibility and bioactivity. HAp nanoparticles were synthesized by the co-precipitation method using cetyltrimethylammonium bromide (CTAB) micelles as a template and are characterized using x-ray diffraction, electron microscopy, and thermal gravimetric measurements. Transmission electron microscope (TEM) demonstrates the formation of rod-shaped HAp. Dynamics of CTAB in HAp-CTAB composite as studied by using quasielastic neutron scattering (QENS) technique is reported here. HAp-CTAB composite provides an ideal system for studying the dynamics of CTAB micelles without any aqueous media. QENS data indicate that the observed dynamics are reminiscent of localized motions in ionic micellar systems, consisting of segmental and fast torsional motions. Segmental dynamics has been described with a model, in which hydrogen atoms in the alkyl chain undergoes localized translation diffusion and the CH3 unit associated with the head group undergo 3-fold jump rotation. Within this model, the hydrogen atoms in the alkyl chain undergo diffusion within spherical domains having different radii and diffusivities. A simple linear distribution of the radius and diffusivity has been assumed, in which the CH2 unit nearest to the head group has the least value and the ones furthest from the head group, that is, at the end of the alkyl chain has the largest value. The fast torsional motion is described by a 2-fold jump rotation model. Quantitative estimate of the different parameters characterizing various dynamical motions active within the time scale of the instrument is also presented. We have provided a detailed description of the observed dynamical features in hybrid HAp-CTAB composite, a potential candidate for biomedical applications.

A specific transition state for S-peptide combining with folded S-protein and then refolding

PubMed Central

Goldberg, Jonathan M.; Baldwin, Robert L.

1999-01-01

We measured the folding and unfolding kinetics of mutants for a simple protein folding reaction to characterize the structure of the transition state. Fluorescently labeled S-peptide analogues combine with S-protein to form ribonuclease S analogues: initially, S-peptide is disordered whereas S-protein is folded. The fluorescent probe provides a convenient spectroscopic probe for the reaction. The association rate constant, kon, and the dissociation rate constant, koff, were both determined for two sets of mutants. The dissociation rate constant is measured by adding an excess of unlabeled S-peptide analogue to a labeled complex (RNaseS*). This strategy allows kon and koff to be measured under identical conditions so that microscopic reversibility applies and the transition state is the same for unfolding and refolding. The first set of mutants tests the role of the α-helix in the transition state. Solvent-exposed residues Ala-6 and Gln-11 in the α-helix of native RNaseS were replaced by the helix destabilizing residues glycine or proline. A plot of log kon vs. log Kd for this series of mutants is linear over a very wide range, with a slope of −0.3, indicating that almost all of the molecules fold via a transition state involving the helix. A second set of mutants tests the role of side chains in the transition state. Three side chains were investigated: Phe-8, His-12, and Met-13, which are known to be important for binding S-peptide to S-protein and which also contribute strongly to the stability of RNaseS*. Only the side chain of Phe-8 contributes significantly, however, to the stability of the transition state. The results provide a remarkably clear description of a folding transition state. PMID:10051587

Pharmaceutical supply chain risk assessment in Iran using analytic hierarchy process (AHP) and simple additive weighting (SAW) methods.

PubMed

Jaberidoost, Mona; Olfat, Laya; Hosseini, Alireza; Kebriaeezadeh, Abbas; Abdollahi, Mohammad; Alaeddini, Mahdi; Dinarvand, Rassoul

2015-01-01

Pharmaceutical supply chain is a significant component of the health system in supplying medicines, particularly in countries where main drugs are provided by local pharmaceutical companies. No previous studies exist assessing risks and disruptions in pharmaceutical companies while assessing the pharmaceutical supply chain. Any risks affecting the pharmaceutical companies could disrupt supply medicines and health system efficiency. The goal of this study was the risk assessment in pharmaceutical industry in Iran considering process's priority, hazard and probability of risks. The study was carried out in 4 phases; risk identification through literature review, risk identification in Iranian pharmaceutical companies through interview with experts, risk analysis through a questionnaire and consultation with experts using group analytic hierarchy process (AHP) method and rating scale (RS) and risk evaluation of simple additive weighting (SAW) method. In total, 86 main risks were identified in the pharmaceutical supply chain with perspective of pharmaceutical companies classified in 11 classes. The majority of risks described in this study were related to the financial and economic category. Also financial management was found to be the most important factor for consideration. Although pharmaceutical industry and supply chain were affected by current political conditions in Iran during the study time, but half of total risks in the pharmaceutical supply chain were found to be internal risks which could be fixed by companies, internally. Likewise, political status and related risks forced companies to focus more on financial and supply management resulting in less attention to quality management.

Translocation of a Polymer Chain across a Nanopore: A Brownian Dynamics Simulation Study

NASA Technical Reports Server (NTRS)

Tian, Pu; Smith, Grant D.

2003-01-01

We carried out Brownian dynamics simulation studies of the translocation of single polymer chains across a nanosized pore under the driving of an applied field (chemical potential gradient). The translocation process can be either dominated by the entropic barrier resulted from restricted motion of flexible polymer chains or by applied forces (or chemical gradient across the wall), we focused on the latter case in our studies. Calculation of radius of gyrations at the two opposite sides of the wall shows that the polymer chains are not in equilibrium during the translocation process. Despite this fact, our results show that the one-dimensional diffusion and the nucleation model provide an excellent description of the dependence of average translocation time on the chemical potential gradients, the polymer chain length and the solvent viscosity. In good agreement with experimental results and theoretical predictions, the translocation time distribution of our simple model shows strong non-Gaussian characteristics. It is observed that even for this simple tubelike pore geometry, more than one peak of translocation time distribution can be generated for proper pore diameter and applied field strengths. Both repulsive Weeks-Chandler-Anderson and attractive Lennard-Jones polymer-nanopore interaction were studied, attraction facilitates the translocation process by shortening the total translocation time and dramatically improve the capturing of polymer chain. The width of the translocation time distribution was found to decrease with increasing temperature, increasing field strength, and decreasing pore diameter.

Stochastic thermodynamics for Ising chain and symmetric exclusion process.

PubMed

Toral, R; Van den Broeck, C; Escaff, D; Lindenberg, Katja

2017-03-01

We verify the finite-time fluctuation theorem for a linear Ising chain in contact with heat reservoirs at its ends. Analytic results are derived for a chain consisting of two spins. The system can be mapped onto a model for particle transport, namely, the symmetric exclusion process in contact with thermal and particle reservoirs. We modify the symmetric exclusion process to represent a thermal engine and reproduce universal features of the efficiency at maximum power.

Reversible geling co-polymer and method of making

DOEpatents

Gutowska, Anna

2005-12-27

The present invention is a thereapeutic agent carrier having a thermally reversible gel or geling copolymer that is a linear random copolymer of an [meth-]acrylamide derivative and a hydrophilic comonomer, wherein the linear random copolymer is in the form of a plurality of linear chains having a plurality of molecular weights greater than or equal to a minimum geling molecular weight cutoff and a therapeutic agent.

Fission Chain Restart Theory

DOE PAGES

Kim, K. S.; Nakae, L. F.; Prasad, M. K.; ...

2017-07-31

We present that fast nanosecond timescale neutron and gamma-ray counting can be performed with a (liquid) scintillator array. Fission chains in metal evolve over a timescale of tens of nanoseconds. If the metal is surrounded by moderator, neutrons leaking from the metal can thermalize and diffuse in the moderator. With finite probability, the diffusing neutrons can return to the metal and restart the fast fission chain. The timescale for this restart process is microseconds. A theory describing time evolving fission chains for metal surrounded by moderator, including this restart process, is presented. Finally, this theory is sufficiently simple for itmore » to be implemented for real-time analysis.« less

Asteroid mass estimation with Markov-chain Monte Carlo

NASA Astrophysics Data System (ADS)

Siltala, L.; Granvik, M.

2017-09-01

We have developed a new Markov-chain Monte Carlo-based algorithm for asteroid mass estimation based on mutual encounters and tested it for several different asteroids. Our results are in line with previous literature values but suggest that uncertainties of prior estimates may be misleading as a consequence of using linearized methods.

UMAP Modules-Units 105, 107-109, 111-112, 158-162.

ERIC Educational Resources Information Center

Keller, Mary K.; And Others

This collection of materials includes six units dealing with applications of matrix methods. These are: 105-Food Service Management; 107-Markov Chains; 108-Electrical Circuits; 109-Food Service and Dietary Requirements; 111-Fixed Point and Absorbing Markov Chains; and 112-Analysis of Linear Circuits. The units contain exercises and model exams,…

KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers.

PubMed

Tubiana, Luca; Polles, Guido; Orlandini, Enzo; Micheletti, Cristian

2018-06-07

The KymoKnot software package and web server identifies and locates physical knots or proper knots in a series of polymer conformations. It is mainly intended as an analysis tool for trajectories of linear or circular polymers, but it can be used on single instances too, e.g. protein structures in PDB format. A key element of the software package is the so-called minimally interfering chain closure algorithm that is used to detect physical knots in open chains and to locate the knotted region in both open and closed chains. The web server offers a user-friendly graphical interface that identifies the knot type and highlights the knotted region on each frame of the trajectory, which the user can visualize interactively from various viewpoints. The dynamical evolution of the knotted region along the chain contour is presented as a kymograph. All data can be downloaded in text format. The KymoKnot package is licensed under the BSD 3-Clause licence. The server is publicly available at http://kymoknot.sissa.it/kymoknot/interactive.php .

Nanoparticle amount, and not size, determines chain alignment and nonlinear hardening in polymer nanocomposites

PubMed Central

Varol, H. Samet; Meng, Fanlong; Hosseinkhani, Babak; Malm, Christian; Bonn, Daniel; Bonn, Mischa; Zaccone, Alessio

2017-01-01

Polymer nanocomposites—materials in which a polymer matrix is blended with nanoparticles (or fillers)—strengthen under sufficiently large strains. Such strain hardening is critical to their function, especially for materials that bear large cyclic loads such as car tires or bearing sealants. Although the reinforcement (i.e., the increase in the linear elasticity) by the addition of filler particles is phenomenologically understood, considerably less is known about strain hardening (the nonlinear elasticity). Here, we elucidate the molecular origin of strain hardening using uniaxial tensile loading, microspectroscopy of polymer chain alignment, and theory. The strain-hardening behavior and chain alignment are found to depend on the volume fraction, but not on the size of nanofillers. This contrasts with reinforcement, which depends on both volume fraction and size of nanofillers, potentially allowing linear and nonlinear elasticity of nanocomposites to be tuned independently. PMID:28377517

rf design of a pulse compressor with correction cavity chain for klystron-based compact linear collider

NASA Astrophysics Data System (ADS)

Wang, Ping; Zha, Hao; Syratchev, Igor; Shi, Jiaru; Chen, Huaibi

2017-11-01

We present an X-band high-power pulse compression system for a klystron-based compact linear collider. In this system design, one rf power unit comprises two klystrons, a correction cavity chain, and two SLAC Energy Doubler (SLED)-type X-band pulse compressors (SLEDX). An rf pulse passes the correction cavity chain, by which the pulse shape is modified. The rf pulse is then equally split into two ways, each deploying a SLEDX to compress the rf power. Each SLEDX produces a short pulse with a length of 244 ns and a peak power of 217 MW to power four accelerating structures. With the help of phase-to-amplitude modulation, the pulse has a dedicated shape to compensate for the beam loading effect in accelerating structures. The layout of this system and the rf design and parameters of the new pulse compressor are described in this work.

Nonequilibrium molecular dynamics study of ring polymer melts under shear and elongation flows: A comparison with their linear analogs

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

Yoon, Jeongha; Kim, Jinseong; Baig, Chunggi, E-mail: cbaig@unist.ac.kr

We present detailed results for the structural and rheological properties of unknotted and unconcatenated ring polyethylene (PE) melts under shear and elongation flows via direct atomistic nonequilibrium molecular dynamics simulations. Short (C{sub 78}H{sub 156}) and long (C{sub 400}H{sub 800}) ring PE melts were subjected to planar Couette flow (PCF) and planar elongational flow (PEF) across a wide range of strain rates from linear to highly nonlinear flow regimes. The results are analyzed in detail through a direct comparison with those of the corresponding linear polymers. We found that, in comparison to their linear analogs, ring melts possess rather compact chainmore » structures at or near the equilibrium state and exhibit a considerably lesser degree of structural deformation with respect to the applied flow strength under both PCF and PEF. The large structural resistance of ring polymers against an external flow field is attributed to the intrinsic closed-loop configuration of the ring and the topological constraint of nonconcatenation between ring chains in the melt. As a result, there appears to be a substantial discrepancy between ring and linear systems in terms of their structural and rheological properties such as chain orientation, the distribution of chain dimensions, viscosity, flow birefringence, hydrostatic pressure, the pair correlation function, and potential interaction energies. The findings and conclusions drawn in this work would be a useful guide in future exploration of the characteristic dynamical and relaxation mechanisms of ring polymers in bulk or confined systems under flowing conditions.« less

Programmable polyproteams built using twin peptide superglues

PubMed Central

Veggiani, Gianluca; Nakamura, Tomohiko; Brenner, Michael D.; Yan, Jun; Robinson, Carol V.; Howarth, Mark

2016-01-01

Programmed connection of amino acids or nucleotides into chains introduced a revolution in control of biological function. Reacting proteins together is more complex because of the number of reactive groups and delicate stability. Here we achieved sequence-programmed irreversible connection of protein units, forming polyprotein teams by sequential amidation and transamidation. SpyTag peptide is engineered to spontaneously form an isopeptide bond with SpyCatcher protein. By engineering the adhesin RrgA from Streptococcus pneumoniae, we developed the peptide SnoopTag, which formed a spontaneous isopeptide bond to its protein partner SnoopCatcher with >99% yield and no cross-reaction to SpyTag/SpyCatcher. Solid-phase attachment followed by sequential SpyTag or SnoopTag reaction between building-blocks enabled iterative extension. Linear, branched, and combinatorial polyproteins were synthesized, identifying optimal combinations of ligands against death receptors and growth factor receptors for cancer cell death signal activation. This simple and modular route to programmable “polyproteams” should enable exploration of a new area of biological space. PMID:26787909

Understanding band gaps of solids in generalized Kohn-Sham theory.

PubMed

Perdew, John P; Yang, Weitao; Burke, Kieron; Yang, Zenghui; Gross, Eberhard K U; Scheffler, Matthias; Scuseria, Gustavo E; Henderson, Thomas M; Zhang, Igor Ying; Ruzsinszky, Adrienn; Peng, Haowei; Sun, Jianwei; Trushin, Egor; Görling, Andreas

2017-03-14

The fundamental energy gap of a periodic solid distinguishes insulators from metals and characterizes low-energy single-electron excitations. However, the gap in the band structure of the exact multiplicative Kohn-Sham (KS) potential substantially underestimates the fundamental gap, a major limitation of KS density-functional theory. Here, we give a simple proof of a theorem: In generalized KS theory (GKS), the band gap of an extended system equals the fundamental gap for the approximate functional if the GKS potential operator is continuous and the density change is delocalized when an electron or hole is added. Our theorem explains how GKS band gaps from metageneralized gradient approximations (meta-GGAs) and hybrid functionals can be more realistic than those from GGAs or even from the exact KS potential. The theorem also follows from earlier work. The band edges in the GKS one-electron spectrum are also related to measurable energies. A linear chain of hydrogen molecules, solid aluminum arsenide, and solid argon provide numerical illustrations.

Template-constrained macrocyclic peptides prepared from native, unprotected precursors

PubMed Central

Lawson, Kenneth V.; Rose, Tristan E.; Harran, Patrick G.

2013-01-01

Peptide–protein interactions are important mediators of cellular-signaling events. Consensus binding motifs (also known as short linear motifs) within these contacts underpin molecular recognition, yet have poor pharmacological properties as discrete species. Here, we present methods to transform intact peptides into stable, templated macrocycles. Two simple steps install the template. The key reaction is a palladium-catalyzed macrocyclization. The catalysis has broad scope and efficiently forms large rings by engaging native peptide functionality including phenols, imidazoles, amines, and carboxylic acids without the necessity of protecting groups. The tunable reactivity of the template gives the process special utility. Defined changes in reaction conditions markedly alter chemoselectivity. In all cases examined, cyclization occurs rapidly and in high yield at room temperature, regardless of peptide composition or chain length. We show that conformational restraints imparted by the template stabilize secondary structure and enhance proteolytic stability in vitro. Palladium-catalyzed internal cinnamylation is a strong complement to existing methods for peptide modification. PMID:24043790

A new code for modelling the near field diffusion releases from the final disposal of nuclear waste

NASA Astrophysics Data System (ADS)

Vopálka, D.; Vokál, A.

2003-01-01

The canisters with spent nuclear fuel produced during the operation of WWER reactors at the Czech power plants are planned, like in other countries, to be disposed of in an underground repository. Canisters will be surrounded by compacted bentonite that will retard the migration of safety-relevant radionuclides into the host rock. A new code that enables the modelling of the critical radionuclides transport from the canister through the bentonite layer in the cylindrical geometry was developed. The code enables to solve the diffusion equation for various types of initial and boundary conditions by means of the finite difference method and to take into account the non-linear shape of the sorption isotherm. A comparison of the code reported here with code PAGODA, which is based on analytical solution of the transport equation, was made for the actinide chain 4N+3 that includes 239Pu. A simple parametric study of the releases of 239Pu, 129I, and 14C into geosphere is discussed.

A fiber orientation-adapted integration scheme for computing the hyperelastic Tucker average for short fiber reinforced composites

NASA Astrophysics Data System (ADS)

Goldberg, Niels; Ospald, Felix; Schneider, Matti

2017-10-01

In this article we introduce a fiber orientation-adapted integration scheme for Tucker's orientation averaging procedure applied to non-linear material laws, based on angular central Gaussian fiber orientation distributions. This method is stable w.r.t. fiber orientations degenerating into planar states and enables the construction of orthotropic hyperelastic energies for truly orthotropic fiber orientation states. We establish a reference scenario for fitting the Tucker average of a transversely isotropic hyperelastic energy, corresponding to a uni-directional fiber orientation, to microstructural simulations, obtained by FFT-based computational homogenization of neo-Hookean constituents. We carefully discuss ideas for accelerating the identification process, leading to a tremendous speed-up compared to a naive approach. The resulting hyperelastic material map turns out to be surprisingly accurate, simple to integrate in commercial finite element codes and fast in its execution. We demonstrate the capabilities of the extracted model by a finite element analysis of a fiber reinforced chain link.

Programmable polyproteams built using twin peptide superglues.

PubMed

Veggiani, Gianluca; Nakamura, Tomohiko; Brenner, Michael D; Gayet, Raphaël V; Yan, Jun; Robinson, Carol V; Howarth, Mark

2016-02-02

Programmed connection of amino acids or nucleotides into chains introduced a revolution in control of biological function. Reacting proteins together is more complex because of the number of reactive groups and delicate stability. Here we achieved sequence-programmed irreversible connection of protein units, forming polyprotein teams by sequential amidation and transamidation. SpyTag peptide is engineered to spontaneously form an isopeptide bond with SpyCatcher protein. By engineering the adhesin RrgA from Streptococcus pneumoniae, we developed the peptide SnoopTag, which formed a spontaneous isopeptide bond to its protein partner SnoopCatcher with >99% yield and no cross-reaction to SpyTag/SpyCatcher. Solid-phase attachment followed by sequential SpyTag or SnoopTag reaction between building-blocks enabled iterative extension. Linear, branched, and combinatorial polyproteins were synthesized, identifying optimal combinations of ligands against death receptors and growth factor receptors for cancer cell death signal activation. This simple and modular route to programmable "polyproteams" should enable exploration of a new area of biological space.

Understanding band gaps of solids in generalized Kohn–Sham theory

PubMed Central

Perdew, John P.; Yang, Weitao; Burke, Kieron; Yang, Zenghui; Gross, Eberhard K. U.; Scheffler, Matthias; Scuseria, Gustavo E.; Henderson, Thomas M.; Zhang, Igor Ying; Ruzsinszky, Adrienn; Peng, Haowei; Sun, Jianwei; Trushin, Egor; Görling, Andreas

2017-01-01

The fundamental energy gap of a periodic solid distinguishes insulators from metals and characterizes low-energy single-electron excitations. However, the gap in the band structure of the exact multiplicative Kohn–Sham (KS) potential substantially underestimates the fundamental gap, a major limitation of KS density-functional theory. Here, we give a simple proof of a theorem: In generalized KS theory (GKS), the band gap of an extended system equals the fundamental gap for the approximate functional if the GKS potential operator is continuous and the density change is delocalized when an electron or hole is added. Our theorem explains how GKS band gaps from metageneralized gradient approximations (meta-GGAs) and hybrid functionals can be more realistic than those from GGAs or even from the exact KS potential. The theorem also follows from earlier work. The band edges in the GKS one-electron spectrum are also related to measurable energies. A linear chain of hydrogen molecules, solid aluminum arsenide, and solid argon provide numerical illustrations. PMID:28265085

A general strategy for synthesis of cyclophane-braced peptide macrocycles via palladium-catalysed intramolecular sp3 C-H arylation

NASA Astrophysics Data System (ADS)

Zhang, Xuekai; Lu, Gang; Sun, Meng; Mahankali, Madhu; Ma, Yanfei; Zhang, Mingming; Hua, Wangde; Hu, Yuting; Wang, Qingbing; Chen, Jinghuo; He, Gang; Qi, Xiangbing; Shen, Weijun; Liu, Peng; Chen, Gong

2018-05-01

New methods capable of effecting cyclization, and forming novel three-dimensional structures while maintaining favourable physicochemical properties are needed to facilitate the development of cyclic peptide-based drugs that can engage challenging biological targets, such as protein-protein interactions. Here, we report a highly efficient and generally applicable strategy for constructing new types of peptide macrocycles using palladium-catalysed intramolecular C(sp3)-H arylation reactions. Easily accessible linear peptide precursors of simple and versatile design can be selectively cyclized at the side chains of either aromatic or modified non-aromatic amino acid units to form various cyclophane-braced peptide cycles. This strategy provides a powerful tool to address the long-standing challenge of size- and composition-dependence in peptide macrocyclization, and generates novel peptide macrocycles with uniquely buttressed backbones and distinct loop-type three-dimensional structures. Preliminary cell proliferation screening of the pilot library revealed a potent lead compound with selective cytotoxicity toward proliferative Myc-dependent cancer cell lines.

Retailer Stackelberg game in a supply chain with pricing and service decisions and simple price discount contract.

PubMed

Sadjadi, Seyed Jafar; Asadi, Hashem; Sadeghian, Ramin; Sahebi, Hadi

2018-01-01

This paper studies the Retailer Stackelberg game in a supply chain consisting of two manufacturers and one retailer where they compete simultaneously under three factors including price, service and simple price discount contract. It is assumed that the second manufacturer provides service directly to his customers, and the retailer provides service for the first product's customers, while the retailer buys the first product under price discount from the first manufacturer. The analysis of the optimal equilibrium solutions and the results of the numerical examples show that if a manufacturer chooses the appropriate range of discount rate, he will gain more profit than when there is no discount given to the retailer. This situation can be considered as an effective tool for the coordination of the first manufacturer and the retailer to offer discount by manufacturer and to provide the service by the retailer. We obtain equilibrium solution of Retailer Stackelberg game and analyze the numerical examples under two cases: a) the manufacturers sell their products to the retailer without price discount contract. b) The first manufacturer sells his products to the retailer with the simple price discount contract. The preliminary results show that the service and the price discount contract can improve the performance of supply chain.

Retailer Stackelberg game in a supply chain with pricing and service decisions and simple price discount contract

PubMed Central

Sadjadi, Seyed Jafar; Sadeghian, Ramin; Sahebi, Hadi

2018-01-01

This paper studies the Retailer Stackelberg game in a supply chain consisting of two manufacturers and one retailer where they compete simultaneously under three factors including price, service and simple price discount contract. It is assumed that the second manufacturer provides service directly to his customers, and the retailer provides service for the first product’s customers, while the retailer buys the first product under price discount from the first manufacturer. The analysis of the optimal equilibrium solutions and the results of the numerical examples show that if a manufacturer chooses the appropriate range of discount rate, he will gain more profit than when there is no discount given to the retailer. This situation can be considered as an effective tool for the coordination of the first manufacturer and the retailer to offer discount by manufacturer and to provide the service by the retailer. We obtain equilibrium solution of Retailer Stackelberg game and analyze the numerical examples under two cases: a) the manufacturers sell their products to the retailer without price discount contract. b) The first manufacturer sells his products to the retailer with the simple price discount contract. The preliminary results show that the service and the price discount contract can improve the performance of supply chain. PMID:29649315

Giant Linear Dunes as the Formation Pathway to Megabarchan Chains: Titan and the Rub 'Al Khali

NASA Astrophysics Data System (ADS)

Lorenz, R. D.; Radebaugh, J.

2015-05-01

We suggest megabarchans cannot grow from barchans. Rather sand accumulates as giant linear dunes in a bidirectional regime which has since become more unidirectional. We see this pattern on Titan and in the field in the .United Arab Emirates.

Packing C60 in Boron Nitride Nanotubes

NASA Astrophysics Data System (ADS)

Mickelson, W.; Aloni, S.; Han, Wei-Qiang; Cumings, John; Zettl, A.

2003-04-01

We have created insulated C60 nanowire by packing C60 molecules into the interior of insulating boron nitride nanotubes (BNNTs). For small-diameter BNNTs, the wire consists of a linear chain of C60 molecules. With increasing BNNT inner diameter, unusual C60 stacking configurations are obtained (including helical, hollow core, and incommensurate) that are unknown for bulk or thin-film forms of C60. C60 in BNNTs thus presents a model system for studying the properties of dimensionally constrained ``silo'' crystal structures. For the linear-chain case, we have fused the C60 molecules to form a single-walled carbon nanotube inside the insulating BNNT.

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

Park, I.Y.; Tirziu, A.; Tseytlin, A.A.

We consider circular strings rotating with equal spins S{sub 1}=S{sub 2}=S in two orthogonal planes in AdS{sub 5} and suggest that they may be dual to long gauge-theory operators built out of self-dual components of gauge field strength. As was found in hep-th/0404187, the one-loop anomalous dimensions of the such gauge-theory operators are described by an antiferromagnetic XXX{sub 1} spin chain and scale linearly with length L>>1. We find that in the case of rigid rotating string both the classical energy E{sub 0} and the 1-loop string correction E{sub 1} depend linearly on the spin S (within the stability regionmore » of the solution). This supports the identification of the rigid rotating string with the gauge-theory operator corresponding to the maximal-spin (ferromagnetic) state of the XXX{sub 1} spin chain. The energy of more general rotating and pulsating strings also happens to scale linearly with both the spin and the oscillation number. Such solutions should be dual to other lower-spin states of the spin chain, with the antiferromagnetic ground state presumably corresponding to the string pulsating in two planes with no rotation.« less

A theoretical investigation of symmetry-origin unidirectional energy gradient in light-harvesting dendrimers.

PubMed

Koda, Shin-ichi

2016-03-21

We theoretically investigate a possibility that the symmetry of the repetitively branched structure of light-harvesting dendrimers creates the energy gradient descending toward inner generations (layers of pigment molecules) of the dendrimers. In the first half of this paper, we define a model system using the Frenkel exciton Hamiltonian that focuses only on the topology of dendrimers and numerically show that excitation energy tends to gather at inner generations of the model system at a thermal equilibrium state. This indicates that an energy gradient is formed in the model system. In the last half, we attribute this result to the symmetry of the model system and propose two symmetry-origin mechanisms creating the energy gradient. The present analysis and proposition are based on the theory of the linear chain (LC) decomposition [S. Koda, J. Chem. Phys. 142, 204112 (2015)], which equivalently transforms the model system into a set of one-dimensional systems on the basis of the symmetry of dendrimers. In the picture of the LC decomposition, we find that energy gradient is formed both in each linear chain and among linear chains, and these two mechanisms explain the numerical results well.

A theoretical investigation of symmetry-origin unidirectional energy gradient in light-harvesting dendrimers

NASA Astrophysics Data System (ADS)

Koda, Shin-ichi

2016-03-01

We theoretically investigate a possibility that the symmetry of the repetitively branched structure of light-harvesting dendrimers creates the energy gradient descending toward inner generations (layers of pigment molecules) of the dendrimers. In the first half of this paper, we define a model system using the Frenkel exciton Hamiltonian that focuses only on the topology of dendrimers and numerically show that excitation energy tends to gather at inner generations of the model system at a thermal equilibrium state. This indicates that an energy gradient is formed in the model system. In the last half, we attribute this result to the symmetry of the model system and propose two symmetry-origin mechanisms creating the energy gradient. The present analysis and proposition are based on the theory of the linear chain (LC) decomposition [S. Koda, J. Chem. Phys. 142, 204112 (2015)], which equivalently transforms the model system into a set of one-dimensional systems on the basis of the symmetry of dendrimers. In the picture of the LC decomposition, we find that energy gradient is formed both in each linear chain and among linear chains, and these two mechanisms explain the numerical results well.

Gas chromatography-mass spectrometry of carbonyl compounds in cigarette mainstream smoke after derivatization with 2,4-dinitrophenylhydrazine.

PubMed

Dong, Ji-Zhou; Moldoveanu, Serban C

2004-02-20

An improved gas chromatography-mass spectrometry (GC-MS) method was described for the analysis of carbonyl compounds in cigarette mainstream smoke (CMS) after 2,4-dinitrophenylhydrazine (DNPH) derivatization. Besides formaldehyde, acetaldehyde, acetone, acrolein, propionaldehyde, methyl ethyl ketone, butyraldehyde, and crotonaldehyde that are routinely analyzed in cigarette smoke, this technique separates and allows the analysis of several C4, C5 and C6 isomeric carbonyl compounds. Differentiation could be made between the linear and branched carbon chain components. In cigarette smoke, the branched chain carbonyls are found at higher level than the linear chain carbonyls. Also, several trace carbonyl compounds such as methoxyacetaldehyde were found for the first time in cigarette smoke. For the analysis, cigarette smoke was collected using DNPH-treated pads, which is a simpler procedure compared to conventional impinger collection. Thermal decomposition of DNPH-carbonyl compounds was minimized by the optimization of the GC conditions. The linear range of the method was significantly improved by using a standard mixture of DNPH-carbonyl compounds instead of individual compounds for calibration. The minimum detectable quantity for the carbonyls ranged from 1.4 to 5.6 microg/cigarette.

Molecular Mobility in Phase Segregated Bottlebrush Block Copolymer Melts

NASA Astrophysics Data System (ADS)

Yavitt, Benjamin; Gai, Yue; Song, Dongpo; Winter, H. Henning; Watkins, James

We investigate the linear viscoelastic behavior of poly(styrene)-block-poly(ethylene oxide) (PS-b-PEO) brush block copolymer (BBCP) materials over a range of vol. fractions and with side chain lengths below the entanglement molecular weights. The high chain mobility of the brush architecture results in rapid micro-phase segregation of the brush copolymer segments, which occurs during thermal annealing at mild temperatures. Master curves of the dynamic moduli were obtained by time-temperature superposition. The reduced degree of chain entanglements leads to a unique liquid-like rheology similar to that of bottlebrush homopolymers, even in the phase segregated state. We also explore the alignment of phase segregated domains at exceptionally low strain amplitudes (γ = 0.01) and mild processing temperatures using small angle X-ray scattering (SAXS). Domain orientation occurred readily at strains within the linear viscoelastic regime without noticeable effect on the moduli. This interplay of high molecular mobility and rapid phase segregation that are exhibited simultaneously in BBCPs is in contrast to the behavior of conventional linear block copolymer (LBCP) analogs and opens up new possibilities for processing BBCP materials for a wide range of nanotechnology applications. NSF Center for Hierarchical Manufacturing at the University of Massachusetts, Amherst (CMMI-1025020).

Acetanilide mediated reversible assembly and disassembly of Au nanoparticles.

PubMed

Murugadoss, A; Kar, Manoranjan; Chattopadhyay, Arun

2008-08-01

Herein we report the generation of Au nanoparticles (NPs) by sparingly soluble acetanilide in water. We also report the formation of linear chain-like superstructures of self-assembled Au NPs, in the presence of excess acetanilide. This was achieved in two different ways. In the first method, acetanilide was added, with increasing concentration, into aqueous HAuCl(4) to produce Au NPs as well as for the formation of assembly, which varied according to the concentration of acetanilide. The other route involved formation of spherical Au NPs at the lowest concentration of acetanilide, which was followed by the formation of assembly of various lengths upon further addition of variable amount of acetanilide. The assemblies were stable in aqueous solution for days with characteristic UV-vis absorption spectra consisting of two peaks. While the wavelength of the first peak remained the same, the position of the second peak changed to longer wavelength with increasing acetanilide concentration. Interestingly, the linear chain-like arrays could be broken into individual particles by first dilution of the solution concentration followed by treatment with ultrasonic waves. The individual Au NPs again formed linear chain-like arrays upon addition of excess acetanilide.

Prediction of the Main Engine Power of a New Container Ship at the Preliminary Design Stage

NASA Astrophysics Data System (ADS)

Cepowski, Tomasz

2017-06-01

The paper presents mathematical relationships that allow us to forecast the estimated main engine power of new container ships, based on data concerning vessels built in 2005-2015. The presented approximations allow us to estimate the engine power based on the length between perpendiculars and the number of containers the ship will carry. The approximations were developed using simple linear regression and multivariate linear regression analysis. The presented relations have practical application for estimation of container ship engine power needed in preliminary parametric design of the ship. It follows from the above that the use of multiple linear regression to predict the main engine power of a container ship brings more accurate solutions than simple linear regression.

Approaching a flat boundary with a block copolymer coated emulsion drop: late stage drainage dynamics

NASA Astrophysics Data System (ADS)

Rozairo, Damith; Croll, Andrew

Understanding the dynamics of the formation and drainage of the thin fluid film that becomes trapped by a deformable droplet as it approaches another object is crucial to the advancement of many industrial and biomedical applications. Adding amphiphilic diblock copolymers, which are becoming more commonly used in drug delivery and oil recovery, only add to the complexity. Despite their increased use, little is known about how long polymer chains fill an emulsion drop's interface or how the molecules influence hydrodynamic processes. We study the drainage dynamics of a thin water film trapped between mica and a diblock copolymer saturated oil droplet. Specifically, we examine several different polystyrene-b-poly(ethylene oxide) (PS-PEO) molecules self-assembled at a toluene-water interface using laser scanning confocal microscopy. Our experiments reveal that the molecular details of the polymer chains deeply influence the drainage times, indicating that they are not acting as a 'simple' surfactant. The presence of the chains creates a much slower dynamic as fluid is forced to drain through an effective polymer brush, the brush itself determined by chain packing at the interface. We present a simple model which accounts for the basic physics of the interface.

Ion solvation in polymer blends and block copolymer melts: effects of chain length and connectivity on the reorganization of dipoles.

PubMed

Nakamura, Issei

2014-05-29

We studied the thermodynamic properties of ion solvation in polymer blends and block copolymer melts and developed a dipolar self-consistent field theory for polymer mixtures. Our theory accounts for the chain connectivity of polymerized monomers, the compressibility of the liquid mixtures under electrostriction, the permanent and induced dipole moments of monomers, and the resultant dielectric contrast among species. In our coarse-grained model, dipoles are attached to the monomers and allowed to rotate freely in response to electrostatic fields. We demonstrate that a strong electrostatic field near an ion reorganizes dipolar monomers, resulting in nonmonotonic changes in the volume fraction profile and the dielectric function of the polymers with respect to those of simple liquid mixtures. For the parameter sets used, the spatial variations near an ion can be in the range of 1 nm or larger, producing significant differences in the solvation energy among simple liquid mixtures, polymer blends, and block copolymers. The solvation energy of an ion depends substantially on the chain length in block copolymers; thus, our theory predicts the preferential solvation of ions arising from differences in chain length.

Plastic deformation in a metallic granular chain

NASA Astrophysics Data System (ADS)

Musson, Ryan W.; Carlson, William

2016-03-01

Solitary wave response was investigated in a metallic granular chain-piston system using LS-DYNA. A power law hardening material model was used to show that localized plastic deformation is present in a metallic granular chain for an impact velocity of 0.5 m/s. This loss due to plastic deformation was quantified via impulse, and it was shown that the loss scales nearly linearly with impact velocity. Therefore, metallic grains may not be suitable for devices that require high-amplitude solitary waves. There would be too much energy lost to plastic deformation. One can assume that ceramics will behave elastically; therefore, the response of an aluminum oxide granular chain was compared to that of a steel chain.

Are V1 Simple Cells Optimized for Visual Occlusions? A Comparative Study

PubMed Central

Bornschein, Jörg; Henniges, Marc; Lücke, Jörg

2013-01-01

Simple cells in primary visual cortex were famously found to respond to low-level image components such as edges. Sparse coding and independent component analysis (ICA) emerged as the standard computational models for simple cell coding because they linked their receptive fields to the statistics of visual stimuli. However, a salient feature of image statistics, occlusions of image components, is not considered by these models. Here we ask if occlusions have an effect on the predicted shapes of simple cell receptive fields. We use a comparative approach to answer this question and investigate two models for simple cells: a standard linear model and an occlusive model. For both models we simultaneously estimate optimal receptive fields, sparsity and stimulus noise. The two models are identical except for their component superposition assumption. We find the image encoding and receptive fields predicted by the models to differ significantly. While both models predict many Gabor-like fields, the occlusive model predicts a much sparser encoding and high percentages of ‘globular’ receptive fields. This relatively new center-surround type of simple cell response is observed since reverse correlation is used in experimental studies. While high percentages of ‘globular’ fields can be obtained using specific choices of sparsity and overcompleteness in linear sparse coding, no or only low proportions are reported in the vast majority of studies on linear models (including all ICA models). Likewise, for the here investigated linear model and optimal sparsity, only low proportions of ‘globular’ fields are observed. In comparison, the occlusive model robustly infers high proportions and can match the experimentally observed high proportions of ‘globular’ fields well. Our computational study, therefore, suggests that ‘globular’ fields may be evidence for an optimal encoding of visual occlusions in primary visual cortex. PMID:23754938

Radiation/Catalytic Augmented Combustion.

DTIC Science & Technology

1984-05-01

interest to compare the experimental results for the solid bluff body with a thuoretical result. Using simple argtinieiiLs from fluid mechanics " one...responsibility through completion. Dr. A. E. Cerkanowlcz assisted in writing this final report. Experimental studies on catalytic augmented combustion...as well as with other combustion species, lead to ignition and sustained combustion via chain reactions. Simple combustion enhancement without

Interfacial friction and adhesion of cross-linked polymer thin films swollen with linear chains.

PubMed

Zhang, Qing; Archer, Lynden A

2007-07-03

The preparation and interfacial properties of a new type of tethered, thin-film lubricant coating are presented. These coatings are composed of three components: a dense self-assembled monolayer (SAM) underlayer that presents reactive vinyl groups at its surface; a cross-linked polydimethylsiloxane (PDMS) overlayer that is covalently tethered to the SAM; and free, mobile linear PDMS chains dispersed in the network. We investigate the influence of the molecular weight (Ms) and concentration of the free PDMS chains on the structure and equilibrium swelling properties of the cross-linked films. Using a bead-probe lateral force microscopy measurement technique, we also quantify the interfacial friction and adhesion characteristics of surfaces functionalized with these coatings. We find that both the volume fraction and the molecular weight of free PDMS molecules in the coatings influence their interfacial friction and adhesion properties. For example, the addition of short PDMS chains in dry, cross-linked PDMS thin films yields tethered surface coatings with ultralow friction coefficients (mu = 5.2 x 10(-3)). An analysis based on classical lubrication theory suggests that the reduction in friction force produced by free polymer is a consequence of the gradual separation of asperities on opposing surfaces and the consequent substitution of solid-solid friction by viscous drag of the free polymer chains in the network.

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

Information Entropy Production of Maximum Entropy Markov Chains from Spike Trains

NASA Astrophysics Data System (ADS)

Cofré, Rodrigo; Maldonado, Cesar

2018-01-01

We consider the maximum entropy Markov chain inference approach to characterize the collective statistics of neuronal spike trains, focusing on the statistical properties of the inferred model. We review large deviations techniques useful in this context to describe properties of accuracy and convergence in terms of sampling size. We use these results to study the statistical fluctuation of correlations, distinguishability and irreversibility of maximum entropy Markov chains. We illustrate these applications using simple examples where the large deviation rate function is explicitly obtained for maximum entropy models of relevance in this field.

Vibrational Markovian modelling of footprints after the interaction of antibiotics with the packaging region of HIV type 1.

PubMed

Díaz, Humberto González; de Armas, Ronal Ramos; Molina, Reinaldo

2003-11-01

The design of novel anti-HIV compounds has now become a crucial area for scientists working in numerous interrelated fields of science such as molecular biology, medicinal chemistry, mathematical biology, molecular modelling and bioinformatics. In this context, the development of simple but physically meaningful mathematical models to represent the interaction between anti-HIV drugs and their biological targets is of major interest. One such area currently under investigation involves the targets in the HIV-RNA-packaging region. In the work described here, we applied Markov chain theory in an attempt to describe the interaction between the antibiotic paromomycin and the packaging region of the RNA in Type-1 HIV. In this model, a nucleic acid squeezed graph is used. The vertices of the graph represent the nucleotides while the edges are the phosphodiester bonds. A stochastic (Markovian) matrix was subsequently defined on this graph, an operation that codifies the probabilities of interaction between specific nucleotides of HIV-RNA and the antibiotic. The strength of these local interactions can be calculated through an inelastic vibrational model. The successive power of this matrix codifies the probabilities with which the vibrations after drug-RNA interactions vanish along the polynucleotide main chain. The sums of self-return probabilities in the k-vicinity of each nucleotide represent physically meaningful descriptors. A linear discriminant function was developed and gave rise to excellent discrimination in 80.8% of interacting and footprinted nucleotides. The Jackknife method was employed to assess the stability and predictability of the model. On the other hand, a linear regression model predicted the local binding affinity constants between a specific nucleotide and the antibiotic (R(2)=0.91, Q(2)=0.86). These kinds of models could play an important role either in the discovery of new anti-HIV compounds or the study of their mode of action.

Determination of linear viscoelastic properties of an entangled polymer melt by probe rheology simulations.

PubMed

Karim, Mir; Indei, Tsutomu; Schieber, Jay D; Khare, Rajesh

2016-01-01

Particle rheology is used to extract the linear viscoelastic properties of an entangled polymer melt from molecular dynamics simulations. The motion of a stiff, approximately spherical particle is tracked in both passive and active modes. We demonstrate that the dynamic modulus of the melt can be extracted under certain limitations using this technique. As shown before for unentangled chains [Karim et al., Phys. Rev. E 86, 051501 (2012)PLEEE81539-375510.1103/PhysRevE.86.051501], the frequency range of applicability is substantially expanded when both particle and medium inertia are properly accounted for by using our inertial version of the generalized Stokes-Einstein relation (IGSER). The system used here introduces an entanglement length d_{T}, in addition to those length scales already relevant: monomer bead size d, probe size R, polymer radius of gyration R_{g}, simulation box size L, shear wave penetration length Δ, and wave period Λ. Previously, we demonstrated a number of restrictions necessary to obtain the relevant fluid properties: continuum approximation breaks down when d≳Λ; medium inertia is important and IGSER is required when R≳Λ; and the probe should not experience hydrodynamic interaction with its periodic images, L≳Δ. These restrictions are also observed here. A simple scaling argument for entangled polymers shows that the simulation box size must scale with polymer molecular weight as M_{w}^{3}. Continuum analysis requires the existence of an added mass to the probe particle from the entrained medium but was not observed in the earlier work for unentangled chains. We confirm here that this added mass is necessary only when the thickness L_{S} of the shell around the particle that contains the added mass, L_{S}>d. We also demonstrate that the IGSER can be used to predict particle displacement over a given timescale from knowledge of medium viscoelasticity; such ability will be of interest for designing nanoparticle-based drug delivery.

Determination of linear viscoelastic properties of an entangled polymer melt by probe rheology simulations

NASA Astrophysics Data System (ADS)

Karim, Mir; Indei, Tsutomu; Schieber, Jay D.; Khare, Rajesh

2016-01-01

Particle rheology is used to extract the linear viscoelastic properties of an entangled polymer melt from molecular dynamics simulations. The motion of a stiff, approximately spherical particle is tracked in both passive and active modes. We demonstrate that the dynamic modulus of the melt can be extracted under certain limitations using this technique. As shown before for unentangled chains [Karim et al., Phys. Rev. E 86, 051501 (2012), 10.1103/PhysRevE.86.051501], the frequency range of applicability is substantially expanded when both particle and medium inertia are properly accounted for by using our inertial version of the generalized Stokes-Einstein relation (IGSER). The system used here introduces an entanglement length dT, in addition to those length scales already relevant: monomer bead size d , probe size R , polymer radius of gyration Rg, simulation box size L , shear wave penetration length Δ , and wave period Λ . Previously, we demonstrated a number of restrictions necessary to obtain the relevant fluid properties: continuum approximation breaks down when d ≳Λ ; medium inertia is important and IGSER is required when R ≳Λ ; and the probe should not experience hydrodynamic interaction with its periodic images, L ≳Δ . These restrictions are also observed here. A simple scaling argument for entangled polymers shows that the simulation box size must scale with polymer molecular weight as Mw3. Continuum analysis requires the existence of an added mass to the probe particle from the entrained medium but was not observed in the earlier work for unentangled chains. We confirm here that this added mass is necessary only when the thickness LS of the shell around the particle that contains the added mass, LS>d . We also demonstrate that the IGSER can be used to predict particle displacement over a given timescale from knowledge of medium viscoelasticity; such ability will be of interest for designing nanoparticle-based drug delivery.

The knowledge-value chain: A conceptual framework for knowledge translation in health.

PubMed

Landry, Réjean; Amara, Nabil; Pablos-Mendes, Ariel; Shademani, Ramesh; Gold, Irving

2006-08-01

This article briefly discusses knowledge translation and lists the problems associated with it. Then it uses knowledge-management literature to develop and propose a knowledge-value chain framework in order to provide an integrated conceptual model of knowledge management and application in public health organizations. The knowledge-value chain is a non-linear concept and is based on the management of five dyadic capabilities: mapping and acquisition, creation and destruction, integration and sharing/transfer, replication and protection, and performance and innovation.

Transition records of stationary Markov chains.

PubMed

Naudts, Jan; Van der Straeten, Erik

2006-10-01

In any Markov chain with finite state space the distribution of transition records always belongs to the exponential family. This observation is used to prove a fluctuation theorem, and to show that the dynamical entropy of a stationary Markov chain is linear in the number of steps. Three applications are discussed. A known result about entropy production is reproduced. A thermodynamic relation is derived for equilibrium systems with Metropolis dynamics. Finally, a link is made with recent results concerning a one-dimensional polymer model.

The knowledge-value chain: A conceptual framework for knowledge translation in health.

PubMed Central

Landry, Réjean; Amara, Nabil; Pablos-Mendes, Ariel; Shademani, Ramesh; Gold, Irving

2006-01-01

This article briefly discusses knowledge translation and lists the problems associated with it. Then it uses knowledge-management literature to develop and propose a knowledge-value chain framework in order to provide an integrated conceptual model of knowledge management and application in public health organizations. The knowledge-value chain is a non-linear concept and is based on the management of five dyadic capabilities: mapping and acquisition, creation and destruction, integration and sharing/transfer, replication and protection, and performance and innovation. PMID:16917645

From bicycle chain ring shape to gear ratio: algorithm and examples.

PubMed

van Soest, A J

2014-01-03

A simple model of the bicycle drive system with a non-circular front chain ring is proposed and an algorithm is devised for calculation of the corresponding Gear Ratio As a Function Of Crank Angle (GRAFOCA). It is shown that the true effective radius of the chain ring is always the perpendicular distance between the crank axis and the line through the chain segment between the chain ring and the cog. It is illustrated that the true effective radius of the chain ring at any crank angle may differ substantially from the maximum vertical distance between the crank axis and the chain ring circumference that is used as a proxy for the effective chain ring radius in several studies; in particular, the crank angle at which the effective chain ring radius is maximal as predicted from the latter approach may deviate by as much as 0.30 rad from the true value. The algorithm proposed may help in designing chain rings that achieve the desired GRAFOCA. © 2013 Published by Elsevier Ltd. All rights reserved.

Beating of grafted chains induced by active Brownian particles

NASA Astrophysics Data System (ADS)

Yang, Qiu-song; Fan, Qing-wei; Shen, Zhuang-lin; Xia, Yi-qi; Tian, Wen-de; Chen, Kang

2018-06-01

We study the interplay between active Brownian particles (ABPs) and a "hairy" surface in two-dimensional geometry. We find that the increase of propelling force leads to and enhances inhomogeneous accumulation of ABPs inside the brush region. Oscillation of chain bundles (beating like cilia) is found in company with the formation and disassembly of a dynamic cluster of ABPs at large propelling forces. Meanwhile chains are stretched and pushed down due to the effective shear force by ABPs. The decrease of the average brush thickness with propelling force reflects the growth of the beating amplitude of chain bundles. Furthermore, the beating phenomenon is investigated in a simple single-chain system. We find that the chain swings regularly with a major oscillatory period, which increases with chain length and decreases with the increase of propelling force. We build a theory to describe the phenomenon and the predictions on the relationship between the period and amplitude for various chain lengths, and propelling forces agree very well with simulation data.

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.

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

Popp, R.A.; Enlow, M.K.

The clinical hematologic change in 2 groups of progeny from mice carrying radiation-induced strain SEC ..cap alpha..-chain deficiencies was found to be similar to the hematologic alterations in persons with ..cap alpha..-thalassemia. The heterozygous deletion or inactivation of the ..cap alpha..-chain gene in mice caused an anemia similar to ..cap alpha..-thalassemina minor in persons. The ..cap alpha..-chain deficiency in mice created an erythrocytosis, reticulocytosis, and microcytic, hypochromic anemia comparable with the changes in human ..cap alpha..-thalassemia minor resulting from deletion of the ..cap alpha..-chain gene. These mouse mutants are the only known animal models of human thalassemia. A comparison ofmore » hematologic values obtained from progeny possessing an ..cap alpha..-chain gene deficiency and from progeny possessing a ..beta..-chain duplication suggested that the deficiency of ..cap alpha..-chain synthesis, rather than a simple imbalance between the amounts of ..cap alpha..- and ..beta..-chains produced, was primarily responsible for the altered hematologic characteristics in these ..cap alpha..-thalassemic mice.« less

New cationic vesicles prepared with double chain surfactants from arginine: Role of the hydrophobic group on the antimicrobial activity and cytotoxicity.

PubMed

Pinazo, A; Petrizelli, V; Bustelo, M; Pons, R; Vinardell, M P; Mitjans, M; Manresa, A; Perez, L

2016-05-01

Cationic double chain surfactants have attracted much interest because they can give rise to cationic vesicles that can be used in biomedical applications. Using a simple and economical synthetic approach, we have synthesized four double-chain surfactants with different alkyl chain lengths (LANHCx). The critical aggregation concentration of the double chain surfactants is at least one order of magnitude lower than the CMC of their corresponding single-chain LAM and the solutions prepared with the LANHCx contain stable cationic vesicles. Encouragingly, these new arginine derivatives show very low haemolytic activity and weaker cytotoxic effects than conventional dialkyl dimethyl ammonium surfactants. In addition, the surfactant with the shortest alkyl chain exhibits good antimicrobial activity against Gram-positive bacteria. The results show that a rational design applied to cationic double chain surfactants might serve as a promising strategy for the development of safe cationic vesicular systems. Copyright © 2016 Elsevier B.V. All rights reserved.

Rheological Behavior of Entangled Polystyrene-Polyhedral Oligosilsesquioxane (POSS) Copolymer

DTIC Science & Technology

2006-08-24

analysis. The effects of the presence of tethered POSS cages on the glass transition were studied using differential scanning...studies mainly focused on the effect of the long chain branches (LCBs) on the linear and non- linear rheological properties. How spherical cage -like...apparent activation energy increasing with increasing iBuPOSS loading. Like linear polymeric coil branches, the iBuPOSS cage plays a negative effect on

Commande optimale minimisant la consommation d'energie d'un drone utilise comme relai de communication

NASA Astrophysics Data System (ADS)

Mechirgui, Monia

The purpose of this project is to implement an optimal control regulator, particularly the linear quadratic regulator in order to control the position of an unmanned aerial vehicle known as a quadrotor. This type of UAV has a symmetrical and simple structure. Thus, its control is relatively easy compared to conventional helicopters. Optimal control can be proven to be an ideal controller to reconcile between the tracking performance and energy consumption. In practice, the linearity requirements are not met, but some elaborations of the linear quadratic regulator have been used in many nonlinear applications with good results. The linear quadratic controller used in this thesis is presented in two forms: simple and adapted to the state of charge of the battery. Based on the traditional structure of the linear quadratic regulator, we introduced a new criterion which relies on the state of charge of the battery, in order to optimize energy consumption. This command is intended to be used to monitor and maintain the desired trajectory during several maneuvers while minimizing energy consumption. Both simple and adapted, linear quadratic controller are implemented in Simulink in discrete time. The model simulates the dynamics and control of a quadrotor. Performance and stability of the system are analyzed with several tests, from the simply hover to the complex trajectories in closed loop.

Arabidopsis GUX Proteins Are Glucuronyltransferases Responsible for the Addition of Glucuronic Acid Side Chains onto Xylan

EPA Science Inventory

Xylan, the second most abundant cell wall polysaccharide, is composed of a linear backbone of β-(1,4)-linked xylosyl residues that are often substituted with sugar side chains, such as glucuronic acid (GlcA) and methylglucuronic acid (MeGlcA). It has recently been shown that muta...

Visualizing the Chain Rule (for Functions over R and C) and More

ERIC Educational Resources Information Center

Kreminski, Rick

2009-01-01

A visual approach to understanding the chain rule and related derivative formulae, for functions from R to R and from C to C, is presented. This apparently novel approach has been successfully used with several audiences: students first studying calculus, students with some background in linear algebra, students beginning study of functions of a…

Simulation of size-exclusion chromatography distribution coefficients of comb-shaped molecules in spherical pores comparison of simulation and experiment.

PubMed

Radke, Wolfgang

2004-03-05

Simulations of the distribution coefficients of linear polymers and regular combs with various spacings between the arms have been performed. The distribution coefficients were plotted as a function of the number of segments in order to compare the size exclusion chromatography (SEC)-elution behavior of combs relative to linear molecules. By comparing the simulated SEC-calibration curves it is possible to predict the elution behavior of comb-shaped polymers relative to linear ones. In order to compare the results obtained by computer simulations with experimental data, a variety of comb-shaped polymers varying in side chain length, spacing between the side chains and molecular weights of the backbone were analyzed by SEC with light-scattering detection. It was found that the computer simulations could predict the molecular weights of linear molecules having the same retention volume with an accuracy of about 10%, i.e. the error in the molecular weight obtained by calculating the molecular weight of the comb-polymer based on a calibration curve constructed using linear standards and the results of the computer simulations are of the same magnitude as the experimental error of absolute molecular weight determination.

Fatty acid composition of polar and neutral meat lipids of goats browsing in native pasture of Brazilian Semiarid.

PubMed

Fonteles, Natália L O; Alves, Susana P; Madruga, Marta Suely; Queiroga, Rita R E; Andrade, Albericio P; Silva, Divan S; Leal, Amanda P; Bessa, Rui J B; Medeiros, Ariosvaldo N

2018-05-01

Thirty six male goats grazing Caatinga native pasture were randomly assigned to 4 concentrate supplementation levels (0, 5, 10 and 15g/kg of body weight) and slaughtered after 120days. Longissimus muscle meat lipids were extracted and fractionated into neutral (NL) and polar (PL) lipids. Supplementation of grazing goats increased linearly (P<0.05) intramuscular fat (1 to 1.5% of meat) and NL (0.3 to 1% of meat) but decreased linearly (P=0.044) the PL (0.66 to 0.50% of meat). On NL, supplementation increased linearly (P=0.047) the proportion of c9-18:1 (31 to 40% of FA) with supplementation. On PL, supplementation reduced linearly (P<0.03) the dimethyl acetals, 18:3n-3 and most of long chain polyunsaturated FA (PUFA) proportions but increased linearly (P<0.001) the c9-18:1. Considering the total meat FA, supplementation led to an increase of the saturated and monounsaturated FA contents and a decrease of the long chain n-6 and n-3 PUFA contents. Copyright © 2018 Elsevier Ltd. All rights reserved.

Magnetization of a quantum spin system induced by a linear polarized laser

NASA Astrophysics Data System (ADS)

Zvyagin, A. A.

2015-08-01

It is shown that a linear polarized laser can cause magnetization of a spin system with magnetic anisotropy, the distinguished axis of which is perpendicular to the polarization of the laser field. In the dynamical regime the magnetization oscillates around the nonzero value determined by the parameters of the system. Oscillations have the frequency of the laser field, modulated by the lower Rabi-like frequencies. In the steady-state regime, for a large time scale greater than the characteristic relaxation time, the Rabi-like oscillations are damped, and the magnetization oscillates with the frequency of the laser field around the value which is determined by the relaxation rate also. Analytic results are presented for the spin-1/2 chain. The most direct manifestation of such a behavior can be observed in spin-1/2 Ising chain materials if the linear polarization of the laser field is chosen to be perpendicular to the Ising axis.

A simple, stable, and accurate linear tetrahedral finite element for transient, nearly, and fully incompressible solid dynamics: A dynamic variational multiscale approach [A simple, stable, and accurate tetrahedral finite element for transient, nearly incompressible, linear and nonlinear elasticity: A dynamic variational multiscale approach

DOE PAGES

Scovazzi, Guglielmo; Carnes, Brian; Zeng, Xianyi; ...

2015-11-12

Here, we propose a new approach for the stabilization of linear tetrahedral finite elements in the case of nearly incompressible transient solid dynamics computations. Our method is based on a mixed formulation, in which the momentum equation is complemented by a rate equation for the evolution of the pressure field, approximated with piece-wise linear, continuous finite element functions. The pressure equation is stabilized to prevent spurious pressure oscillations in computations. Incidentally, it is also shown that many stabilized methods previously developed for the static case do not generalize easily to transient dynamics. Extensive tests in the context of linear andmore » nonlinear elasticity are used to corroborate the claim that the proposed method is robust, stable, and accurate.« less

A simple, stable, and accurate linear tetrahedral finite element for transient, nearly, and fully incompressible solid dynamics: A dynamic variational multiscale approach [A simple, stable, and accurate tetrahedral finite element for transient, nearly incompressible, linear and nonlinear elasticity: A dynamic variational multiscale approach

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

Scovazzi, Guglielmo; Carnes, Brian; Zeng, Xianyi

Here, we propose a new approach for the stabilization of linear tetrahedral finite elements in the case of nearly incompressible transient solid dynamics computations. Our method is based on a mixed formulation, in which the momentum equation is complemented by a rate equation for the evolution of the pressure field, approximated with piece-wise linear, continuous finite element functions. The pressure equation is stabilized to prevent spurious pressure oscillations in computations. Incidentally, it is also shown that many stabilized methods previously developed for the static case do not generalize easily to transient dynamics. Extensive tests in the context of linear andmore » nonlinear elasticity are used to corroborate the claim that the proposed method is robust, stable, and accurate.« less

Asymptotic Linear Spectral Statistics for Spiked Hermitian Random Matrices

NASA Astrophysics Data System (ADS)

Passemier, Damien; McKay, Matthew R.; Chen, Yang

2015-07-01

Using the Coulomb Fluid method, this paper derives central limit theorems (CLTs) for linear spectral statistics of three "spiked" Hermitian random matrix ensembles. These include Johnstone's spiked model (i.e., central Wishart with spiked correlation), non-central Wishart with rank-one non-centrality, and a related class of non-central matrices. For a generic linear statistic, we derive simple and explicit CLT expressions as the matrix dimensions grow large. For all three ensembles under consideration, we find that the primary effect of the spike is to introduce an correction term to the asymptotic mean of the linear spectral statistic, which we characterize with simple formulas. The utility of our proposed framework is demonstrated through application to three different linear statistics problems: the classical likelihood ratio test for a population covariance, the capacity analysis of multi-antenna wireless communication systems with a line-of-sight transmission path, and a classical multiple sample significance testing problem.

Review of Statistical Methods for Analysing Healthcare Resources and Costs

PubMed Central

Mihaylova, Borislava; Briggs, Andrew; O'Hagan, Anthony; Thompson, Simon G

2011-01-01

We review statistical methods for analysing healthcare resource use and costs, their ability to address skewness, excess zeros, multimodality and heavy right tails, and their ease for general use. We aim to provide guidance on analysing resource use and costs focusing on randomised trials, although methods often have wider applicability. Twelve broad categories of methods were identified: (I) methods based on the normal distribution, (II) methods following transformation of data, (III) single-distribution generalized linear models (GLMs), (IV) parametric models based on skewed distributions outside the GLM family, (V) models based on mixtures of parametric distributions, (VI) two (or multi)-part and Tobit models, (VII) survival methods, (VIII) non-parametric methods, (IX) methods based on truncation or trimming of data, (X) data components models, (XI) methods based on averaging across models, and (XII) Markov chain methods. Based on this review, our recommendations are that, first, simple methods are preferred in large samples where the near-normality of sample means is assured. Second, in somewhat smaller samples, relatively simple methods, able to deal with one or two of above data characteristics, may be preferable but checking sensitivity to assumptions is necessary. Finally, some more complex methods hold promise, but are relatively untried; their implementation requires substantial expertise and they are not currently recommended for wider applied work. Copyright © 2010 John Wiley & Sons, Ltd. PMID:20799344

A simple device using magnetic transportation for droplet-based PCR.

PubMed

Ohashi, Tetsuo; Kuyama, Hiroki; Hanafusa, Nobuhiro; Togawa, Yoshiyuki

2007-10-01

The Polymerase chain reaction (PCR) was successfully and rapidly performed in a simple reaction device devoid of channels, pumps, valves, or other control elements used in conventional lab-on-a-chip technology. The basic concept of this device is the transportation of aqueous droplets containing hydrophilic magnetic beads in a flat-bottomed, tray-type reactor filled with silicone oil. The whole droplets sink to the bottom of the reactor because their specific gravity is greater than that of the silicone oil used here. The droplets follow the movement of a magnet located underneath the reactor. The notable advantage of the droplet-based PCR is the ability to switch rapidly the proposed reaction temperature by moving the droplets to the required temperature zones in the temperature gradient. The droplet-based reciprocative thermal cycling was performed by moving the droplets composed of PCR reaction mixture to the designated temperature zones on a linear temperature gradient from 50 degrees C to 94 degrees C generated on the flat bottom plate of the tray reactor. Using human-derived DNA containing the mitochondria genes as the amplification targets, the droplet-based PCR with magnetic reciprocative thermal cycling successfully provided the five PCR products ranging from 126 to 1,219 bp in 11 min with 30 cycles. More remarkably, the human genomic gene amplification targeting glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene was accomplished rapidly in 3.6 min with 40 cycles.

Real-time forecasting of an epidemic using a discrete time stochastic model: a case study of pandemic influenza (H1N1-2009).

PubMed

Nishiura, Hiroshi

2011-02-16

Real-time forecasting of epidemics, especially those based on a likelihood-based approach, is understudied. This study aimed to develop a simple method that can be used for the real-time epidemic forecasting. A discrete time stochastic model, accounting for demographic stochasticity and conditional measurement, was developed and applied as a case study to the weekly incidence of pandemic influenza (H1N1-2009) in Japan. By imposing a branching process approximation and by assuming the linear growth of cases within each reporting interval, the epidemic curve is predicted using only two parameters. The uncertainty bounds of the forecasts are computed using chains of conditional offspring distributions. The quality of the forecasts made before the epidemic peak appears largely to depend on obtaining valid parameter estimates. The forecasts of both weekly incidence and final epidemic size greatly improved at and after the epidemic peak with all the observed data points falling within the uncertainty bounds. Real-time forecasting using the discrete time stochastic model with its simple computation of the uncertainty bounds was successful. Because of the simplistic model structure, the proposed model has the potential to additionally account for various types of heterogeneity, time-dependent transmission dynamics and epidemiological details. The impact of such complexities on forecasting should be explored when the data become available as part of the disease surveillance.

Dual-primer self-generation SERS signal amplification assay for PDGF-BB using label-free aptamer.

PubMed

Ye, SuJuan; Zhai, XiaoMo; Wu, YanYing; Kuang, ShaoPing

2016-05-15

Highly sensitive detection of proteins, especially those associated with cancers, is essential to biomedical research as well as clinical diagnosis. In this work, a simple and novel one-two-three signal amplification surface-enhanced Raman scattering (SERS) method for the detection of protein is fabricated by using label-free aptamer and dual-primer self-generation. Platelet-derived growth factor B-chain (PDGF-BB) is selected as the model protein. The one-two-three cascade DNA amplification means one target-aptamer binding event, two hairpin DNA switches and three DNA amplification reactions. This strategy possesses some remarkable features compared to conventional signal amplification methods: (i) A smart probe including a label-free aptamer is fabricated, for suitable hybridization without hindering the affinity of the aptamer toward its target. (ii) Using the unique structure switch of the aptamer and cooperator, a one-two-three working mode is developed to amplify the SERS signal. The amplification efficiency is enhanced. Given the unique and attractive characteristics, a simple and universal strategy is designed to accomplish ultrasensitive detection of proteins. The detection limit of PDGF-BB via SERS detection is 0.42 pM, with the linear range from 1.0×10(-12)M to 10(-8)M. It is potentially universal because the aptamer can be easily designed for biomolecules whose aptamers undergo similar conformational changes. Copyright © 2015 Elsevier B.V. All rights reserved.

Antagonistic and synergistic toxic effects of Pb and Cd in a simple food chain: nematodes feeding on bacteria and fungi

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

Doelman, P.; Nieboer, G.; Schrooten, J.

1984-06-01

Soil pollution with heavy metals may affect the functioning of the soil biota by inhibiting the decomposition of organic matter and may also influence food chains. This paper presents the results of an investigation on how the reproduction of soil nematodes can be influenced by feeding on bacteria or fungi contaminated with lead and cadmium.

The surprising dynamics of a chain on a pulley: lift off and snapping

PubMed Central

Audoly, Basile

2016-01-01

The motion of weights attached to a chain or string moving on a frictionless pulley is a classic problem of introductory physics used to understand the relationship between force and acceleration. Here, we consider the dynamics of the chain when one of the weights is removed and, thus, one end is pulled with constant acceleration. This simple change has dramatic consequences for the ensuing motion: at a finite time, the chain ‘lifts off’ from the pulley, and the free end subsequently accelerates faster than the end that is pulled. Eventually, the chain undergoes a dramatic reversal of curvature reminiscent of the crack or snap, of a whip. We combine experiments, numerical simulations and theoretical arguments to explain key aspects of this dynamical problem. PMID:27436987

The surprising dynamics of a chain on a pulley: lift off and snapping.

PubMed

Brun, P-T; Audoly, Basile; Goriely, Alain; Vella, Dominic

2016-06-01

The motion of weights attached to a chain or string moving on a frictionless pulley is a classic problem of introductory physics used to understand the relationship between force and acceleration. Here, we consider the dynamics of the chain when one of the weights is removed and, thus, one end is pulled with constant acceleration. This simple change has dramatic consequences for the ensuing motion: at a finite time, the chain 'lifts off' from the pulley, and the free end subsequently accelerates faster than the end that is pulled. Eventually, the chain undergoes a dramatic reversal of curvature reminiscent of the crack or snap, of a whip. We combine experiments, numerical simulations and theoretical arguments to explain key aspects of this dynamical problem.

Practical Use Of It In Traceability In Food Value Chains

NASA Astrophysics Data System (ADS)

Ratcliff, Jon; Boddington, Michael

Traceability is today considered an essential requirement for the food value chain due to the need to provide consumers with accurate information in the event of food safety recalls, to provide assurance with regard the source and production systems for food products and in certain countries to comply with government legislation. Within an individual business traceability can be quite simple to implement, however, in a global trading market, traceability of the entire supply chain, including logistics is extremely complex. For this reason IT solutions such as TraceTracker have been developed which not only provide electronic solutions for complete traceability but also allow products to be tracked at any point in the supply chain.

Solid-phase submonomer synthesis of peptoid polymers and their self-assembly into highly-ordered nanosheets.

PubMed

Tran, Helen; Gael, Sarah L; Connolly, Michael D; Zuckermann, Ronald N

2011-11-02

Peptoids are a novel class of biomimetic, non-natural, sequence-specific heteropolymers that resist proteolysis, exhibit potent biological activity, and fold into higher order nanostructures. Structurally similar to peptides, peptoids are poly N-substituted glycines, where the side chains are attached to the nitrogen rather than the alpha-carbon. Their ease of synthesis and structural diversity allows testing of basic design principles to drive de novo design and engineering of new biologically-active and nanostructured materials. Here, a simple manual peptoid synthesis protocol is presented that allows the synthesis of long chain polypeptoids (up to 50mers) in excellent yields. Only basic equipment, simple techniques (e.g. liquid transfer, filtration), and commercially available reagents are required, making peptoids an accessible addition to many researchers' toolkits. The peptoid backbone is grown one monomer at a time via the submonomer method which consists of a two-step monomer addition cycle: acylation and displacement. First, bromoacetic acid activated in situ with N,N'-diisopropylcarbodiimide acylates a resin-bound secondary amine. Second, nucleophilic displacement of the bromide by a primary amine follows to introduce the side chain. The two-step cycle is iterated until the desired chain length is reached. The coupling efficiency of this two-step cycle routinely exceeds 98% and enables the synthesis of peptoids as long as 50 residues. Highly tunable, precise and chemically diverse sequences are achievable with the submonomer method as hundreds of readily available primary amines can be directly incorporated. Peptoids are emerging as a versatile biomimetic material for nanobioscience research because of their synthetic flexibility, robustness, and ordering at the atomic level. The folding of a single-chain, amphiphilic, information-rich polypeptoid into a highly-ordered nanosheet was recently demonstrated. This peptoid is a 36-mer that consists of only three different commercially available monomers: hydrophobic, cationic and anionic. The hydrophobic phenylethyl side chains are buried in the nanosheet core whereas the ionic amine and carboxyl side chains align on the hydrophilic faces. The peptoid nanosheets serve as a potential platform for membrane mimetics, protein mimetics, device fabrication, and sensors. Methods for peptoid synthesis, sheet formation, and microscopy imaging are described and provide a simple method to enable future peptoid nanosheet designs.

Resultant as the determinant of a Koszul complex

NASA Astrophysics Data System (ADS)

Anokhina, A. S.; Morozov, A. Yu.; Shakirov, Sh. R.

2009-09-01

The determinant is a very important characteristic of a linear map between vector spaces. Two generalizations of linear maps are intensively used in modern theory: linear complexes (nilpotent chains of linear maps) and nonlinear maps. The determinant of a complex and the resultant are then the corresponding generalizations of the determinant of a linear map. It turns out that these two quantities are related: the resultant of a nonlinear map is the determinant of the corresponding Koszul complex. We give an elementary introduction into these notions and relations, which will definitely play a role in the future development of theoretical physics.

Nonsimultaneous chains and dominos in kidney- paired donation-revisited.

PubMed

Ashlagi, I; Gilchrist, D S; Roth, A E; Rees, M A

2011-05-01

Since 2008, kidney exchange in America has grown in part from the incorporation of nondirected donors in transplant chains rather than simple exchanges. It is controversial whether these chains should be performed simultaneously 'domino-paired donation', (DPD) or nonsimultaneously 'nonsimultaneous extended altruistic donor, chains (NEAD). NEAD chains create 'bridge donors' whose incompatible recipients receive kidneys before the bridge donor donates, and so risk reneging by bridge donors, but offer the opportunity to create more transplants by overcoming logistical barriers inherent in simultaneous chains. Gentry et al. simulated whether DPD or NEAD chains would produce more transplants when chain segment length was limited to three transplants, and reported that DPD performed at least as well as NEAD chains. As this finding contrasts with the experience of several groups involved in kidney-paired donation, we performed simulations that allowed for longer chain segments and used actual patient data from the Alliance for Paired Donation. When chain segments of 4-6 transplants are allowed in the simulations, NEAD chains produce more transplants than DPD. Our simulations showed not only more transplants as chain length increased, but also that NEAD chains produced more transplants for highly sensitized and blood type O recipients. ©2011 The Authors Journal compilation©2011 The American Society of Transplantation and the American Society of Transplant Surgeons.

Robust design of (s, S) inventory policy parameters in supply chains with demand and lead time uncertainties

NASA Astrophysics Data System (ADS)

Karimi Movahed, Kamran; Zhang, Zhi-Hai

2015-09-01

Demand and lead time uncertainties have significant effects on supply chain behaviour. In this paper, we present a single-product three-level multi-period supply chain with uncertain demands and lead times by using robust techniques to study the managerial insights of the supply chain inventory system under uncertainty. We formulate this problem as a robust mixed-integer linear program with minimised expected cost and total cost variation to determine the optimal (s, S) values of the inventory parameters. Several numerical studies are performed to investigate the supply chain behaviour. Useful guidelines for the design of a robust supply chain are also provided. Results show that the order variance and the expected cost in a supply chain significantly increase when the manufacturer's review period is an integer ratio of the distributor's and the retailer's review periods.

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.

Synthesis of diketopyrrolopyrrole-based polymers with polydimethylsiloxane side chains and their application in organic field-effect transistors

NASA Astrophysics Data System (ADS)

Ohnishi, Inori; Hashimoto, Kazuhito; Tajima, Keisuke

2018-03-01

Linear polydimethylsiloxane (PDMS) was investigated as a solubilizing group for π-conjugated polymers with the aim of combining high solubility in organic solvents with the molecular packing in solid films that is advantageous for charge transport. Diketopyrrolopyrrole-based copolymers with different contents and substitution patterns of the PDMS side chains were synthesized and evaluated for application in organic field-effect transistors. The PDMS side chains greatly increased the solubility of the polymers and led to shorter d-spacings of the π-stacking in the thin films compared with polymers containing conventional branched alkyl side chains.

Statistical mechanics of Fermi-Pasta-Ulam chains with the canonical ensemble

NASA Astrophysics Data System (ADS)

Demirel, Melik C.; Sayar, Mehmet; Atılgan, Ali R.

1997-03-01

Low-energy vibrations of a Fermi-Pasta-Ulam-Β (FPU-Β) chain with 16 repeat units are analyzed with the aid of numerical experiments and the statistical mechanics equations of the canonical ensemble. Constant temperature numerical integrations are performed by employing the cubic coupling scheme of Kusnezov et al. [Ann. Phys. 204, 155 (1990)]. Very good agreement is obtained between numerical results and theoretical predictions for the probability distributions of the generalized coordinates and momenta both of the chain and of the thermal bath. It is also shown that the average energy of the chain scales linearly with the bath temperature.

A simple linear regression method for quantitative trait loci linkage analysis with censored observations.

PubMed

Anderson, Carl A; McRae, Allan F; Visscher, Peter M

2006-07-01

Standard quantitative trait loci (QTL) mapping techniques commonly assume that the trait is both fully observed and normally distributed. When considering survival or age-at-onset traits these assumptions are often incorrect. Methods have been developed to map QTL for survival traits; however, they are both computationally intensive and not available in standard genome analysis software packages. We propose a grouped linear regression method for the analysis of continuous survival data. Using simulation we compare this method to both the Cox and Weibull proportional hazards models and a standard linear regression method that ignores censoring. The grouped linear regression method is of equivalent power to both the Cox and Weibull proportional hazards methods and is significantly better than the standard linear regression method when censored observations are present. The method is also robust to the proportion of censored individuals and the underlying distribution of the trait. On the basis of linear regression methodology, the grouped linear regression model is computationally simple and fast and can be implemented readily in freely available statistical software.

Formation of printable granular and colloidal chains through capillary effects and dielectrophoresis

PubMed Central

Rozynek, Zbigniew; Han, Ming; Dutka, Filip; Garstecki, Piotr; Józefczak, Arkadiusz; Luijten, Erik

2017-01-01

One-dimensional conductive particle assembly holds promise for a variety of practical applications, in particular for a new generation of electronic devices. However, synthesis of such chains with programmable shapes outside a liquid environment has proven difficult. Here we report a route to simply ‘pull' flexible granular and colloidal chains out of a dispersion by combining field-directed assembly and capillary effects. These chains are automatically stabilized by liquid bridges formed between adjacent particles, without the need for continuous energy input or special particle functionalization. They can further be deposited onto any surface and form desired conductive patterns, potentially applicable to the manufacturing of simple electronic circuits. Various aspects of our route, including the role of particle size and the voltages needed, are studied in detail. Looking towards practical applications, we also present the possibility of two-dimensional writing, rapid solidification of chains and methods to scale up chain production. PMID:28497791

Formation of printable granular and colloidal chains through capillary effects and dielectrophoresis

NASA Astrophysics Data System (ADS)

Rozynek, Zbigniew; Han, Ming; Dutka, Filip; Garstecki, Piotr; Józefczak, Arkadiusz; Luijten, Erik

2017-05-01

One-dimensional conductive particle assembly holds promise for a variety of practical applications, in particular for a new generation of electronic devices. However, synthesis of such chains with programmable shapes outside a liquid environment has proven difficult. Here we report a route to simply `pull' flexible granular and colloidal chains out of a dispersion by combining field-directed assembly and capillary effects. These chains are automatically stabilized by liquid bridges formed between adjacent particles, without the need for continuous energy input or special particle functionalization. They can further be deposited onto any surface and form desired conductive patterns, potentially applicable to the manufacturing of simple electronic circuits. Various aspects of our route, including the role of particle size and the voltages needed, are studied in detail. Looking towards practical applications, we also present the possibility of two-dimensional writing, rapid solidification of chains and methods to scale up chain production.

Near-optimal alternative generation using modified hit-and-run sampling for non-linear, non-convex problems

NASA Astrophysics Data System (ADS)

Rosenberg, D. E.; Alafifi, A.

2016-12-01

Water resources systems analysis often focuses on finding optimal solutions. Yet an optimal solution is optimal only for the modelled issues and managers often seek near-optimal alternatives that address un-modelled objectives, preferences, limits, uncertainties, and other issues. Early on, Modelling to Generate Alternatives (MGA) formalized near-optimal as the region comprising the original problem constraints plus a new constraint that allowed performance within a specified tolerance of the optimal objective function value. MGA identified a few maximally-different alternatives from the near-optimal region. Subsequent work applied Markov Chain Monte Carlo (MCMC) sampling to generate a larger number of alternatives that span the near-optimal region of linear problems or select portions for non-linear problems. We extend the MCMC Hit-And-Run method to generate alternatives that span the full extent of the near-optimal region for non-linear, non-convex problems. First, start at a feasible hit point within the near-optimal region, then run a random distance in a random direction to a new hit point. Next, repeat until generating the desired number of alternatives. The key step at each iterate is to run a random distance along the line in the specified direction to a new hit point. If linear equity constraints exist, we construct an orthogonal basis and use a null space transformation to confine hits and runs to a lower-dimensional space. Linear inequity constraints define the convex bounds on the line that runs through the current hit point in the specified direction. We then use slice sampling to identify a new hit point along the line within bounds defined by the non-linear inequity constraints. This technique is computationally efficient compared to prior near-optimal alternative generation techniques such MGA, MCMC Metropolis-Hastings, evolutionary, or firefly algorithms because search at each iteration is confined to the hit line, the algorithm can move in one step to any point in the near-optimal region, and each iterate generates a new, feasible alternative. We use the method to generate alternatives that span the near-optimal regions of simple and more complicated water management problems and may be preferred to optimal solutions. We also discuss extensions to handle non-linear equity constraints.

Conserving the linear momentum in stochastic dynamics: Dissipative particle dynamics as a general strategy to achieve local thermostatization in molecular dynamics simulations.

PubMed

Passler, Peter P; Hofer, Thomas S

2017-02-15

Stochastic dynamics is a widely employed strategy to achieve local thermostatization in molecular dynamics simulation studies; however, it suffers from an inherent violation of momentum conservation. Although this short-coming has little impact on structural and short-time dynamic properties, it can be shown that dynamics in the long-time limit such as diffusion is strongly dependent on the respective thermostat setting. Application of the methodically similar dissipative particle dynamics (DPD) provides a simple, effective strategy to ensure the advantages of local, stochastic thermostatization while at the same time the linear momentum of the system remains conserved. In this work, the key parameters to employ the DPD thermostats in the framework of periodic boundary conditions are investigated, in particular the dependence of the system properties on the size of the DPD-region as well as the treatment of forces near the cutoff. Structural and dynamical data for light and heavy water as well as a Lennard-Jones fluid have been compared to simulations executed via stochastic dynamics as well as via use of the widely employed Nose-Hoover chain and Berendsen thermostats. It is demonstrated that a small size of the DPD region is sufficient to achieve local thermalization, while at the same time artifacts in the self-diffusion characteristic for stochastic dynamics are eliminated. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

A Rigidity-Enhanced Antimicrobial Activity: A Case for Linear Cationic α-Helical Peptide HP(2–20) and Its Four Analogues

PubMed Central

Liu, Li; Fang, Ying; Huang, Qingsheng; Wu, Jianhua

2011-01-01

Linear cationic α-helical antimicrobial peptides are referred to as one of the most likely substitutes for common antibiotics, due to their relatively simple structures (≤40 residues) and various antimicrobial activities against a wide range of pathogens. Of those, HP(2–20) was isolated from Helicobacter pylori ribosomal protein. To reveal a mechanical determinant that may mediate the antimicrobial activities, we examined the mechanical properties and structural stabilities of HP(2–20) and its four analogues of same chain length by steered molecular dynamics simulation. The results indicated the following: the resistance of H-bonds to the tensile extension mediated the early extensive stage; with the loss of H-bonds, the tensile force was dispensed to prompt the conformational phase transition; and Young's moduli (N/m2) of the peptides were about 4∼8×109. These mechanical features were sensitive to the variation of the residue compositions. Furthermore, we found that the antimicrobial activity is rigidity-enhanced, that is, a harder peptide has stronger antimicrobial activity. It suggests that the molecular spring constant may be used to seek a new structure-activity relationship for different α-helical peptide groups. This exciting result was reasonably explained by a possible mechanical mechanism that regulates both the membrane pore formation and the peptide insertion. PMID:21283643

Cyclic Macromolecules: Dynamics and Nonlinear Rheology, Final Report DOE Award # DE-FG02-05ER46218, Texas Tech University

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

McKenna, Gregory B.; Grubbs, Robert H.; Kornfield, Julia A.

2012-04-25

The work described in the present report had the original goal to produce large, entangled, ring polymers that were uncontaminated by linear chains and to characterize by rheological methods the dynamics of these rings. While the work fell short of this specific goal, the outcomes of the research performed under support from this grant provided novel macromolecular synthesis methods, new separation methods for ring and linear chains, and novel rheological data on bottle brush polymers, wedge polymers and dendron-based ring molecules. The grant funded a total of 8 archival manuscripts and one patent, all of which are attached to themore » present report.« less

Mixed Integer Linear Programming model for Crude Palm Oil Supply Chain Planning

NASA Astrophysics Data System (ADS)

Sembiring, Pasukat; Mawengkang, Herman; Sadyadharma, Hendaru; Bu'ulolo, F.; Fajriana

2018-01-01

The production process of crude palm oil (CPO) can be defined as the milling process of raw materials, called fresh fruit bunch (FFB) into end products palm oil. The process usually through a series of steps producing and consuming intermediate products. The CPO milling industry considered in this paper does not have oil palm plantation, therefore the FFB are supplied by several public oil palm plantations. Due to the limited availability of FFB, then it is necessary to choose from which plantations would be appropriate. This paper proposes a mixed integer linear programming model the supply chain integrated problem, which include waste processing. The mathematical programming model is solved using neighborhood search approach.

On the Effect of Variability on Fermi, Pasta and Ulam Matrices

NASA Astrophysics Data System (ADS)

Nelson, Heather; Choubey, Bhaskar

The first numerical experiment by Fermi, Pasta, Ulam and Tsingou in 1955 observed recurrence in an array of non-linear systems. This has led to a large number of nonlinear numerical experiments with various new results from a chain of ideal oscillators. FPUT arrays consists of linear oscillators connected nonlinearly which leads to recurrence of energy mode with time. However, if such a system were to be physically constructed, inherent process variations would introduce a manufacturing tolerance into the parameters of the system. This abstract reports investigation into the effects of these tolerances on the FPU matrices. It has been observed that tolerance in the oscillators can degrade the observance of recurrence and with a chain of even 64 oscillators, recurrence cannot be observed with tolerances more than 10%. It has also been observed that linear oscillators tolerances have more effects on recurrence than those of the nonlinear coupling. Even with very small tolerances of +/- 1% on the linear components, one start to observe variations in the quality and magnitude of the recurrence and at +/- 5%, recurrence is starting to break down.

A mathematical/physics carbon emission reduction strategy for building supply chain network based on carbon tax policy

NASA Astrophysics Data System (ADS)

Li, Xueying; Peng, Ying; Zhang, Jing

2017-03-01

Under the background of a low carbon economy, this paper examines the impact of carbon tax policy on supply chain network emission reduction. The integer linear programming method is used to establish a supply chain network emission reduction such a model considers the cost of CO2 emissions, and analyses the impact of different carbon price on cost and carbon emissions in supply chains. The results show that the implementation of a carbon tax policy can reduce CO2 emissions in building supply chain, but the increase in carbon price does not produce a reduction effect, and may bring financial burden to the enterprise. This paper presents a reasonable carbon price range and provides decision makers with strategies towards realizing a low carbon building supply chain in an economical manner.

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

Xing, Kunyue; Chatterjee, Sabornie; Saito, Tomonori

Dielectric spectroscopy, rheology, and differential scanning calorimetry were employed to study the effect of chain-end hydrogen bonding on the dynamics of hydroxylterminated polydimethylsiloxane. We demonstrate that hydrogen bonding has a strong influence on both segmental and slower dynamics in the systems with low molecular weights. In particular, the decrease in the chain length leads to an increase of the glass transition temperature, viscosity, and fragility index, at variance with the usual behavior of nonassociating polymers. The supramolecular association of hydroxylterminated chains leads to the emergence in dielectric and mechanical relaxation spectra of the so-called Debye process traditionally observed in monohydroxymore » alcohols. Our analysis suggests that the hydroxyl-terminated PDMS oligomers may associate in brush-like or chain-like structures, depending on the size of their covalent chains. Finally, the effective length of the linear-associated chains was estimated from the rheological measurements.« less

Forecasting Workload for Defense Logistics Agency Distribution

DTIC Science & Technology

2014-12-01

Distribution workload ...........................18 Monthly DD Sales for the four primary supply chains ( Avn , Land, Maritime, Ind HW) plotted to...average AVN Aviation BSM Business Systems Modernization CIT consumable items transfer C&E Construction and Equipment C&T Clothing...992081.437 See Figure 2 below for the graphical output of the linear regression. Monthly DD Sales for the four primary supply chains ( Avn , Land

29 CFR 570.65 - Occupations involving the operation of circular saws, band saws, guillotine shears, chain saws...

Code of Federal Regulations, 2013 CFR

2013-07-01

... notches or teeth, running over wheels or pulleys, and used for sawing materials. Chain saw shall mean a... machine equipped with a moveable blade operated vertically and used to shear materials. The term shall not... moving blade that alternately changes direction on a linear cutting axis used for sawing materials. Wood...

29 CFR 570.65 - Occupations involving the operation of circular saws, band saws, guillotine shears, chain saws...

Code of Federal Regulations, 2012 CFR

2012-07-01

... notches or teeth, running over wheels or pulleys, and used for sawing materials. Chain saw shall mean a... machine equipped with a moveable blade operated vertically and used to shear materials. The term shall not... moving blade that alternately changes direction on a linear cutting axis used for sawing materials. Wood...

29 CFR 570.65 - Occupations involved in the operations of circular saws, band saws, guillotine shears, chain saws...

Code of Federal Regulations, 2011 CFR

2011-07-01

... notches or teeth, running over wheels or pulleys, and used for sawing materials. Chain saw shall mean a... machine equipped with a moveable blade operated vertically and used to shear materials. The term shall not... moving blade that alternately changes direction on a linear cutting axis used for sawing materials. Wood...

29 CFR 570.65 - Occupations involving the operation of circular saws, band saws, guillotine shears, chain saws...

Code of Federal Regulations, 2014 CFR

2014-07-01

... notches or teeth, running over wheels or pulleys, and used for sawing materials. Chain saw shall mean a... machine equipped with a moveable blade operated vertically and used to shear materials. The term shall not... moving blade that alternately changes direction on a linear cutting axis used for sawing materials. Wood...

A High-Linearity, Ring-Oscillator-Based, Vernier Time-to-Digital Converter Utilizing Carry Chains in FPGAs

NASA Astrophysics Data System (ADS)

Cui, Ke; Ren, Zhongjie; Li, Xiangyu; Liu, Zongkai; Zhu, Rihong

2017-01-01

Time-to-digital converters (TDCs) using dedicated carry chains of field programmable gate arrays (FPGAs) are usually organized in tapped-delay-line type which are intensively researched in recent years. However this method incurs poor differential nonlinearity (DNL) which arises from the inherent uneven bin granularity. This paper proposes a TDC architecture which utilizes the carry chains in a quite different manner in order to alleviate this long-standing problem. Two independent carry chains working as the delay lines for the fine time interpolation are organized in a ring-oscillator-based Vernier style and the time difference between them is finely adjusted by assigning different number of basic delay cells. A specific design flow is described to obtain the desired delay difference. The TDC was implemented on a Stratix III FPGA. Test results show that the obtained resolution is 31 ps and the DNL\\INL is in the range of (-0.080 LSB, 0.073 LSB)(-0.087 LSB, 0.091 LSB). This demonstrates that the proposed architecture greatly improves linearity compared to previous techniques. Additionally the resource cost is rather low which uses only 319 LUTs and 104 registers per TDC channel.

Room temperature structures and odd even behaviour of a homologous series of anhydrous lithium n-alkanoates

NASA Astrophysics Data System (ADS)

White, Nicole A. S.; Ellis, Henry A.

2008-10-01

The molecular structures of a homologous series of lithium n-alkanoates have been determined at room temperature using infrared spectroscopy, polarizing light microscopy and X-ray powder diffraction in conjunction with density and melting point measurements. For all the compounds investigated, asymmetric ionic metal-carboxylate coordination is proposed, with the molecules located within a triclinic crystal system with P1¯ space group. The molecules are nearly all of similar structure and are arranged within lamellar layers with four molecules per unit cell. The hydrocarbon chains, in nearly all trans conformation, are arranged tail-to-tail and tilted at an average angle of 55 ο to the planes containing lithium ions. The unit cell parameters such as sides: b and c increase linearly with increasing chain length whilst side a shows a linear decrease. Furthermore, the measured densities and melting points show odd-even behaviour, suggesting differences in molecular packing between odd and even chain length homologues. Geometric models are proposed to explain molecular orientation within a lamella and odd-even behaviour, involving the influence of terminal groups on the packing geometry of hydrocarbon chains within the lattice.

A Simple Piece of Apparatus to Aid the Understanding of the Relationship between Angular Velocity and Linear Velocity

ERIC Educational Resources Information Center

Unsal, Yasin

2011-01-01

One of the subjects that is confusing and difficult for students to fully comprehend is the concept of angular velocity and linear velocity. It is the relationship between linear and angular velocity that students find difficult; most students understand linear motion in isolation. In this article, we detail the design, construction and…

Ergonomics and sustainability--challenges from global supply chains.

PubMed

Hasle, Peter; Jensen, Per Langaa

2012-01-01

The development of globalised supply chains is a major challenge for sustainability. For several years, there has been discussion within the profession whether and how ergonomics and human factors can play a role. Based on our research, we have identified five major challenges from global supply chains especially related to the social aspects of sustainability: (1) criteria for social sustainability, (2) the role of key performance indicators in the management of supply chains, (3) the constant changes in supply chains, (4) the challenge in establishing participation, and (5) the development of agency and regulatory mechanisms. There are obviously no clear and simple solutions to these challenges. One possible avenue for progress might lie in acquiring a greater understanding of the challenges from global supply chains and developing a strategy which combines social and long-term business sustainability. Starting from such a basis, the next step would be to find ways for the ergonomics and human factors community to create international collaboration which can impact specific global supply chains.

Domain walls in single-chain magnets

NASA Astrophysics Data System (ADS)

Pianet, Vivien; Urdampilleta, Matias; Colin, Thierry; Clérac, Rodolphe; Coulon, Claude

2017-12-01

The topology and creation energy of domain walls in different magnetic chains (called Single-Chain Magnets or SCMs) are discussed. As these domain walls, that can be seen as "defects", are known to control both static and dynamic properties of these one-dimensional systems, their study and understanding are necessary first steps before a deeper discussion of the SCM properties at finite temperature. The starting point of the paper is the simple regular ferromagnetic chain for which the characteristics of the domain walls are well known. Then two cases will be discussed (i) the "mixed chains" in which isotropic and anisotropic classical spins alternate, and (ii) the so-called "canted chains" where two different easy axis directions are present. In particular, we show that "strictly narrow" domain walls no longer exist in these more complex cases, while a cascade of phase transitions is found for canted chains as the canting angle approaches 45∘. The consequence for thermodynamic properties is briefly discussed in the last part of the paper.

Optimal clinical trial design based on a dichotomous Markov-chain mixed-effect sleep model.

PubMed

Steven Ernest, C; Nyberg, Joakim; Karlsson, Mats O; Hooker, Andrew C

2014-12-01

D-optimal designs for discrete-type responses have been derived using generalized linear mixed models, simulation based methods and analytical approximations for computing the fisher information matrix (FIM) of non-linear mixed effect models with homogeneous probabilities over time. In this work, D-optimal designs using an analytical approximation of the FIM for a dichotomous, non-homogeneous, Markov-chain phase advanced sleep non-linear mixed effect model was investigated. The non-linear mixed effect model consisted of transition probabilities of dichotomous sleep data estimated as logistic functions using piecewise linear functions. Theoretical linear and nonlinear dose effects were added to the transition probabilities to modify the probability of being in either sleep stage. D-optimal designs were computed by determining an analytical approximation the FIM for each Markov component (one where the previous state was awake and another where the previous state was asleep). Each Markov component FIM was weighted either equally or by the average probability of response being awake or asleep over the night and summed to derive the total FIM (FIM(total)). The reference designs were placebo, 0.1, 1-, 6-, 10- and 20-mg dosing for a 2- to 6-way crossover study in six dosing groups. Optimized design variables were dose and number of subjects in each dose group. The designs were validated using stochastic simulation/re-estimation (SSE). Contrary to expectations, the predicted parameter uncertainty obtained via FIM(total) was larger than the uncertainty in parameter estimates computed by SSE. Nevertheless, the D-optimal designs decreased the uncertainty of parameter estimates relative to the reference designs. Additionally, the improvement for the D-optimal designs were more pronounced using SSE than predicted via FIM(total). Through the use of an approximate analytic solution and weighting schemes, the FIM(total) for a non-homogeneous, dichotomous Markov-chain phase advanced sleep model was computed and provided more efficient trial designs and increased nonlinear mixed-effects modeling parameter precision.

Intrinsic energy localization through discrete gap breathers in one-dimensional diatomic granular crystals.

PubMed

Theocharis, G; Boechler, N; Kevrekidis, P G; Job, S; Porter, Mason A; Daraio, C

2010-11-01

We present a systematic study of the existence and stability of discrete breathers that are spatially localized in the bulk of a one-dimensional chain of compressed elastic beads that interact via Hertzian contact. The chain is diatomic, consisting of a periodic arrangement of heavy and light spherical particles. We examine two families of discrete gap breathers: (1) an unstable discrete gap breather that is centered on a heavy particle and characterized by a symmetric spatial energy profile and (2) a potentially stable discrete gap breather that is centered on a light particle and is characterized by an asymmetric spatial energy profile. We investigate their existence, structure, and stability throughout the band gap of the linear spectrum and classify them into four regimes: a regime near the lower optical band edge of the linear spectrum, a moderately discrete regime, a strongly discrete regime that lies deep within the band gap of the linearized version of the system, and a regime near the upper acoustic band edge. We contrast discrete breathers in anharmonic Fermi-Pasta-Ulam (FPU)-type diatomic chains with those in diatomic granular crystals, which have a tensionless interaction potential between adjacent particles, and note that the asymmetric nature of the tensionless interaction potential can lead to hybrid bulk-surface localized solutions.

Intrinsic energy localization through discrete gap breathers in one-dimensional diatomic granular crystals

NASA Astrophysics Data System (ADS)

Theocharis, G.; Boechler, N.; Kevrekidis, P. G.; Job, S.; Porter, Mason A.; Daraio, C.

2010-11-01

We present a systematic study of the existence and stability of discrete breathers that are spatially localized in the bulk of a one-dimensional chain of compressed elastic beads that interact via Hertzian contact. The chain is diatomic, consisting of a periodic arrangement of heavy and light spherical particles. We examine two families of discrete gap breathers: (1) an unstable discrete gap breather that is centered on a heavy particle and characterized by a symmetric spatial energy profile and (2) a potentially stable discrete gap breather that is centered on a light particle and is characterized by an asymmetric spatial energy profile. We investigate their existence, structure, and stability throughout the band gap of the linear spectrum and classify them into four regimes: a regime near the lower optical band edge of the linear spectrum, a moderately discrete regime, a strongly discrete regime that lies deep within the band gap of the linearized version of the system, and a regime near the upper acoustic band edge. We contrast discrete breathers in anharmonic Fermi-Pasta-Ulam (FPU)-type diatomic chains with those in diatomic granular crystals, which have a tensionless interaction potential between adjacent particles, and note that the asymmetric nature of the tensionless interaction potential can lead to hybrid bulk-surface localized solutions.

Impact of Linear Alkyl Length on the Assembly of Twisted Perylene Bisimides: From Molecular Arrangement to Nanostructures.

PubMed

Guo, Zongxia; Wang, Kun; Yu, Ping; Wang, Xiangnan; Lan, Shusha; Sun, Kai; Yi, Yuanping; Li, Zhibo

2017-11-02

The effect of the length of linear alkyl chains substituted at imine positions on the assembly of tetrachlorinated perylene bisimides (1: PBI with -C 6 H 13 ; 2: PBI with -C 12 H 25 ) has been investigated. Solvent-induced assembly was performed in solutions of THF and methanol with varying volume ratios. Morphological (SEM, AFM, and TEM) and spectral (UV/Vis, fluorescence, FTIR, and XRD) methods were used to characterize the assembled nanostructures and the molecular arrangement in the aggregates. It was found that uniform structures could be obtained for both molecules in solutions with a high ratio of methanol. PBI 1 formed rigid nanosheets, whereas 2 assembled into longer nanostripes with a high ratio of length to width. On combining the morphological data with the spectral data, it was suggested that π-π stacking predominated in assemblies of 1, and the synergetic effect of van der Waals interactions from the long alkyl chains and π-π stacking between neighboring building blocks facilitated the growth of the long-range-ordered nanostructures of 2. By changing the linear chain length, the hierarchical assembly of PBIs modified on bay positions could be manipulated effectively. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Improving validation methods for molecular diagnostics: application of Bland-Altman, Deming and simple linear regression analyses in assay comparison and evaluation for next-generation sequencing

PubMed Central

Misyura, Maksym; Sukhai, Mahadeo A; Kulasignam, Vathany; Zhang, Tong; Kamel-Reid, Suzanne; Stockley, Tracy L

2018-01-01

Aims A standard approach in test evaluation is to compare results of the assay in validation to results from previously validated methods. For quantitative molecular diagnostic assays, comparison of test values is often performed using simple linear regression and the coefficient of determination (R2), using R2 as the primary metric of assay agreement. However, the use of R2 alone does not adequately quantify constant or proportional errors required for optimal test evaluation. More extensive statistical approaches, such as Bland-Altman and expanded interpretation of linear regression methods, can be used to more thoroughly compare data from quantitative molecular assays. Methods We present the application of Bland-Altman and linear regression statistical methods to evaluate quantitative outputs from next-generation sequencing assays (NGS). NGS-derived data sets from assay validation experiments were used to demonstrate the utility of the statistical methods. Results Both Bland-Altman and linear regression were able to detect the presence and magnitude of constant and proportional error in quantitative values of NGS data. Deming linear regression was used in the context of assay comparison studies, while simple linear regression was used to analyse serial dilution data. Bland-Altman statistical approach was also adapted to quantify assay accuracy, including constant and proportional errors, and precision where theoretical and empirical values were known. Conclusions The complementary application of the statistical methods described in this manuscript enables more extensive evaluation of performance characteristics of quantitative molecular assays, prior to implementation in the clinical molecular laboratory. PMID:28747393

An analytical equation of state for describing isotropic-nematic phase equilibria of Lennard-Jones chain fluids with variable degree of molecular flexibility

NASA Astrophysics Data System (ADS)

van Westen, Thijs; Oyarzún, Bernardo; Vlugt, Thijs J. H.; Gross, Joachim

2015-06-01

We develop an equation of state (EoS) for describing isotropic-nematic (IN) phase equilibria of Lennard-Jones (LJ) chain fluids. The EoS is developed by applying a second order Barker-Henderson perturbation theory to a reference fluid of hard chain molecules. The chain molecules consist of tangentially bonded spherical segments and are allowed to be fully flexible, partially flexible (rod-coil), or rigid linear. The hard-chain reference contribution to the EoS is obtained from a Vega-Lago rescaled Onsager theory. For the description of the (attractive) dispersion interactions between molecules, we adopt a segment-segment approach. We show that the perturbation contribution for describing these interactions can be divided into an "isotropic" part, which depends only implicitly on orientational ordering of molecules (through density), and an "anisotropic" part, for which an explicit dependence on orientational ordering is included (through an expansion in the nematic order parameter). The perturbation theory is used to study the effect of chain length, molecular flexibility, and attractive interactions on IN phase equilibria of pure LJ chain fluids. Theoretical results for the IN phase equilibrium of rigid linear LJ 10-mers are compared to results obtained from Monte Carlo simulations in the isobaric-isothermal (NPT) ensemble, and an expanded formulation of the Gibbs-ensemble. Our results show that the anisotropic contribution to the dispersion attractions is irrelevant for LJ chain fluids. Using the isotropic (density-dependent) contribution only (i.e., using a zeroth order expansion of the attractive Helmholtz energy contribution in the nematic order parameter), excellent agreement between theory and simulations is observed. These results suggest that an EoS contribution for describing the attractive part of the dispersion interactions in real LCs can be obtained from conventional theoretical approaches designed for isotropic fluids, such as a Perturbed-Chain Statistical Associating Fluid Theory approach.

Tuning of chain chirality by interchain stacking forces and the structure-property relationship in coordination systems constructed by meridional FeIII cyanide and MnIII Schiff bases.

PubMed

Sohn, Ah Ram; Lim, Kwang Soo; Kang, Dong Won; Song, Jeong Hwa; Koh, Eui Kwan; Moon, Dohyun; Hong, Chang Seop

2016-12-06

We synthesized six Fe(iii)-Mn(iii) bimetallic compounds by self-assembling the newly developed mer-Fe cyanide PPh 4 [Fe(Clqpa)(CN) 3 ]·H 2 O (1) and PPh 4 [Fe(Brqpa)(CN) 3 ]·H 2 O (2) with Mn Schiff base Mn(5-Xsalen) + cations. These compounds include [Fe(Xqpa)(CN) 3 ][Mn(5-Ysalen)]·pMeOH·qH 2 O [qpaH 2 = N-(quinolin-8-yl)picolinamide; salen = N,N'-ethylenebis(salicylideneiminato) dianion; X = Cl, Y = H (3); X = Cl, Y = Br (4); X = Br, Y = H (5); X = Br, Y = F (6); X = Br, Y = Cl (7); X = Br, Y = Br (8)]. When precursor 1 was used, compounds 3 and 4 were isolated to give a dinuclear entity and a linear chain structure, respectively. The reaction of precursor 2 with the Schiff bases afforded four linear Fe(iii)-Mn(iii) chain complexes. Chain chirality with P- and M-helicity emerges in 4, 7, and 8, while 5 exhibits chain helicity opposite to the previous chain complexes and 6 presents no chain helicity. Such a structural feature is heavily dependent on the interchain π-π contacts and the Fe precursor bridging unit. Chiral induction from a local ethylenediamine link of Y-salen is propagated over the chain via noncovalent π-π interactions. All the bimetallic compounds show antiferromagnetic interactions transmitted by the cyanide linkage. A field-induced metamagnetic transition is involved in 4, 7, and 8, while a field-induced two-step transition is evident in 6. From a magnetostructural viewpoint, the coupling constant is primarily governed by the Mn-N ax -C ax angle (ax = axial) in the bimetallic chain complexes composed of mer-Fe(iii) tricyanides, although the torsion angle plays a role.

Synthesis and Solution Properties of Adamantane Containing Quaternary Ammonium Salt-type Cationic Surfactants: Hydrocarbon-based, Fluorocarbonbased and Bola-type.

PubMed

Yoshimura, Tomokazu; Okada, Mari; Matsuoka, Keisuke

2016-10-01

Quaternary ammonium salt-type cationic surfactants with an adamantyl group (hydrocarbon-type; C n AdAB, fluorocarbon-type; C m F C 3 AdAB, bola-type; Ad-s-Ad, where n, m and s represent hydrocarbon chain lengths of 8-16, fluorocarbon chain lengths of 4-8, and spacer chain length of 10-12) were synthesized via quaternization of N, N-dimethylaminoadamantane and n-alkyl bromide or 1, n-dibromoalkane. Conductivity and surface tension were measured to characterize the solution properties of the synthesized adamantyl group-containing cationic surfactants. In addition, the effects of hydrocarbon and fluorocarbon chain lengths and spacer chain length between headgroups on the measured properties were evaluated by comparison with those of conventional cationic surfactants. The critical micelle concentration (CMC) of C n AdAB and Ad-s-Ad was 2/5 of that for the corresponding conventional surfactants C n TAB and bola-type surfactants with similar number of carbons in the alkyl or alkylene chain; this was because of the increased hydrophobicity due to the adamantyl group. A linear relationship between the logarithm of CMC and the hydrocarbon chain length for C n AdAB was observed, as well as for C n TAB. The slope of the linear correlation for both surfactants was almost the same, indicating that the adamantyl group does not affect the CMC with variations in the hydrocarbon chain length. Similar to conventional surfactants C n TAB, the hydrocarbon-type C n AdAB is highly efficient in reducing the surface tension of water, despite the large occupied area per molecule resulting from the relatively bulky structure of the adamantane skeleton. On the other hand, the bola-type Ad-s-Ad resulted in increased surface tension compared to C n AdAB, indicating that the curved chain between adamantyl groups leads to poor adsorption and orientation at the air-water interface.

Entanglement Dynamics in Miscible Polyisoprene / Poly(p-tert-butyl styrene) Blends

NASA Astrophysics Data System (ADS)

Watanabe, Hiroshi

2011-03-01

Viscoelastic and dielectric behavior was examined for well entangled, miscible blends of high- M cis-polyisoprene (PI) and poly(p-tert-butyl styrene) (PtBS). The dielectric data of the blends, reflecting the global motion of the PI chains having the type-A dipoles, indicated that PI and PtBS were the fast and slow components therein. At high temperatures T , the blends exhibited two-step entanglement plateau. The high frequency (ω) plateau height was well described by a simple mixing rule of the entanglement length based on the number fraction of the Kuhn segments. At low T , the blend exhibited the Rouse-like power-law behavior of storage and loss moduli, G ' = G ~ω0.5 , in the range of ω where the high- ω plateau was supposed to emerge. This lack of the high- ω plateau was attributed to retardation of the Rouse equilibration of the PI chain over the entanglement length due to the hindrance from the slow PtBS chains: The PI and PtBS chains were equilibrated cooperatively, and the retardation due to PtBS shortened the plateau for PI to a width not resolved experimentally. A simple model for this cooperative equilibration formulated on the basis of the dielectric data described the viscoelastic data surprisingly well.

Networks 90: Polymer Networks Group Meeting (10th) and IUPAC international Symposium on Polymer Networks (10th) Held in Jerusalem on 20-25 May 1990. Programme and Abstracts

DTIC Science & Technology

1990-05-25

INCLUDING ORIENTATIONAL INTERACTIONS BETWEEN CHAIN SEGMENTS B. Deloche, E.T. Samulski (France, USA) CHAIN SEGMENT ORDERING IN STRAINED BIMODAL P-2 PDMS...theory of elastomers is difficult because it requires a detailed study of many body interactions . A theory of elasticity must address the following: (1...a Kirchhoff matrix which describes the connectivity of the network (Kc) or the linear chains (Ku). The nonbonded interactions are handled with the

Magnonic analog of relativistic Zitterbewegung in an antiferromagnetic spin chain

NASA Astrophysics Data System (ADS)

Wang, Weiwei; Gu, Chenjie; Zhou, Yan; Fangohr, Hans

2017-07-01

We theoretically investigate the spin-wave (magnon) excitations in a classical antiferromagnetic spin chain with easy-axis anisotropy. We obtain a Dirac-like equation by linearizing the Landau-Lifshitz-Gilbert equation in this antiferromagnetic system, in contrast to the ferromagnetic system in which a Schrödinger-type equation is derived. The Hamiltonian operator in the Dirac-like equation is a pseudo-Hermitian. We compute and demonstrate relativistic Zitterbewegung (trembling motion) in the antiferromagnetic spin chain by measuring the expectation values of the wave-packet position.

Structural differences among alkali-soluble arabinoxylans from maize (Zea mays), rice (Oryza sativa), and wheat (Triticum aestivum) brans influence human fecal fermentation profiles.

PubMed

Rose, Devin J; Patterson, John A; Hamaker, Bruce R

2010-01-13

Human fecal fermentation profiles of maize, rice, and wheat bran and their dietary fiber fractions released by alkaline-hydrogen peroxide treatment (principally arabinoxylan) were obtained with the aim of identifying and characterizing fractions associated with high production of short chain fatty acids and a linear fermentation profile for possible application as a slowly fermentable dietary fiber. The alkali-soluble fraction from maize bran resulted in the highest short chain fatty acid production among all samples tested, and was linear over the 24 h fermentation period. Size-exclusion chromatography and (1)H NMR suggested that higher molecular weight and uniquely substituted arabinose side chains may contribute to these properties. Monosaccharide disappearance data suggest that maize and rice bran arabinoxylans are fermented by a debranching mechanism, while wheat bran arabinoxylans likely contain large unsubstituted xylose regions that are fermented preferentially, followed by poor fermentation of the remaining, highly branched oligosaccharides.

Primitive chain network simulations for entangled DNA solutions

NASA Astrophysics Data System (ADS)

Masubuchi, Yuichi; Furuichi, Kenji; Horio, Kazushi; Uneyama, Takashi; Watanabe, Hiroshi; Ianniruberto, Giovanni; Greco, Francesco; Marrucci, Giuseppe

2009-09-01

Molecular theories for polymer rheology are based on conformational dynamics of the polymeric chain. Hence, measurements directly related to molecular conformations appear more appealing than indirect ones obtained from rheology. In this study, primitive chain network simulations are compared to experimental data of entangled DNA solutions [Teixeira et al., Macromolecules 40, 2461 (2007)]. In addition to rheological comparisons of both linear and nonlinear viscoelasticities, a molecular extension measure obtained by Teixeira et al. through fluorescent microscopy is compared to simulations, in terms of both averages and distributions. The influence of flow on conformational distributions has never been simulated for the case of entangled polymers, and how DNA molecular individualism extends to the entangled regime is not known. The linear viscoelastic response and the viscosity growth curve in the nonlinear regime are found in good agreement with data for various DNA concentrations. Conversely, the molecular extension measure shows significant departures, even under equilibrium conditions. The reason for such discrepancies remains unknown.

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.

Lattice cluster theory of associating polymers. I. Solutions of linear telechelic polymer chains.

PubMed

Dudowicz, Jacek; Freed, Karl F

2012-02-14

The lattice cluster theory (LCT) for the thermodynamics of a wide array of polymer systems has been developed by using an analogy to Mayer's virial expansions for non-ideal gases. However, the high-temperature expansion inherent to the LCT has heretofore precluded its application to systems exhibiting strong, specific "sticky" interactions. The present paper describes a reformulation of the LCT necessary to treat systems with both weak and strong, "sticky" interactions. This initial study concerns solutions of linear telechelic chains (with stickers at the chain ends) as the self-assembling system. The main idea behind this extension of the LCT lies in the extraction of terms associated with the strong interactions from the cluster expansion. The generalized LCT for sticky systems reduces to the quasi-chemical theory of hydrogen bonding of Panyioutou and Sanchez when correlation corrections are neglected in the LCT. A diagrammatic representation is employed to facilitate the evaluation of the corrections to the zeroth-order approximation from short range correlations. © 2012 American Institute of Physics

Chemistry of anthracene-acetylene oligomers XXV: on-surface chirality of a self-assembled molecular network of a fan-blade-shaped anthracene-acetylene macrocycle with a long alkyl chain.

PubMed

Tsuya, Takuya; Iritani, Kohei; Tahara, Kazukuni; Tobe, Yoshito; Iwanaga, Tetsuo; Toyota, Shinji

2015-03-27

An anthracene cyclic dimer with two different linkers and a dodecyl group was synthesized by means of coupling reactions. The calculated structure had a planar macrocyclic π core and a linear alkyl chain. Scanning tunneling microscopy observations at the 1-phenyloctane/graphite interface revealed that the molecules formed a self-assembled monolayer that consisted of linear striped bright and dark bands. In each domain, the molecular network consisted of either Re or Si molecules that differed in the two-dimensional chirality about the macrocyclic faces, which led to a unique conglomerate-type self-assembly. The molecular packing mode and the conformation of the alkyl chains are discussed in terms of the intermolecular interactions and the interactions between the molecules and the graphite surface with the aid of MM3 simulations of a model system. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Assembly and Architecture of Biogenesis of Lysosome-related Organelles Complex-1 (BLOC-1)*

PubMed Central

Lee, Hyung Ho; Nemecek, Daniel; Schindler, Christina; Smith, William J.; Ghirlando, Rodolfo; Steven, Alasdair C.; Bonifacino, Juan S.; Hurley, James H.

2012-01-01

BLOC-1 (biogenesis of lysosome-related organelles complex-1) is critical for melanosome biogenesis and has also been implicated in neurological function and disease. We show that BLOC-1 is an elongated complex that contains one copy each of the eight subunits pallidin, Cappuccino, dysbindin, Snapin, Muted, BLOS1, BLOS2, and BLOS3. The complex appears as a linear chain of eight globular domains, ∼300 Å long and ∼30 Å in diameter. The individual domains are flexibly connected such that the linear chain undergoes bending by as much as 45°. Two stable subcomplexes were defined, pallidin-Cappuccino-BLOS1 and dysbindin-Snapin-BLOS2. Both subcomplexes are 1:1:1 heterotrimers that form extended structures as indicated by their hydrodynamic properties. The two subcomplexes appear to constitute flexible units within the larger BLOC-1 chain, an arrangement conducive to simultaneous interactions with multiple BLOC-1 partners in the course of tubular endosome biogenesis and sorting. PMID:22203680

Molecular structure, supramolecular organization and thermotropic phase behavior of N-acylglycine alkyl esters with matched acyl and alkyl chains.

PubMed

Reddy, S Thirupathi; Swamy, Musti J

2017-11-01

N-Acylglycines (NAGs), the endogenous single-tailed lipids present in rat brain and other mammalian tissues, play significant roles in cell physiology and exhibit interesting pharmacological properties. In the present study, a homologous series of N-acylglycine alkyl esters (NAGEs) with matched chains were synthesized and characterized. Results of differential scanning calorimetric studies revealed that all NAGEs exhibit a single sharp phase transition and that the transition enthalpy and entropy show a linear dependence on the N-acyl and ester alkyl chain length. The structure of N-myristoylglycine myristyl ester (NMGME), solved by single-crystal X-ray diffraction, showed that the molecule adopts a linear geometry and revealed that the structure of N-myristoyl glycyl moiety in NMGME is identical to that in N-myristoylglycine. The molecules are packed in layers with the polar functional groups of the ester and amide functionalities located at the center of the layer. The crystal packing is stabilized by NH⋯O hydrogen bonds between the amide CO and NH groups of adjacent molecules as well as by CH⋯O hydrogen bonds between the amide carbonyl and the methylene CH adjacent to the ester carbonyl of neighboring molecules as well as between ester carbonyl and methylene group of the glycine moiety of adjacent molecules. Powder X-ray diffraction studies showed a linear dependence of the d-spacings on the acyl chain length, suggesting that all NAGEs adopt a structure similar to the packing exhibited in the crystal lattice of NMGME. Copyright © 2017 Elsevier B.V. All rights reserved.

Computer Simulations of Bottlebrush Melts and Soft Networks

NASA Astrophysics Data System (ADS)

Cao, Zhen; Carrillo, Jan-Michael; Sheiko, Sergei; Dobrynin, Andrey

We have studied dense bottlebrush systems in a melt and network state using a combination of the molecular dynamics simulations and analytical calculations. Our simulations show that the bottlebrush macromolecules in a melt behave as ideal chains with the effective Kuhn length bK. The bottlebrush induced bending rigidity is due to redistribution of the side chains upon backbone bending. Kuhn length of the bottlebrushes increases with increasing the side-chain degree of polymerization nsc as bK ~nsc0 . 46 . This model of bottlebrush macromolecules is extended to describe mechanical properties of bottlebrush networks in linear and nonlinear deformation regimes. In the linear deformation regime, the network shear modulus scales with the degree of polymerization of the side chains as G0 ~nsc + 1 - 1 as long as the ratio of the Kuhn length to the size of the fully extended bottlebrush backbone between crosslinks, Rmax, is smaller than unity, bK /Rmax < < 1 . Bottlebrush networks with bK /Rmax ~ 1 demonstrate behavior similar to that of networks of semiflexible chains with G0 ~nsc- 0 . 5 . In the nonlinear deformation regime, the deformation dependent shear modulus is a universal function of the first strain invariant I1 and bottlebrush backbone deformation ratio β describing stretching ability of the bottlebrush backbone between crosslinks. Nsf DMR-1409710 DMR-1436201.

A Simple Demonstration of Atomic and Molecular Orbitals Using Circular Magnets

ERIC Educational Resources Information Center

Chakraborty, Maharudra; Mukhopadhyay, Subrata; Das, Ranendu Sekhar

2014-01-01

A quite simple and inexpensive technique is described here to represent the approximate shapes of atomic orbitals and the molecular orbitals formed by them following the principles of the linear combination of atomic orbitals (LCAO) method. Molecular orbitals of a few simple molecules can also be pictorially represented. Instructors can employ the…

Familial hypofibrinogenaemia associated with heterozygous substitution of a conserved arginine residue; Bbeta255 Arg-->His (Fibrinogen Merivale).

PubMed

Maghzal, Ghassan J; Brennan, Stephen O; Fellowes, Andrew P; Spearing, Ruth; George, Peter M

2003-02-21

Sequencing of all three fibrinogen genes from an individual with hypofibrinogenaemia led to the identification of two new point mutations in the Bbeta gene. Family studies showed the mutations Bbeta255 Arg-->His (Fibrinogen Merivale) and Bbeta148 Lys-->Asn (Fibrinogen Merivale II) were on different alleles and that only the Bbeta255 Arg-->His mutation segregated with hypofibrinogenaemia. Three simple heterozygotes for this mutation had mean fibrinogen concentrations of 1.4 mg/ml, while heterozygotes for the Bbeta148 Lys-->Asn mutation had normal fibrinogen concentrations. ESI MS analysis of endoproteinase Asp-N digests of Bbeta chains showed that the Bbeta255 Arg-->His substitution was not expressed in plasma, confirming it as the cause of the hypofibrinogenaemia. The Bbeta148 Lys-->Asn chains, on the other hand, were equally expressed with wild-type Bbeta chains in simple heterozygotes. Genotype analysis failed to detect either substitution in 182 healthy controls. Arg(255) is located in the first strand of the five-stranded sheet that forms the main feature of the betaD domain and appears to form an essential H bond with Gly(414). Both the Arg and Gly are absolutely conserved, not only in all known Bbeta chains, but also in all homologous alphaE and gamma chains and in all fibrinogen-related proteins. Protein instability from loss of this contact could easily explain the association of this mutation with hypofibrinogenaemia.

Simple linear and multivariate regression models.

PubMed

Rodríguez del Águila, M M; Benítez-Parejo, N

2011-01-01

In biomedical research it is common to find problems in which we wish to relate a response variable to one or more variables capable of describing the behaviour of the former variable by means of mathematical models. Regression techniques are used to this effect, in which an equation is determined relating the two variables. While such equations can have different forms, linear equations are the most widely used form and are easy to interpret. The present article describes simple and multiple linear regression models, how they are calculated, and how their applicability assumptions are checked. Illustrative examples are provided, based on the use of the freely accessible R program. Copyright © 2011 SEICAP. Published by Elsevier Espana. All rights reserved.

Evaluation of strategies to control Fab light chain dimer during mammalian expression and purification: A universal one-step process for purification of correctly assembled Fab.

PubMed

Spooner, Jennifer; Keen, Jenny; Nayyar, Kalpana; Birkett, Neil; Bond, Nicholas; Bannister, David; Tigue, Natalie; Higazi, Daniel; Kemp, Benjamin; Vaughan, Tristan; Kippen, Alistair; Buchanan, Andrew

2015-07-01

Fabs are an important class of antibody fragment as both research reagents and therapeutic agents. There are a plethora of methods described for their recombinant expression and purification. However, these do not address the issue of excessive light chain production that forms light chain dimers nor do they describe a universal purification strategy. Light chain dimer impurities and the absence of a universal Fab purification strategy present persistent challenges for biotechnology applications using Fabs, particularly around the need for bespoke purification strategies. This study describes methods to address light chain dimer formation during Fab expression and identifies a novel CH 1 affinity resin as a simple and efficient one-step purification for correctly assembled Fab. © 2015 Wiley Periodicals, Inc.

Effect of reinforcement learning on coordination of multiangent systems

NASA Astrophysics Data System (ADS)

Bukkapatnam, Satish T. S.; Gao, Greg

2000-12-01

For effective coordination of distributed environments involving multiagent systems, learning ability of each agent in the environment plays a crucial role. In this paper, we develop a simple group learning method based on reinforcement, and study its effect on coordination through application to a supply chain procurement scenario involving a computer manufacturer. Here, all parties are represented by self-interested, autonomous agents, each capable of performing specific simple tasks. They negotiate with each other to perform complex tasks and thus coordinate supply chain procurement. Reinforcement learning is intended to enable each agent to reach a best negotiable price within a shortest possible time. Our simulations of the application scenario under different learning strategies reveals the positive effects of reinforcement learning on an agent's as well as the system's performance.

Two-channel spin-chain communication line and simple quantum gates

NASA Astrophysics Data System (ADS)

Stolze, J.; Zenchuk, A. I.

2017-08-01

We consider the remote creation of a mixed state in a one-qubit receiver connected to two two-qubit senders via different channels. Channels are assumed to be chains of spins (qubits) with nearest-neighbor interactions, no external fields are being applied. The problem of sharing the creatable region of the receiver's state-space between two senders is considered for a communication line with the receiver located asymmetrically with respect to these senders (asymmetric communication line). An example of a quantum register realizing simple functions is constructed on the basis of a symmetric communication line. In that setup, the initial states of the two senders serve as input and control signals, respectively, while the state of the receiver at a proper time instant is considered as the output signal.

Theoretical analysis of flux amplification by soft magnetic material in a putative biological magnetic-field receptor.

PubMed

Shcherbakov, Valera P; Winklhofer, Michael

2010-03-01

Birds are endowed with a magnetic sense that allows them to detect Earth's magnetic field and to use it for orientation. Physiological and behavioral experiments have shown the upper beak to host a magnetoreceptor. Putative magnetoreceptive structures in the beak are nerve terminals that each contain a dozen or so of micrometer-sized clusters of superparamagnetic nanocrystals made of magnetite/maghemite and numerous electron-opaque platelets filled with a so far unidentified, amorphous ferric iron compound. The platelets typically form chainlike structures, which have been proposed to function as magnetic flux focusers for detecting the intensity of the geomagnetic field. Here, we test that proposition from first principles and develop an unconstrained model to determine the equilibrium distribution of magnetization along a linear chain of platelets which we assume to behave magnetically soft and to have no magnetic remanence. Our analysis, which is valid for arbitrary values of the intrinsic magnetic susceptibility chi , shows that chi needs to be much greater than unity to amplify the external field by two orders of magnitude in a chain of platelets. However, the high amplification is confined to the central region of the chain and subsides quadratically toward the ends of the chain. For large values of chi , the possibility opens up of realizing magnetoreceptor mechanisms on the basis of attraction forces between adjacent platelets in a linear chain. The force in the central region of the chain may amount to several pN, which would be sufficient to convert magnetic input energy into mechanical output energy. The striking feature of an ensemble of platelets is its ability to organize into tightly spaced chains under the action of an external field of given strength. We discuss how this property can be exploited for a magnetoreception mechanism.

Partitioning of electron flux between the respiratory chains of the yeast Candida parapsilosis: parallel working of the two chains.

PubMed

Guerin, M G; Camougrand, N M

1994-02-08

Partitioning of the electron flux between the classical and the alternative respiratory chains of the yeast Candida parapsilosis, was measured as a function of the oxidation rate and of the Q-pool redox poise. At low respiration rate, electrons from external NADH travelled preferentially through the alternative pathway as indicated by the antimycin A-insensitivity of electron flow. Inhibition of the alternative pathway by SHAM restored full antimycin A-sensitivity to the remaining electro flow. The dependence of the respiratory rate on the redox poise of the quinone pool was investigated when the electron flux was mediated either by the main respiratory chain (growth in the absence of antimycin A) or by the second respiratory chain (growth in the presence of antimycin A). In the former case, a linear relationship was found between these two parameters. In contrast, in the latter case, the relationship between Q-pool reduction level and electron flux was non-linear, but it could be resolved into two distinct curves. This second quinone is not reducible in the presence of antimycin A but only in the presence of high concentrations of myxothiazol or cyanide. Since two quinone species exist in C. parapsilosis, UQ9 and Qx (C33H54O4), we hypothesized that these two curves could correspond to the functioning of the second quinone engaged during the alternative pathway activity. Partitioning of electrons between both respiratory chains could occur upstream of complex III with the second chain functioning in parallel to the main one, and with the additional possibility of merging into the main one at the complex IV level.

Prefrontal Markers and Cognitive Performance Are Dissociated during Progressive Dopamine Lesion

PubMed Central

Wilson, Charles R. E.; Vezoli, Julien; Faraut, Maïlys C. M.; Leviel, Vincent; Knoblauch, Kenneth; Procyk, Emmanuel

2016-01-01

Dopamine is thought to directly influence the neurophysiological mechanisms of both performance monitoring and cognitive control—two processes that are critically linked in the production of adapted behaviour. Changing dopamine levels are also thought to induce cognitive changes in several neurological and psychiatric conditions. But the working model of this system as a whole remains untested. Specifically, although many researchers assume that changing dopamine levels modify neurophysiological mechanisms and their markers in frontal cortex, and that this in turn leads to cognitive changes, this causal chain needs to be verified. Using longitudinal recordings of frontal neurophysiological markers over many months during progressive dopaminergic lesion in non-human primates, we provide data that fail to support a simple interaction between dopamine, frontal function, and cognition. Feedback potentials, which are performance-monitoring signals sometimes thought to drive successful control, ceased to differentiate feedback valence at the end of the lesion, just before clinical motor threshold. In contrast, cognitive control performance and beta oscillatory markers of cognitive control were unimpaired by the lesion. The differing dynamics of these measures throughout a dopamine lesion suggests they are not all driven by dopamine in the same way. These dynamics also demonstrate that a complex non-linear set of mechanisms is engaged in the brain in response to a progressive dopamine lesion. These results question the direct causal chain from dopamine to frontal physiology and on to cognition. They imply that biomarkers of cognitive functions are not directly predictive of dopamine loss. PMID:27824858

Determination of short chain chlorinated paraffins in water by stir bar sorptive extraction-thermal desorption-gas chromatography-triple quadrupole tandem mass spectrometry.

PubMed

Tölgyessy, P; Nagyová, S; Sládkovičová, M

2017-04-21

A simple, robust, sensitive and environment friendly method for the determination of short chain chlorinated paraffins (SCCPs) in water using stir bar sorptive extraction (SBSE) coupled to thermal desorption-gas chromatography-triple quadrupole tandem mass spectrometry (TD-GC-QqQ-MS/MS) was developed. SBSE was performed using 100mL of water sample, 20mL of methanol as a modifier, and a commercial sorptive stir bar (with 10mm×0.5mm PDMS layer) during extraction period of 16h. After extraction, the sorptive stir bar was thermally desorbed and online analysed by GC-MS/MS. Method performance was evaluated for MilliQ and surface water spiked samples. For both types of matrices, a linear dynamic range of 0.5-3.0μgL -1 with correlation coefficients >0.999 and relative standard deviations (RSDs) of the relative response factors (RRFs) <12% was established. The limits of quantification (LOQs) of 0.06 and 0.08μgL -1 , and the precision (repeatability) of 6.4 and 7.7% (RSDs) were achieved for MilliQ and surface water, respectively. The method also showed good robustness, recovery and accuracy. The obtained performance characteristics indicate that the method is suitable for screening and monitoring and compliance checking with environmental quality standards (EQS, set by the EU) for SCCPs in surface waters. Copyright © 2017 Elsevier B.V. All rights reserved.

The stretch to stray on time: Resonant length of random walks in a transient

NASA Astrophysics Data System (ADS)

Falcke, Martin; Friedhoff, Victor Nicolai

2018-05-01

First-passage times in random walks have a vast number of diverse applications in physics, chemistry, biology, and finance. In general, environmental conditions for a stochastic process are not constant on the time scale of the average first-passage time or control might be applied to reduce noise. We investigate moments of the first-passage time distribution under an exponential transient describing relaxation of environmental conditions. We solve the Laplace-transformed (generalized) master equation analytically using a novel method that is applicable to general state schemes. The first-passage time from one end to the other of a linear chain of states is our application for the solutions. The dependence of its average on the relaxation rate obeys a power law for slow transients. The exponent ν depends on the chain length N like ν = - N / ( N + 1 ) to leading order. Slow transients substantially reduce the noise of first-passage times expressed as the coefficient of variation (CV), even if the average first-passage time is much longer than the transient. The CV has a pronounced minimum for some lengths, which we call resonant lengths. These results also suggest a simple and efficient noise control strategy and are closely related to the timing of repetitive excitations, coherence resonance, and information transmission by noisy excitable systems. A resonant number of steps from the inhibited state to the excitation threshold and slow recovery from negative feedback provide optimal timing noise reduction and information transmission.

Jeffamine® based polymers as highly conductive polymer electrolytes and cathode binder materials for battery application

NASA Astrophysics Data System (ADS)

Aldalur, Itziar; Zhang, Heng; Piszcz, Michał; Oteo, Uxue; Rodriguez-Martinez, Lide M.; Shanmukaraj, Devaraj; Rojo, Teofilo; Armand, Michel

2017-04-01

We report a simple synthesis route towards a new type of comb polymer material based on polyether amines oligomer side chains (i.e., Jeffamine® compounds) and a poly(ethylene-alt-maleic anhydride) backbone. Reaction proceeds by imide ring formation through the NH2 group allowing for attachment of side chains. By taking advantage of the high configurational freedoms and flexibility of propylene oxide/ethylene oxide units (PO/EO) in Jeffamine® compounds, novel polymer matrices were obtained with good elastomeric properties. Fully amorphous solid polymer electrolytes (SPEs) based on lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) and Jeffamine®-based polymer matrices show low glass transition temperatures around -40 °C, high ionic conductivities and good electrochemical stabilities. The ionic conductivities of Jeffamine-based SPEs (5.3 × 10-4 S cm-1 at 70 °C and 4.5 × 10-5 S cm-1 at room temperature) are higher than those of the conventional SPEs comprising of LiTFSI and linear poly(ethylene oxide) (PEO), due to the amorphous nature and the high concentration of mobile end-groups of the Jeffamine-based polymer matrices rather than the semi-crystalline PEO The feasibility of Jeffamine-based compounds in lithium metal batteries is further demonstrated by the implementation of Jeffamine®-based polymer as a binder for cathode materials, and the stable cycling of Li|SPE|LiFePO4 and Li|SPE|S cells using Jeffamine-based SPEs.

Pyrosequencing-based validation of a simple cell-suspension polymerase chain reaction assay for Campylobacter... of high-processivity polymerase with novel internal amplification controls for rapid and specific detection.

USDA-ARS?s Scientific Manuscript database

Although Campylobacter is an important food-borne human pathogen, there remains a lack of molecular diagnostic assays that are simple to use, cost-effective, and provide rapid results in research, clinical, or regulatory laboratories. Of the numerous Campylobacter assays that do exist, to our knowl...

Verge and Foliot Clock Escapement: A Simple Dynamical System

ERIC Educational Resources Information Center

Denny, Mark

2010-01-01

The earliest mechanical clocks appeared in Europe in the 13th century. From about 1250 CE to 1670 CE, these simple clocks consisted of a weight suspended from a rope or chain that was wrapped around a horizontal axle. To tell time, the weight must fall with a slow uniform speed, but, under the action of gravity alone, such a suspended weight would…

Increasing Capacity Exploitation in Food Supply Chains Using Grid Concepts

NASA Astrophysics Data System (ADS)

Volk, Eugen; Müller, Marcus; Jacob, Ansger; Racz, Peter; Waldburger, Martin

Food supply chains today are characterized by fixed trade relations with long term contracts established between heterogeneous supply chain companies. Production and logistics capacities of these companies are often utilized in an economically inefficient manner only. In addition, increased consumer awareness in food safety issues renders supply chain management even more challenging, since integrated tracking and tracing along the whole food supply chain is needed. Facing these issues of supply chain management complexity and completely documented product quality, this paper proposes a full lifecycle solution for dynamic capacity markets based on concepts used in the field of Grid [1], like management of Virtual Organization (VO) combined with Service Level Agreement (SLA). The solution enables the cost-efficient utilization of real world capacities (e.g., production capacities or logistics facilities) by using a simple, browser-based portal. Users are able to enter into product-specific negotiations with buyers and suppliers of a food supply chain, and to obtain real-time access to product information including SLA evaluation reports. Thus, business opportunities in wider market access, process innovation, and trustworthy food products are offered for participating supply chain companies.

Simulation study of the initial crystallization processes of poly(3-hexylthiophene) in solution: ordering dynamics of main chains and side chains.

PubMed

Takizawa, Yuumi; Shimomura, Takeshi; Miura, Toshiaki

2013-05-23

We study the initial nucleation dynamics of poly(3-hexylthiophene) (P3HT) in solution, focusing on the relationship between the ordering process of main chains and that of side chains. We carried out Langevin dynamics simulation and found that the initial nucleation processes consist of three steps: the ordering of ring orientation, the ordering of main-chain vectors, and the ordering of side chains. At the start, the normal vectors of thiophene rings aligned in a very short time, followed by alignment of main-chain end-to-end vectors. The flexible side-chain ordering took almost 5 times longer than the rigid-main-chain ordering. The simulation results indicated that the ordering of side chains was induced after the formation of the regular stack structure of main chains. This slow ordering dynamics of flexible side chains is one of the factors that cause anisotropic nuclei growth, which would be closely related to the formation of nanofiber structures without external flow field. Our simulation results revealed how the combined structure of the planar and rigid-main-chain backbones and the sparse flexible side chains lead to specific ordering behaviors that are not observed in ordinary linear polymer crystallization processes.

Structure of Salt-free Linear Polyelectrolytes in the Debye-Hückel Approximation

NASA Astrophysics Data System (ADS)

Stevens, Mark J.; Kremer, Kurt

1996-11-01

We examine the effects of the common Debye-Hückel approximation used in theories of polyelectrolytes. Molecular dynamics simulations using the Debye-Hückel pair potential of salt-free polyelectrolytes have been performed. The results of these simulations are compared to earlier “Coulomb" simulations which explicitly treated the counterions. We report here the comparisons of the osmotic pressure, the end-to-end distance and the single chain structure factor. In the dilute regime the Debye-Hückel chains are more elongated than the Coulomb chains implying that the counterion screening is stronger than the Debye-Hückel prediction. Like the Coulomb chains the Debye-Hückel chains contract significantly below the overlap density in contradiction to all theories. Entropy thus plays an important and sorely neglected role in theory.

A simple quantitative approach for the determination of long and medium chain lipids in bio-relevant matrices by high performance liquid chromatography with refractive index detection.

PubMed

Lee, Kathy Wai Yu; Porter, Christopher J H; Boyd, Ben J

2013-09-01

There is increasing attention in the literature towards understanding the behaviour of lipid-based drug formulations under digestion conditions using in vitro and in vivo methods. This necessitates a convenient method for quantitation of lipids and lipid digestion products. In this study, a simple and accessible method for the separation and quantitative determination of typical formulation and digested lipids using high performance liquid chromatography coupled to refractive index detection (HPLC-RI) is described. Long and medium chain lipids were separated and quantified in a biological matrix (gastrointestinal content) without derivatisation using HPLC-RI on C18 and C8 columns, respectively. The intra- and inter-assay accuracy was between 92% and 106%, and the assays were precise to within a coefficient of variation of less than 10% over the range of 0.1-2 mg/mL for both long and medium chain lipids. This method is also shown to be suitable for quantifying the lipolysis products collected from the gastrointestinal tract in the course of in vivo lipid digestion studies.

Guidelines and Procedures for Computing Time-Series Suspended-Sediment Concentrations and Loads from In-Stream Turbidity-Sensor and Streamflow Data

USGS Publications Warehouse

Rasmussen, Patrick P.; Gray, John R.; Glysson, G. Douglas; Ziegler, Andrew C.

2009-01-01

In-stream continuous turbidity and streamflow data, calibrated with measured suspended-sediment concentration data, can be used to compute a time series of suspended-sediment concentration and load at a stream site. Development of a simple linear (ordinary least squares) regression model for computing suspended-sediment concentrations from instantaneous turbidity data is the first step in the computation process. If the model standard percentage error (MSPE) of the simple linear regression model meets a minimum criterion, this model should be used to compute a time series of suspended-sediment concentrations. Otherwise, a multiple linear regression model using paired instantaneous turbidity and streamflow data is developed and compared to the simple regression model. If the inclusion of the streamflow variable proves to be statistically significant and the uncertainty associated with the multiple regression model results in an improvement over that for the simple linear model, the turbidity-streamflow multiple linear regression model should be used to compute a suspended-sediment concentration time series. The computed concentration time series is subsequently used with its paired streamflow time series to compute suspended-sediment loads by standard U.S. Geological Survey techniques. Once an acceptable regression model is developed, it can be used to compute suspended-sediment concentration beyond the period of record used in model development with proper ongoing collection and analysis of calibration samples. Regression models to compute suspended-sediment concentrations are generally site specific and should never be considered static, but they represent a set period in a continually dynamic system in which additional data will help verify any change in sediment load, type, and source.

Rheology of Hyperbranched Poly(triglyceride)-Based Thermoplastic Elastomers via RAFT polymerization

NASA Astrophysics Data System (ADS)

Yan, Mengguo; Cochran, Eric

2014-03-01

In this contribution we discuss how melt- and solid-state properties are influenced by the degree of branching and molecular weight in a family of hyperbranched thermoplastics derived from soybean oil. Acrylated epoxidized triglycerides from soybean oils have been polymerized to hyperbranched thermoplastic elastomers using reversible addition-fragmentation chain transfer (RAFT) polymerization. With the proper choice of chain transfer agent, both homopolymer and block copolymer can be synthesized. By changing the number of acrylic groups per triglycerides, the chain architectures can range from nearly linear to highly branched. We show how the fundamental viscoelastic properties (e.g. entanglement molecular weight, plateau modulus, etc.) are influenced by chain architecture and molecular weight.

Study of structural morphologies of thermoresponsive diblock AB and triblock BAB copolymers (A = poly(N-isopropylacrylamide), B = polystyrene)

NASA Astrophysics Data System (ADS)

Rodríguez-Hidalgo, María del Rosario; Soto-Figueroa, César; Vicente, Luis

2018-03-01

Structural morphologies of diblock AB and triblock BAB copolymers (A = poly(N-isopropylacrylamide), B = polystyrene) in aqueous environment have been investigated by dissipative particle dynamics (DPD). In triblock copolymers insoluble PS blocks contract while soluble pNIPAM blocks stay at the periphery forming looped chains as corona. As the temperature is increased there is a continuous morphological transition and micelles form ellipsoidal structures with segregated polymer zones. The phase transition of looped pNIPAM chains occurs at lower temperature than for linear chains and within broader temperature range. It is discussed how the chain topology of pNIPAM affects the phase transition.

The Role of the Side Chain on the Performance of N-type Conjugated Polymers in Aqueous Electrolytes

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

Giovannitti, Alexander; Maria, Iuliana P.; Hanifi, David

Here, we report a design strategy that allows the preparation of solution processable n-type materials from low boiling point solvents for organic electrochemical transistors (OECTs). The polymer backbone is based on NDI-T2 copolymers where a branched alkyl side chain is gradually exchanged for a linear ethylene glycol-based side chain. A series of random copolymers was prepared with glycol side chain percentages of 0, 10, 25, 50, 75, 90, and 100 with respect to the alkyl side chains. These were characterized to study the influence of the polar side chains on interaction with aqueous electrolytes, their electrochemical redox reactions, and performancemore » in OECTs when operated in aqueous electrolytes. We observed that glycol side chain percentages of >50% are required to achieve volumetric charging, while lower glycol chain percentages show a mixed operation with high required voltages to allow for bulk charging of the organic semiconductor. A strong dependence of the electron mobility on the fraction of glycol chains was found for copolymers based on NDI-T2, with a significant drop as alkyl side chains are replaced by glycol side chains.« less

The Role of the Side Chain on the Performance of N-type Conjugated Polymers in Aqueous Electrolytes.

PubMed

Giovannitti, Alexander; Maria, Iuliana P; Hanifi, David; Donahue, Mary J; Bryant, Daniel; Barth, Katrina J; Makdah, Beatrice E; Savva, Achilleas; Moia, Davide; Zetek, Matyáš; Barnes, Piers R F; Reid, Obadiah G; Inal, Sahika; Rumbles, Garry; Malliaras, George G; Nelson, Jenny; Rivnay, Jonathan; McCulloch, Iain

2018-05-08

We report a design strategy that allows the preparation of solution processable n-type materials from low boiling point solvents for organic electrochemical transistors (OECTs). The polymer backbone is based on NDI-T2 copolymers where a branched alkyl side chain is gradually exchanged for a linear ethylene glycol-based side chain. A series of random copolymers was prepared with glycol side chain percentages of 0, 10, 25, 50, 75, 90, and 100 with respect to the alkyl side chains. These were characterized to study the influence of the polar side chains on interaction with aqueous electrolytes, their electrochemical redox reactions, and performance in OECTs when operated in aqueous electrolytes. We observed that glycol side chain percentages of >50% are required to achieve volumetric charging, while lower glycol chain percentages show a mixed operation with high required voltages to allow for bulk charging of the organic semiconductor. A strong dependence of the electron mobility on the fraction of glycol chains was found for copolymers based on NDI-T2, with a significant drop as alkyl side chains are replaced by glycol side chains.

The Role of the Side Chain on the Performance of N-type Conjugated Polymers in Aqueous Electrolytes

DOE PAGES

Giovannitti, Alexander; Maria, Iuliana P.; Hanifi, David; ...

2018-04-24

Here, we report a design strategy that allows the preparation of solution processable n-type materials from low boiling point solvents for organic electrochemical transistors (OECTs). The polymer backbone is based on NDI-T2 copolymers where a branched alkyl side chain is gradually exchanged for a linear ethylene glycol-based side chain. A series of random copolymers was prepared with glycol side chain percentages of 0, 10, 25, 50, 75, 90, and 100 with respect to the alkyl side chains. These were characterized to study the influence of the polar side chains on interaction with aqueous electrolytes, their electrochemical redox reactions, and performancemore » in OECTs when operated in aqueous electrolytes. We observed that glycol side chain percentages of >50% are required to achieve volumetric charging, while lower glycol chain percentages show a mixed operation with high required voltages to allow for bulk charging of the organic semiconductor. A strong dependence of the electron mobility on the fraction of glycol chains was found for copolymers based on NDI-T2, with a significant drop as alkyl side chains are replaced by glycol side chains.« less

An Evaluation of Kernel Equating: Parallel Equating with Classical Methods in the SAT Subject Tests[TM] Program. Research Report. ETS RR-09-06

ERIC Educational Resources Information Center

Grant, Mary C.; Zhang, Lilly; Damiano, Michele

2009-01-01

This study investigated kernel equating methods by comparing these methods to operational equatings for two tests in the SAT Subject Tests[TM] program. GENASYS (ETS, 2007) was used for all equating methods and scaled score kernel equating results were compared to Tucker, Levine observed score, chained linear, and chained equipercentile equating…

Using crosscorrelation techniques to determine the impulse response of linear systems

NASA Technical Reports Server (NTRS)

Dallabetta, Michael J.; Li, Harry W.; Demuth, Howard B.

1993-01-01

A crosscorrelation method of measuring the impulse response of linear systems is presented. The technique, implementation, and limitations of this method are discussed. A simple system is designed and built using discrete components and the impulse response of a linear circuit is measured. Theoretical and software simulation results are presented.

Impact of hydrogen bonding on dynamics of hydroxyl-terminated polydimethylsiloxane

DOE PAGES

Xing, Kunyue; Chatterjee, Sabornie; Saito, Tomonori; ...

2016-04-06

Dielectric spectroscopy, rheology, and differential scanning calorimetry were employed to study the effect of chain-end hydrogen bonding on the dynamics of hydroxylterminated polydimethylsiloxane. We demonstrate that hydrogen bonding has a strong influence on both segmental and slower dynamics in the systems with low molecular weights. In particular, the decrease in the chain length leads to an increase of the glass transition temperature, viscosity, and fragility index, at variance with the usual behavior of nonassociating polymers. The supramolecular association of hydroxylterminated chains leads to the emergence in dielectric and mechanical relaxation spectra of the so-called Debye process traditionally observed in monohydroxymore » alcohols. Our analysis suggests that the hydroxyl-terminated PDMS oligomers may associate in brush-like or chain-like structures, depending on the size of their covalent chains. Finally, the effective length of the linear-associated chains was estimated from the rheological measurements.« less

Linear alkane polymerization on a gold surface.

PubMed

Zhong, Dingyong; Franke, Jörn-Holger; Podiyanachari, Santhosh Kumar; Blömker, Tobias; Zhang, Haiming; Kehr, Gerald; Erker, Gerhard; Fuchs, Harald; Chi, Lifeng

2011-10-14

In contrast to the many methods of selectively coupling olefins, few protocols catenate saturated hydrocarbons in a predictable manner. We report here the highly selective carbon-hydrogen (C-H) activation and subsequent dehydrogenative C-C coupling reaction of long-chain (>C(20)) linear alkanes on an anisotropic gold(110) surface, which undergoes an appropriate reconstruction by adsorption of the molecules and subsequent mild annealing, resulting in nanometer-sized channels (1.22 nanometers in width). Owing to the orientational constraint of the reactant molecules in these one-dimensional channels, the reaction takes place exclusively at specific sites (terminal CH(3) or penultimate CH(2) groups) in the chains at intermediate temperatures (420 to 470 kelvin) and selects for aliphatic over aromatic C-H activation.

Linear and nonlinear Fano resonance in the main chain-structure of additional defects with an isolated ring composed of defects

NASA Astrophysics Data System (ADS)

Ding, Xiu-Huan; Wang, Rui; Qiao, Qian; Zhang, Cun-Xi

2018-03-01

As is well known, Fano resonance originates from the interference between a continuum energy band and an embedded discrete energy level. We study transmission properties of the discrete chain-structure of additional defects with an isolated ring composed of N defect states, and obtain the analytical transmission coefficient of similar Fano formula. Using the formula, we reveal conditions for perfect reflections and transmissions due to either destructive or constructive interferences. It is found that a nonlinear Kerr-like response leads to bistable transmission, and for either linear cases or nonlinear ones, the defects in main arrays have a major impact on perfect reflections, but has no effect on perfect transmission.

Direction-dependent secondary bonds and their stepwise melting in a uracil-based molecular crystal studied by infrared spectroscopy and theoretical modeling

NASA Astrophysics Data System (ADS)

Szekrényes, Zsolt; Nagy, Péter R.; Tarczay, György; Maggini, Laura; Bonifazi, Davide; Kamarás, Katalin

2018-01-01

Three types of supramolecular interactions are identified in the three crystallographic directions in crystals of 1,4-bis[(1-hexylurac-6-yl) ethynyl]benzene, a uracil-based molecule with a linear backbone. These three interactions, characterized by their strongest component, are: intermolecular double H-bonds along the molecular axis, London dispersion interaction of hexyl chains connecting these linear assemblies, and π - π stacking of the aromatic rings perpendicular to the molecular planes. On heating, two transitions happen, disordering of hexyl chains at 473 K, followed by H-bond melting at 534 K. The nature of the bonds and transitions was established by matrix-isolation and temperature-dependent infrared spectroscopy and supported by theoretical computations.

Numerical approach of the quantum circuit theory

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

Silva, J.J.B., E-mail: jaedsonfisica@hotmail.com; Duarte-Filho, G.C.; Almeida, F.A.G.

2017-03-15

In this paper we develop a numerical method based on the quantum circuit theory to approach the coherent electronic transport in a network of quantum dots connected with arbitrary topology. The algorithm was employed in a circuit formed by quantum dots connected each other in a shape of a linear chain (associations in series), and of a ring (associations in series, and in parallel). For both systems we compute two current observables: conductance and shot noise power. We find an excellent agreement between our numerical results and the ones found in the literature. Moreover, we analyze the algorithm efficiency formore » a chain of quantum dots, where the mean processing time exhibits a linear dependence with the number of quantum dots in the array.« less

Analysis of scattering by a linear chain of spherical inclusions in an optical fiber

NASA Astrophysics Data System (ADS)

Chremmos, Ioannis D.; Uzunoglu, Nikolaos K.

2006-12-01

The scattering by a linear chain of spherical dielectric inclusions, embedded along the axis of an optical fiber, is analyzed using a rigorous integral equation formulation, based on the dyadic Green's function theory. The coupled electric field integral equations are solved by applying the Galerkin technique with Mie-type expansion of the field inside the spheres in terms of spherical waves. The analysis extends the previously studied case of a single spherical inhomogeneity inside a fiber to the multisphere-scattering case, by utilizing the classic translational addition theorems for spherical waves in order to analytically extract the direct-intersphere-coupling coefficients. Results for the transmitted and reflected power, on incidence of the fundamental HE11 mode, are presented for several cases.

Ergosterol in POPC membranes: physical properties and comparison with structurally similar sterols.

PubMed

Hsueh, Ya-Wei; Chen, Mei-Ting; Patty, Philipus J; Code, Christian; Cheng, John; Frisken, Barbara J; Zuckermann, Martin; Thewalt, Jenifer

2007-03-01

The physical properties of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/ergosterol bilayers in the liquid-crystalline phase were determined using deuterium nuclear magnetic resonance ((2)H NMR) and vesicle extrusion. For the (2)H NMR experiments, the sn-1 chain of POPC was perdeuterated, and spectra were taken as a function of ergosterol concentration and temperature. Analysis of the liquid-crystalline spectra provides clear evidence that two types of liquid-crystalline domains, neither of which is a liquid-ordered phase, having distinct average chain conformations coexist in 80:20 and 75:25 POPC/ergosterol membranes over a wide temperature range (from -2 to at least 31 degrees C). Adding ergosterol to a concentration of 25 mol % increases POPC-d(31) chain ordering as measured by the NMR spectral first moment M(1) and also increases the membrane lysis tension, obtained from vesicle extrusion. Further addition of ergosterol had no effect on either chain order or lysis tension. This behavior is in marked contrast to the effect of cholesterol on POPC membranes: POPC/cholesterol membranes have a linear dependence of chain order on sterol concentration to at least 40 mol %. To investigate further we compared the dependence on sterol structure and concentration of the NMR spectra and lysis tension for several POPC/sterol membranes at 25 degrees C. For all POPC/sterol membranes investigated in this study, we observed a universal linear relation between lysis tension and M(1). This suggests that changes in acyl chain ordering directly affect the tensile properties of the membrane.

Ergosterol in POPC Membranes: Physical Properties and Comparison with Structurally Similar Sterols

PubMed Central

Hsueh, Ya-Wei; Chen, Mei-Ting; Patty, Philipus J.; Code, Christian; Cheng, John; Frisken, Barbara J.; Zuckermann, Martin; Thewalt, Jenifer

2007-01-01

The physical properties of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/ergosterol bilayers in the liquid-crystalline phase were determined using deuterium nuclear magnetic resonance (2H NMR) and vesicle extrusion. For the 2H NMR experiments, the sn-1 chain of POPC was perdeuterated, and spectra were taken as a function of ergosterol concentration and temperature. Analysis of the liquid-crystalline spectra provides clear evidence that two types of liquid-crystalline domains, neither of which is a liquid-ordered phase, having distinct average chain conformations coexist in 80:20 and 75:25 POPC/ergosterol membranes over a wide temperature range (from −2 to at least 31°C). Adding ergosterol to a concentration of 25 mol % increases POPC-d31 chain ordering as measured by the NMR spectral first moment M1 and also increases the membrane lysis tension, obtained from vesicle extrusion. Further addition of ergosterol had no effect on either chain order or lysis tension. This behavior is in marked contrast to the effect of cholesterol on POPC membranes: POPC/cholesterol membranes have a linear dependence of chain order on sterol concentration to at least 40 mol %. To investigate further we compared the dependence on sterol structure and concentration of the NMR spectra and lysis tension for several POPC/sterol membranes at 25°C. For all POPC/sterol membranes investigated in this study, we observed a universal linear relation between lysis tension and M1. This suggests that changes in acyl chain ordering directly affect the tensile properties of the membrane. PMID:17142279

A simple-shear rheometer for linear viscoelastic characterization of vocal fold tissues at phonatory frequencies.

PubMed

Chan, Roger W; Rodriguez, Maritza L

2008-08-01

Previous studies reporting the linear viscoelastic shear properties of the human vocal fold cover or mucosa have been based on torsional rheometry, with measurements limited to low audio frequencies, up to around 80 Hz. This paper describes the design and validation of a custom-built, controlled-strain, linear, simple-shear rheometer system capable of direct empirical measurements of viscoelastic shear properties at phonatory frequencies. A tissue specimen was subjected to simple shear between two parallel, rigid acrylic plates, with a linear motor creating a translational sinusoidal displacement of the specimen via the upper plate, and the lower plate transmitting the harmonic shear force resulting from the viscoelastic response of the specimen. The displacement of the specimen was measured by a linear variable differential transformer whereas the shear force was detected by a piezoelectric transducer. The frequency response characteristics of these system components were assessed by vibration experiments with accelerometers. Measurements of the viscoelastic shear moduli (G' and G") of a standard ANSI S2.21 polyurethane material and those of human vocal fold cover specimens were made, along with estimation of the system signal and noise levels. Preliminary results showed that the rheometer can provide valid and reliable rheometric data of vocal fold lamina propria specimens at frequencies of up to around 250 Hz, well into the phonatory range.

The clustering of QSOs and the dark matter halos that host them

NASA Astrophysics Data System (ADS)

Zhao, Dong-Yao; Yan, Chang-Shuo; Lu, Youjun

2013-10-01

The spatial clustering of QSOs is an important measurable quantity which can be used to infer the properties of dark matter halos that host them. We construct a simple QSO model to explain the linear bias of QSOs measured by recent observations and explore the properties of dark matter halos that host a QSO. We assume that major mergers of dark matter halos can lead to the triggering of QSO phenomena, and the evolution of luminosity for a QSO generally shows two accretion phases, i.e., initially having a constant Eddington ratio due to the self-regulation of the accretion process when supply is sufficient, and then declining in rate with time as a power law due to either diminished supply or long term disk evolution. Using a Markov Chain Monte Carlo method, the model parameters are constrained by fitting the observationally determined QSO luminosity functions (LFs) in the hard X-ray and in the optical band simultaneously. Adopting the model parameters that best fit the QSO LFs, the linear bias of QSOs can be predicted and then compared with the observational measurements by accounting for various selection effects in different QSO surveys. We find that the latest measurements of the linear bias of QSOs from both the SDSS and BOSS QSO surveys can be well reproduced. The typical mass of SDSS QSOs at redshift 1.5 < z < 4.5 is ~ (3 - 6) × 1012 h-1 Msolar and the typical mass of BOSS QSOs at z ~ 2.4 is ~ 2 × 1012 h-1 Msolar. For relatively faint QSOs, the mass distribution of their host dark matter halos is wider than that of bright QSOs because faint QSOs can be hosted in both big halos and smaller halos, but bright QSOs are only hosted in big halos, which is part of the reason for the predicted weak dependence of the linear biases on the QSO luminosity.

A simple attitude control of quadrotor helicopter based on Ziegler-Nichols rules for tuning PD parameters.

PubMed

He, ZeFang; Zhao, Long

2014-01-01

An attitude control strategy based on Ziegler-Nichols rules for tuning PD (proportional-derivative) parameters of quadrotor helicopters is presented to solve the problem that quadrotor tends to be instable. This problem is caused by the narrow definition domain of attitude angles of quadrotor helicopters. The proposed controller is nonlinear and consists of a linear part and a nonlinear part. The linear part is a PD controller with PD parameters tuned by Ziegler-Nichols rules and acts on the quadrotor decoupled linear system after feedback linearization; the nonlinear part is a feedback linearization item which converts a nonlinear system into a linear system. It can be seen from the simulation results that the attitude controller proposed in this paper is highly robust, and its control effect is better than the other two nonlinear controllers. The nonlinear parts of the other two nonlinear controllers are the same as the attitude controller proposed in this paper. The linear part involves a PID (proportional-integral-derivative) controller with the PID controller parameters tuned by Ziegler-Nichols rules and a PD controller with the PD controller parameters tuned by GA (genetic algorithms). Moreover, this attitude controller is simple and easy to implement.