Calculations of critical micelle concentration by dissipative particle dynamics simulations: the role of chain rigidity.

PubMed

Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V

2013-09-05

Micelle formation in surfactant solutions is a self-assembly process governed by complex interplay of solvent-mediated interactions between hydrophilic and hydrophobic groups, which are commonly called heads and tails. However, the head-tail repulsion is not the only factor affecting the micelle formation. For the first time, we present a systematic study of the effect of chain rigidity on critical micelle concentration and micelle size, which is performed with the dissipative particle dynamics simulation method. Rigidity of the coarse-grained surfactant molecule was controlled by the harmonic bonds set between the second-neighbor beads. Compared to flexible molecules with the nearest-neighbor bonds being the only type of bonded interactions, rigid molecules exhibited a lower critical micelle concentration and formed larger and better-defined micelles. By varying the strength of head-tail repulsion and the chain rigidity, we constructed two-dimensional diagrams presenting how the critical micelle concentration and aggregation number depend on these parameters. We found that the solutions of flexible and rigid molecules that exhibited approximately the same critical micelle concentration could differ substantially in the micelle size and shape depending on the chain rigidity. With the increase of surfactant concentration, primary micelles of more rigid molecules were found less keen to agglomeration and formation of nonspherical aggregates characteristic of flexible molecules.

Solvothermal synthesis and structure of coordination polymers of Nd(III) and Dy(III) with rigid isophthalic acid derivatives and flexible adipic acid

NASA Astrophysics Data System (ADS)

Kariem, Mukaddus; Kumar, Manesh; Yawer, Mohd; Sheikh, Haq Nawaz

2017-12-01

Two new coordination polymers (CPs) with the formula [Nd(hip)(adip) 0.5(H2O)2]n.nH2O (1) and [Dy(aip)(adip)0.5(H2O)2]n.nH2O (2) were synthesized by self-assembly of lanthanide salts with rigid [5-hydroxyisophthalic acid (H2hip)], [5-aminoisophthalic acid (H2aip)] and flexible [adipic acid (H2adip)] linkers under solvothermal conditions. The CPs 1 &2 crystallize in monoclinic C2/c space group. Both the CPs have 1D linear ladder shaped extension with the linkages having the backbone of hip2-, aip2- and adip2- ligands. The 1D linear ladder chains generate three dimensional (3D) supramolecular frameworks via significant π-π and hydrogen bonding interactions. The CP 2 (Dy) emit strong ligand sensitized characteristic f-f luminescence emission. The CP 2 also exhibit weak ferromagnetic interactions at low temperatures.

Looped star polymers show conformational transition from spherical to flat toroidal shapes.

PubMed

Reiss, Pascal; Fritsche, Miriam; Heermann, Dieter W

2011-11-01

Inspired by the topological organization of the circular Escherichia coli chromosome, which is compacted by separate domains, we study a polymer architecture consisting of a central ring to which either looped or linear side chains are grafted. A shape change from a spherical to a toroidal organization takes place as soon as the inner ring becomes large enough for the attached arms to fit within its circumference. Building up a torus, the system flattens, depending on the effective bending rigidity of the chain induced by entropic repulsion of the attached loops and, to a lesser extent, linear arms. Our results suggest that the natural formation of a toroidal structure with a decreased amount of writhe induced by a specific underlying topology could be one driving force, among others, that nature exploits to ensure proper packaging of the genetic material within a rod-shaped, bacterial envelope.

Chain stiffness, salt valency, and concentration influences on titration curves of polyelectrolytes: Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Carnal, Fabrice; Stoll, Serge

2011-01-01

Monte Carlo simulations have been used to study two different models of a weak linear polyelectrolyte surrounded by explicit counterions and salt particles: (i) a rigid rod and (ii) a flexible chain. We focused on the influence of the pH, chain stiffness, salt concentration, and valency on the polyelectrolyte titration process and conformational properties. It is shown that chain acid-base properties and conformational properties are strongly modified when multivalent salt concentration variation ranges below the charge equivalence. Increasing chain stiffness allows to minimize intramolecular electrostatic monomer interactions hence improving the deprotonation process. The presence of di and trivalent salt cations clearly promotes the chain degree of ionization but has only a limited effect at very low salt concentration ranges. Moreover, folded structures of fully charged chains are only observed when multivalent salt at a concentration equal or above charge equivalence is considered. Long-range electrostatic potential is found to influence the distribution of charges along and around the polyelectrolyte backbones hence resulting in a higher degree of ionization and a lower attraction of counterions and salt particles at the chain extremities.

Chain stiffness, salt valency, and concentration influences on titration curves of polyelectrolytes: Monte Carlo simulations.

PubMed

Carnal, Fabrice; Stoll, Serge

2011-01-28

Monte Carlo simulations have been used to study two different models of a weak linear polyelectrolyte surrounded by explicit counterions and salt particles: (i) a rigid rod and (ii) a flexible chain. We focused on the influence of the pH, chain stiffness, salt concentration, and valency on the polyelectrolyte titration process and conformational properties. It is shown that chain acid-base properties and conformational properties are strongly modified when multivalent salt concentration variation ranges below the charge equivalence. Increasing chain stiffness allows to minimize intramolecular electrostatic monomer interactions hence improving the deprotonation process. The presence of di and trivalent salt cations clearly promotes the chain degree of ionization but has only a limited effect at very low salt concentration ranges. Moreover, folded structures of fully charged chains are only observed when multivalent salt at a concentration equal or above charge equivalence is considered. Long-range electrostatic potential is found to influence the distribution of charges along and around the polyelectrolyte backbones hence resulting in a higher degree of ionization and a lower attraction of counterions and salt particles at the chain extremities.

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.

Momentum-Based Dynamics for Spacecraft with Chained Revolute Appendages

NASA Technical Reports Server (NTRS)

Queen, Steven; London, Ken; Gonzalez, Marcelo

2005-01-01

An efficient formulation is presented for a sub-class of multi-body dynamics problems that involve a six degree-of-freedom base body and a chain of N rigid linkages connected in series by single degree-of-freedom revolute joints. This general method is particularly well suited for simulations of spacecraft dynamics and control that include the modeling of an orbiting platform with or without internal degrees of freedom such as reaction wheels, dampers, and/or booms. In the present work, particular emphasis is placed on dynamic simulation of multi-linkage robotic manipulators. The differential equations of motion are explicitly given in terms of linear and angular momentum states, which can be evaluated recursively along a serial chain of linkages for an efficient real-time solution on par with the best of the O(N3) methods.

Effect of chain rigidity on network architecture and deformation behavior of glassy polymer networks

NASA Astrophysics Data System (ADS)

Knowles, Kyler Reser

Processing carbon fiber composite laminates creates molecular-level strains in the thermoset matrix upon curing and cooling which can lead to failures such as geometry deformations, micro-cracking, and other issues. It is known strain creation is attributed to the significant volume and physical state changes undergone by the polymer matrix throughout the curing process, though storage and relaxation of cure-induced strains remain poorly understood. This dissertation establishes two approaches to address the issue. The first establishes testing methods to simultaneously measure key volumetric properties of a carbon fiber composite laminate and its polymer matrix. The second approach considers the rigidity of the polymer matrix in regards to strain storage and relaxation mechanisms which ultimately control composite performance throughout manufacturing and use. Through the use of a non-contact, full-field strain measurement technique known as digital image correlation (DIC), we describe and implement useful experiments which quantify matrix and composite parameters necessary for simulation efforts and failure models. The methods are compared to more traditional techniques and show excellent correlation. Further, we established relationships which represent matrix-fiber compatibility in regards to critical processing constraints. The second approach involves a systematic study of epoxy-amine networks which are chemically-similar but differ in chain segment rigidity. Prior research has investigated the isomer effect of glassy polymers, showing sizeable differences in thermal, volumetric, physical, and mechanical properties. This work builds on these themes and shows the apparent isomer effect is rather an effect of chain rigidity. Indeed, it was found that structurally-dissimilar polymer networks exhibit very similar properties as a consequence of their shared average network rigidity. Differences in chain packing, as a consequence of chain rigidity, were shown to alter the physical, volumetric, and mechanical properties of the glassy networks. Chain rigidity was found to directly control deformation mechanisms, which were related to the yielding behavior of the epoxy network series. The unique benefit to our approach is the ability to separate the role of rigidity - an intramolecular parameter - from intermolecular phenomena which otherwise influence network properties.

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.

Synthesis and characterization of shape memory poly (epsilon-caprolactone) polyurethane-ureas

NASA Astrophysics Data System (ADS)

Ren, Hongfeng

Shape memory polymers (SMPs) have attracted significant interest in recent times because of their potential applications in a number of areas, such as medical devices and textiles. However, there are some major drawbacks of SMPs, such as their relatively low moduli resulting in small recovery stresses, and their long response times compared with shape memory alloys (SMAs). A suitable recovery stress which comes from the elastic recovery stress generated in the deformation process is critical in some medical devices. To address some of these shortcomings, the work in this dissertation mainly focuses on the design and synthesis of linear shape memory polymers with higher recovery stress. A series of segmented poly (epsilon-caprolactone) polyurethane-ureas (PCLUUs) were prepared from poly (epsilon-caprolactone) (PCL) diol, different dissociates and chain extenders. NMR and FT-IR were used to identify the structure of the synthesized shape memory polyurethane-ureas. Parameters such as soft segment content (molecular weight and content), chain extender and the rigidity of the main chain were investigated to understand the structure-property relationships of the shape memory polymer systems through DSC, DMA, physical property test, etc. Cyclic thermal mechanic tests were applied to measure the shape memory properties which showed that the recovery stress can be improved above 200% simply by modifying the chain extender. Meanwhile, the synthesis process was optimized to be similar to that of Spandex /LYCRA®. Continuous fibers form shape memory polyurethane-ureas were made from a wet spinning process, which indicated excellent spinnability of the polymer solution. Small angle neutron scattering (SANS) was used to study the morphology of the hard segment at different temperatures and stretch rates and found that the monodisperse rigid cylinder model fit the SANS data quite well. From the cylinder model, the radius of the cylinder increased with increasing hard segment content. The SANS results revealed phase separation of hard and soft segments into nano scale domains. The overall objectives of this dissertation were: ■ To improve the recovery stress of linear shape memory polymers. ■ To study the morphology and structure property relationships of shape memory polymers. Chapter 1 reviews the literature on SMAs and SMPs, especially on linear SMPs. Chapter 2 is devoted to SMPUUs with the aliphatic amine 1, 4-Butanediamine (BDA) as chain extender. Chapter 3 reports the effects of different aliphatic diamines as the chain extenders. Chapter 4 covers the results for shape memory polyurethane-ureas with aromatic diamine 4, 4’-Methylenedianiline (MDA) as the chain extender. The effect of different diisocyanates is covered in Chapter 5. Chapter 6-7 show some synthesized polymer systems with unimproved recovery stress or even no shape memory properties. The overall conclusions of this work are reported in Chapter 8.

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.

Influence of chain rigidity on the conformation of model lipid membranes in the presence of cylindrical nanoparticle inclusions

NASA Astrophysics Data System (ADS)

Diloreto, Chris; Wickham, Robert

2012-02-01

We employ real-space self-consistent field theory to study the conformation of model lipid membranes in the presence of solvent and cylindrical nanoparticle inclusions (''peptides''). Whereas it is common to employ a polymeric Gaussian chain model for the lipids, here we model the lipids as persistent, worm-like chains. Our motivation is to develop a more realistic field theory to describe the action of pore-forming anti-microbial peptides that disrupt the bacterial cell membrane. We employ operator-splitting and a pseudo-spectral algorithm, using SpharmonicKit for the chain tangent degrees of freedom, to solve for the worm-like chain propagator. The peptides, modelled using a mask function, have a surface patterned with hydrophobic and hydrophillic patches, but no charge. We examine the role chain rigidity plays in the hydrophobic mismatch, the membrane-mediated interaction between two peptides, the size and structure of pores formed by peptide aggregates, and the free-energy barrier for peptide insertion into the membrane. Our results suggest that chain rigidity influences both the pore structure and the mechanism of pore formation.

Model systems for single molecule polymer dynamics

PubMed Central

Latinwo, Folarin

2012-01-01

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

Anomalous interlayer vibrations in strongly coupled layered PdSe 2

DOE PAGES

Puretzky, Alexander A.; Oyedele, Akinola D.; Xiao, Kai; ...

2018-05-04

In this work, we show unusual effects of strong interlayer coupling on low-frequency (LF) Raman scattering in exfoliated PdSe 2 crystals with different number of layers. Unlike many other layered materials, it is found that the measured frequencies of the breathing modes cannot be simply described by a conventional linear chain model (LCM) that treats each layer as a single rigid object. By using first-principles calculations, we show that strong deviations from layer rigidity can occur for the LF breathing vibrations of PdSe 2, which accounts for the observed disagreement with the conventional LCM. The layer non-rigidity and strong interlayermore » coupling could also explain the unusual strong intensities of the LF breathing modes that are comparable with those of the high-frequency Raman modes. These strong intensities allowed us to use a set of the measured LF Raman lines as unique fingerprints for a precise assignment of the layer numbers. The assignment of the layer numbers was further confirmed using second harmonic generation that appeared only in the noncentrosymmetric even-layer PdSe 2 crystals. In conclusion, this work thus demonstrates a simple and fast approach for the determination of the number of layers in 2D materials with strong interlayer coupling and non-rigid interlayer vibrations.« less

Simulations of dynamics of plunge and pitch of a three-dimensional flexible wing in a low Reynolds number flow

NASA Astrophysics Data System (ADS)

Qi, Dewei; Liu, Yingming; Shyy, Wei; Aono, Hikaru

2010-09-01

The lattice Boltzmann flexible particle method (LBFPM) is used to simulate fluid-structure interaction and motion of a flexible wing in a three-dimensional space. In the method, a beam with rectangular cross section has been discretized into a chain of rigid segments. The segments are connected through ball and socket joints at their ends and may be bent and twisted. Deformation of flexible structure is treated with a linear elasticity model through bending and twisting. It is demonstrated that the flexible particle method (FPM) can approximate the nonlinear Euler-Bernoulli beam equation without resorting to a nonlinear elasticity model. Simulations of plunge and pitch of flexible wing at Reynolds number Re=136 are conducted in hovering condition by using the LBFPM. It is found that both lift and drag forces increase first, then decrease dramatically as the bending rigidity in spanwise direction decreases and that the lift and drag forces are sensitive to rigidity in a certain range. It is shown that the downwash flows induced by wing tip and trailing vortices in wake area are larger for a flexible wing than for a rigid wing, lead to a smaller effective angle of attack, and result in a larger lift force.

Anomalous interlayer vibrations in strongly coupled layered PdSe 2

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

Puretzky, Alexander A.; Oyedele, Akinola D.; Xiao, Kai

In this work, we show unusual effects of strong interlayer coupling on low-frequency (LF) Raman scattering in exfoliated PdSe 2 crystals with different number of layers. Unlike many other layered materials, it is found that the measured frequencies of the breathing modes cannot be simply described by a conventional linear chain model (LCM) that treats each layer as a single rigid object. By using first-principles calculations, we show that strong deviations from layer rigidity can occur for the LF breathing vibrations of PdSe 2, which accounts for the observed disagreement with the conventional LCM. The layer non-rigidity and strong interlayermore » coupling could also explain the unusual strong intensities of the LF breathing modes that are comparable with those of the high-frequency Raman modes. These strong intensities allowed us to use a set of the measured LF Raman lines as unique fingerprints for a precise assignment of the layer numbers. The assignment of the layer numbers was further confirmed using second harmonic generation that appeared only in the noncentrosymmetric even-layer PdSe 2 crystals. In conclusion, this work thus demonstrates a simple and fast approach for the determination of the number of layers in 2D materials with strong interlayer coupling and non-rigid interlayer vibrations.« less

Improved genetic algorithm for the protein folding problem by use of a Cartesian combination operator.

PubMed Central

Rabow, A. A.; Scheraga, H. A.

1996-01-01

We have devised a Cartesian combination operator and coding scheme for improving the performance of genetic algorithms applied to the protein folding problem. The genetic coding consists of the C alpha Cartesian coordinates of the protein chain. The recombination of the genes of the parents is accomplished by: (1) a rigid superposition of one parent chain on the other, to make the relation of Cartesian coordinates meaningful, then, (2) the chains of the children are formed through a linear combination of the coordinates of their parents. The children produced with this Cartesian combination operator scheme have similar topology and retain the long-range contacts of their parents. The new scheme is significantly more efficient than the standard genetic algorithm methods for locating low-energy conformations of proteins. The considerable superiority of genetic algorithms over Monte Carlo optimization methods is also demonstrated. We have also devised a new dynamic programming lattice fitting procedure for use with the Cartesian combination operator method. The procedure finds excellent fits of real-space chains to the lattice while satisfying bond-length, bond-angle, and overlap constraints. PMID:8880904

The electrostatic persistence length of polymers beyond the OSF limit.

PubMed

Everaers, R; Milchev, A; Yamakov, V

2002-05-01

We use large-scale Monte Carlo simulations to test scaling theories for the electrostatic persistence length l(e) of isolated, uniformly charged polymers with Debye-Hückel intrachain interactions in the limit where the screening length kappa(-1) exceeds the intrinsic persistence length of the chains. Our simulations cover a significantly larger part of the parameter space than previous studies. We observe no significant deviations from the prediction l(e) proportional to kappa(-2) by Khokhlov and Khachaturian which is based on applying the Odijk-Skolnick-Fixman theories of electrostatic bending rigidity and electrostatically excluded volume to the stretched de Gennes-Pincus-Velasco-Brochard polyelectrolyte blob chain. A linear or sublinear dependence of the persistence length on the screening length can be ruled out. We show that previous results pointing into this direction are due to a combination of excluded-volume and finite chain length effects. The paper emphasizes the role of scaling arguments in the development of useful representations for experimental and simulation data.

A combinatorial approach to protein docking with flexible side chains.

PubMed

Althaus, Ernst; Kohlbacher, Oliver; Lenhof, Hans-Peter; Müller, Peter

2002-01-01

Rigid-body docking approaches are not sufficient to predict the structure of a protein complex from the unbound (native) structures of the two proteins. Accounting for side chain flexibility is an important step towards fully flexible protein docking. This work describes an approach that allows conformational flexibility for the side chains while keeping the protein backbone rigid. Starting from candidates created by a rigid-docking algorithm, we demangle the side chains of the docking site, thus creating reasonable approximations of the true complex structure. These structures are ranked with respect to the binding free energy. We present two new techniques for side chain demangling. Both approaches are based on a discrete representation of the side chain conformational space by the use of a rotamer library. This leads to a combinatorial optimization problem. For the solution of this problem, we propose a fast heuristic approach and an exact, albeit slower, method that uses branch-and-cut techniques. As a test set, we use the unbound structures of three proteases and the corresponding protein inhibitors. For each of the examples, the highest-ranking conformation produced was a good approximation of the true complex structure.

Parameterization of a mesoscopic model for the self-assembly of linear sodium alkyl sulfates

NASA Astrophysics Data System (ADS)

Mai, Zhaohuan; Couallier, Estelle; Rakib, Mohammed; Rousseau, Bernard

2014-05-01

A systematic approach to develop mesoscopic models for a series of linear anionic surfactants (CH3(CH2)n - 1OSO3Na, n = 6, 9, 12, 15) by dissipative particle dynamics (DPD) simulations is presented in this work. The four surfactants are represented by coarse-grained models composed of the same head group and different numbers of identical tail beads. The transferability of the DPD model over different surfactant systems is carefully checked by adjusting the repulsive interaction parameters and the rigidity of surfactant molecules, in order to reproduce key equilibrium properties of the aqueous micellar solutions observed experimentally, including critical micelle concentration (CMC) and average micelle aggregation number (Nag). We find that the chain length is a good index to optimize the parameters and evaluate the transferability of the DPD model. Our models qualitatively reproduce the essential properties of these surfactant analogues with a set of best-fit parameters. It is observed that the logarithm of the CMC value decreases linearly with the surfactant chain length, in agreement with Klevens' rule. With the best-fit and transferable set of parameters, we have been able to calculate the free energy contribution to micelle formation per methylene unit of -1.7 kJ/mol, very close to the experimentally reported value.

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

PubMed

Jeon, Jonggu; Chun, Myung-Suk

2007-04-21

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

Computer Simulations of Bottle Brushes: From Melts to Soft Networks

DOE PAGES

Cao, Zhen; Carrillo, Jan-Michael Y.; Sheiko, Sergei S.; ...

2015-07-13

We use a combination of Molecular dynamics simulations and analytical calculations, and study dens bottle-brush systems in a melt and network State. Analysis of our simulation results shows that bottle-brush macromolecules in melt behave as ideal chains with effective Kuhn length b K. Simulations show that the bottle-brush-induced bending rigidity is due to an entropy decrease caused by redistribution of the side chains upon backbone bending. The Kuhn length of the bottle:brushes increases with increasing the side-chain degree of polymerization n sc as b K proportional to n sc 0.46. Moreover, this model of bottle brush macromolecules is extended tomore » describe mechanical properties of bottle brush 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 G 0 proportional to (n sc + 1) -1 as long as the ratio of the Kuhn length, b K, to the size of the fully extended bottle-brush backbone between cross-links, R-max, is smaller than unity, b K/R max << 1. Bottle-brush networks With b K/R max proportional to 1 demonstrate behavior similar to that of networks Of semiflexible chains with G 0 proportional to n sc -0.5. Finally, in the nonlinear network deformation regime, the deformation-dependent shear modulus is a universal function of the first strain invariant I 1 and bottle-brush backbone deformation ratio beta describing stretching ability of the bottle-brush backbone between cross-links.« less

Manipulator control by exact linearization

NASA Technical Reports Server (NTRS)

Kruetz, K.

1987-01-01

Comments on the application to rigid link manipulators of geometric control theory, resolved acceleration control, operational space control, and nonlinear decoupling theory are given, and the essential unity of these techniques for externally linearizing and decoupling end effector dynamics is discussed. Exploiting the fact that the mass matrix of a rigid link manipulator is positive definite, a consequence of rigid link manipulators belonging to the class of natural physical systems, it is shown that a necessary and sufficient condition for a locally externally linearizing and output decoupling feedback law to exist is that the end effector Jacobian matrix be nonsingular. Furthermore, this linearizing feedback is easy to produce.

Influence of RNA Strand Rigidity on Polyion Complex Formation with Block Catiomers.

PubMed

Hayashi, Kotaro; Chaya, Hiroyuki; Fukushima, Shigeto; Watanabe, Sumiyo; Takemoto, Hiroyasu; Osada, Kensuke; Nishiyama, Nobuhiro; Miyata, Kanjiro; Kataoka, Kazunori

2016-03-01

Polyion complexes (b-PICs) are prepared by mixing single- or double-stranded oligo RNA (aniomer) with poly(ethylene glycol)-b-poly(L-lysine) (PEG-PLL) (block catiomer) to clarify the effect of aniomer chain rigidity on association behaviors at varying concentrations. Here, a 21-mer single-stranded RNA (ssRNA) (persistence length: 1.0 nm) and a 21-mer double-stranded RNA (small interfering RNA, siRNA) (persistence length: 62 nm) are compared. Both oligo RNAs form a minimal charge-neutralized ionomer pair with a single PEG-PLL chain, termed unit b-PIC (uPIC), at low concentrations (<≈ 0.01 mg mL(-1)). Above the critical association concentration (≈ 0.01 mg mL(-1)), ssRNA b-PICs form secondary associates, PIC micelles, with sizes up to 30-70 nm, while no such multimolecular assembly is observed for siRNA b-PICs. The entropy gain associated with the formation of a segregated PIC phase in the multimolecular PIC micelles may not be large enough for rigid siRNA strands to compensate with appreciably high steric repulsion derived from PEG chains. Chain rigidity appears to be a critical parameter in polyion complex association. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Delocalization of Coherent Triplet Excitons in Linear Rigid Rod Conjugated Oligomers.

PubMed

Hintze, Christian; Korf, Patrick; Degen, Frank; Schütze, Friederike; Mecking, Stefan; Steiner, Ulrich E; Drescher, Malte

2017-02-02

In this work, the triplet state delocalization in a series of monodisperse oligo(p-phenyleneethynylene)s (OPEs) is studied by pulsed electron paramagnetic resonance (EPR) and pulsed electron nuclear double resonance (ENDOR) determining zero-field splitting, optical spin polarization, and proton hyperfine couplings. Neither the zero-field splitting parameters nor the optical spin polarization change significantly with OPE chain length, in contrast to the hyperfine coupling constants, which showed a systematic decrease with chain length n according to a 2/(1 + n) decay law. The results provide striking evidence for the Frenkel-type nature of the triplet excitons exhibiting full coherent delocalization in the OPEs under investigation with up to five OPE repeat units and with a spin density distribution described by a nodeless particle in the box wave function. The same model is successfully applied to recently published data on π-conjugated porphyrin oligomers.

Design and preparation of novel polyarylene ether materials based on Diels-Alder reaction as the crosslinker for electrooptical modulators

NASA Astrophysics Data System (ADS)

Gao, Wu; Hou, Wenjun; Zhen, Zhen; Liu, Xinhou; Liu, Jialei; Fedorchuk, A. A.; Czaja, P.

2016-07-01

Novel crosslinkable organic linear electro-optical (EO) material based on polyarylene ether as the main chain host polymer was designed and prepared. The host polymer with rigid aromatic has demonstrated a good compatibility with the guest chromophore. Long side chain with anthracene ensured the crosslinkable reaction and appropriate glass transition temperature of the host polymer (55 °C). The EO r33 tensor coefficient for this novel EO material has been magnitude of 66 pm/V at 1310 nm and the excellent long term stability at 85 °C. These parameters permit to consider their application in fabrication of organic electro optical devices. The semi-empirical and DFT quantum chemical simulations were performed for 4 principal chromophores to clarify a role of cross-linker in the enhancement of the ground state dipole moments and effective hyperpolarizabilities.

The Advanced Part of a Treatise on the Dynamics of a System of Rigid Bodies

NASA Astrophysics Data System (ADS)

Routh, Edward John

2013-03-01

Preface; 1. Moving axes and relative motion; 2. Oscillations about equilibrium; 3. Oscillations about a state of motion; 4. Motion of a body under no forces; 5. Motion of a body under any forces; 6. Nature of the motion given by linear equations and the conditions of stability; 7. Free and forced oscillations; 8. Determination of the constants of integration in terms of the initial conditions; 9. Calculus of finite differences; 10. Calculus of variations; 11. Precession and nutation; 12. Motion of the moon about its centre; 13. Motion of a string or chain; 14. Motion of a membrane; Notes.

Compression induced phase transition of nematic brush: A mean-field theory study

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

Tang, Jiuzhou; Zhang, Xinghua, E-mail: zhangxh@bjtu.edu.cn; Yan, Dadong, E-mail: yandd@bnu.edu.cn

2015-11-28

Responsive behavior of polymer brush to the external compression is one of the most important characters for its application. For the flexible polymer brush, in the case of low grafting density, which is widely studied by the Gaussian chain model based theory, the compression leads to a uniform deformation of the chain. However, in the case of high grafting density, the brush becomes anisotropic and the nematic phase will be formed. The normal compression tends to destroy the nematic order, which leads to a complex responsive behaviors. Under weak compression, chains in the nematic brush are buckled, and the bendingmore » energy and Onsager interaction give rise to the elasticity. Under deep compression, the responsive behaviors of the nematic polymer brush depend on the chain rigidity. For the compressed rigid polymer brush, the chains incline to re-orientate randomly to maximize the orientational entropy and its nematic order is destroyed. For the compressed flexible polymer brush, the chains incline to fold back to keep the nematic order. A buckling-folding transition takes place during the compressing process. For the compressed semiflexible brush, the chains are collectively tilted to a certain direction, which leads to the breaking of the rotational symmetry in the lateral plane. These responsive behaviors of nematic brush relate to the properties of highly frustrated worm-like chain, which is hard to be studied by the traditional self-consistent field theory due to the difficulty to solve the modified diffusion equation. To overcome this difficulty, a single chain in mean-field theory incorporating Monte Carlo simulation and mean-field theory for the worm-like chain model is developed in present work. This method shows high performance for entire region of chain rigidity in the confined condition.« 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.

The isotropic-nematic phase transition of tangent hard-sphere chain fluids—Pure components

NASA Astrophysics Data System (ADS)

van Westen, Thijs; Oyarzún, Bernardo; Vlugt, Thijs J. H.; Gross, Joachim

2013-07-01

An extension of Onsager's second virial theory is developed to describe the isotropic-nematic phase transition of tangent hard-sphere chain fluids. Flexibility is introduced by the rod-coil model. The effect of chain-flexibility on the second virial coefficient is described using an accurate, analytical approximation for the orientation-dependent pair-excluded volume. The use of this approximation allows for an analytical treatment of intramolecular flexibility by using a single pure-component parameter. Two approaches to approximate the effect of the higher virial coefficients are considered, i.e., the Vega-Lago rescaling and Scaled Particle Theory (SPT). The Onsager trial function is employed to describe the orientational distribution function. Theoretical predictions for the equation of state and orientational order parameter are tested against the results from Monte Carlo (MC) simulations. For linear chains of length 9 and longer, theoretical results are in excellent agreement with MC data. For smaller chain lengths, small errors introduced by the approximation of the higher virial coefficients become apparent, leading to a small under- and overestimation of the pressure and density difference at the phase transition, respectively. For rod-coil fluids of reasonable rigidity, a quantitative comparison between theory and MC simulations is obtained. For more flexible chains, however, both the Vega-Lago rescaling and SPT lead to a small underestimation of the location of the phase transition.

Coordinate measuring system

DOEpatents

Carlisle, Keith [Discovery Bay, CA

2003-04-08

An apparatus and method is utilized to measure relative rigid body motion between two bodies by measuring linear motion in the principal axis and linear motion in an orthogonal axis. From such measurements it is possible to obtain displacement, departure from straightness, and angular displacement from the principal axis of a rigid body.

Effect of Chain Rigidity on the Decoupling of Ion Motion from Segmental Relaxation in Polymerized Ionic Liquids: Ambient and Elevated Pressure Studies

DOE PAGES

Wojnarowska, Zaneta; Feng, Hongbo; Fu, Yao; ...

2017-08-21

Conductivity in polymer electrolytes has been generally discussed with the assumption that the segmental motions control charge transport. However, much less attention has been paid to the mechanism of ion conductivity where the motions of ions are less dependent (decoupled) on segmental dynamics. We present that this phenomenon is observed in ionic materials as they approach their glass transition temperature and becomes essential for design and development of highly conducting solid polymer electrolytes. In this paper, we study the effect of chain rigidity on the decoupling of ion transport from segmental motion in three polymerized ionic liquids (polyILs) containing themore » same cation–anion pair but differing in flexibility of the polymer backbones and side groups. Analysis of dielectric and rheology data reveals that decoupling is strong in vinyl-based rigid polymers while almost negligible in novel siloxane-based flexible polyILs. To explain this behavior, we investigated ion and chain dynamics at ambient and elevated pressure. Our results suggest that decoupling has a direct relationship to the frustration in chain packing and free volume. Finally, these conclusions are also supported by coarse-grained molecular dynamics simulations.« less

Effect of Chain Rigidity on the Decoupling of Ion Motion from Segmental Relaxation in Polymerized Ionic Liquids: Ambient and Elevated Pressure Studies

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

Wojnarowska, Zaneta; Feng, Hongbo; Fu, Yao

Conductivity in polymer electrolytes has been generally discussed with the assumption that the segmental motions control charge transport. However, much less attention has been paid to the mechanism of ion conductivity where the motions of ions are less dependent (decoupled) on segmental dynamics. We present that this phenomenon is observed in ionic materials as they approach their glass transition temperature and becomes essential for design and development of highly conducting solid polymer electrolytes. In this paper, we study the effect of chain rigidity on the decoupling of ion transport from segmental motion in three polymerized ionic liquids (polyILs) containing themore » same cation–anion pair but differing in flexibility of the polymer backbones and side groups. Analysis of dielectric and rheology data reveals that decoupling is strong in vinyl-based rigid polymers while almost negligible in novel siloxane-based flexible polyILs. To explain this behavior, we investigated ion and chain dynamics at ambient and elevated pressure. Our results suggest that decoupling has a direct relationship to the frustration in chain packing and free volume. Finally, these conclusions are also supported by coarse-grained molecular dynamics simulations.« less

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

Rotationally Molded Liquid Crystalline Polymers

NASA Technical Reports Server (NTRS)

Rogers, Martin; Stevenson, Paige; Scribben, Eric; Baird, Donald; Hulcher, Bruce

2002-01-01

Rotational molding is a unique process for producing hollow plastic parts. Rotational molding offers advantages of low cost tooling and can produce very large parts with complicated shapes. Products made by rotational molding include water tanks with capacities up to 20,000 gallons, truck bed liners, playground equipment, air ducts, Nylon fuel tanks, pipes, toys, stretchers, kayaks, pallets, and many others. Thermotropic liquid crystalline polymers are an important class of engineering resins employed in a wide variety of applications. Thermotropic liquid crystalline polymers resins are composed of semi-rigid, nearly linear polymeric chains resulting in an ordered mesomorphic phase between the crystalline solid and the isotropic liquid. Ordering of the rigid rod-like polymers in the melt phase yields microfibrous, self-reinforcing polymer structures with outstanding mechanical and thermal properties. Rotational molding of liquid crystalline polymer resins results in high strength and high temperature hollow structures useful in a variety of applications. Various fillers and reinforcements can potentially be added to improve properties of the hollow structures. This paper focuses on the process and properties of rotationally molded liquid crystalline polymers.

Electrostatic stiffening and induced persistence length for coassembled molecular bottlebrushes

NASA Astrophysics Data System (ADS)

Storm, Ingeborg M.; Stuart, Martien A. Cohen; de Vries, Renko; Leermakers, Frans A. M.

2018-03-01

A self-consistent field analysis for tunable contributions to the persistence length of isolated semiflexible polymer chains including electrostatically driven coassembled deoxyribonucleic acid (DNA) bottlebrushes is presented. When a chain is charged, i.e., for polyelectrolytes, there is, in addition to an intrinsic rigidity, an electrostatic stiffening effect, because the electric double layer resists bending. For molecular bottlebrushes, there is an induced contribution due to the grafts. We explore cases beyond the classical phantom main-chain approximation and elaborate molecularly more realistic models where the backbone has a finite volume, which is necessary for treating coassembled bottlebrushes. We find that the way in which the linear charge density or the grafting density is regulated is important. Typically, the stiffening effect is reduced when there is freedom for these quantities to adapt to the curvature stresses. Electrostatically driven coassembled bottlebrushes, however, are relatively stiff because the chains have a low tendency to escape from the compressed regions and the electrostatic binding force is largest in the convex part. For coassembled bottlebrushes, the induced persistence length is a nonmonotonic function of the polymer concentration: For low polymer concentrations, the stiffening grows quadratically with coverage; for semidilute polymer concentrations, the brush chains retract and regain their Gaussian size. When doing so, they lose their induced persistence length contribution. Our results correlate well with observed physical characteristics of electrostatically driven coassembled DNA-bioengineered protein-polymer bottlebrushes.

Self-assembly of coordination polymers of Pr(III), Nd(III), Tb(III), Dy(III) and Ho(III) with 5-hydroxyisophthalic acid and adipic acid: Syntheses, structures, porosity, luminescence and magnetic properties

NASA Astrophysics Data System (ADS)

Kariem, Mukaddus; Yawer, Mohd; Kumar, Manesh; Nawaz Sheikh, Haq; Sood, Puneet; Kolekar, Sanjay S.

2017-11-01

Five novel coordination polymers (CPs) with the formula [Ln (hip) (adip)0.5(H2O)2]n. nH2O [Ln = Pr (1), Nd (2), Tb (3), Dy (4) and Ho (5)] were synthesized by self-organization of lanthanide salts with rigid [5-hydroxyisophthalic acid (H2hip)] and flexible [adipic acid (H2adip)] linkers under solvothermal condition. X-ray diffraction revealed data that all five CPs 1-5 are isostructural and crystallizes in monoclinic C2/c space group. Coordination polymers 1-5 exhibit 1D linear ladder shaped extension with the linkage of lanthanide carboxylate chains having the backbone of H2hip and H2adip ligands. The 1D linear ladder chains get transformed into three dimensional (3D) supramolecular network via non-covalent interactions (π-π and H - bonding). The porosity study showed that 20.34 mL of N2 gets adsorbed per 1.0 g of sample at 1 atm pressure. The CP 3 (Tb) and 4 (Dy) emit strong ligand sensitized characteristic f-f luminescence emission. The CPs 3 and 4 exhibit weak ferromagnetic interactions at lower temperatures.

Astronaut mass measurement using linear acceleration method and the effect of body non-rigidity

NASA Astrophysics Data System (ADS)

Yan, Hui; Li, LuMing; Hu, ChunHua; Chen, Hao; Hao, HongWei

2011-04-01

Astronaut's body mass is an essential factor of health monitoring in space. The latest mass measurement device for the International Space Station (ISS) has employed a linear acceleration method. The principle of this method is that the device generates a constant pulling force, and the astronaut is accelerated on a parallelogram motion guide which rotates at a large radius to achieve a nearly linear trajectory. The acceleration is calculated by regression analysis of the displacement versus time trajectory and the body mass is calculated by using the formula m= F/ a. However, in actual flight, the device is instable that the deviation between runs could be 6-7 kg. This paper considers the body non-rigidity as the major cause of error and instability and analyzes the effects of body non-rigidity from different aspects. Body non-rigidity makes the acceleration of the center of mass (C.M.) oscillate and fall behind the point where force is applied. Actual acceleration curves showed that the overall effect of body non-rigidity is an oscillation at about 7 Hz and a deviation of about 25%. To enhance body rigidity, better body restraints were introduced and a prototype based on linear acceleration method was built. Measurement experiment was carried out on ground on an air table. Three human subjects weighing 60-70 kg were measured. The average variance was 0.04 kg and the average measurement error was 0.4%. This study will provide reference for future development of China's own mass measurement device.

Modeling the interactions between a prosthetic socket, polyurethane liners and the residual limb in transtibial amputees using non-linear finite element analysis.

PubMed

Simpson, G; Fisher, C; Wright, D K

2001-01-01

Continuing earlier studies into the relationship between the residual limb, liner and socket in transtibial amputees, we describe a geometrically accurate non-linear model simulating the donning of a liner and then a socket. The socket is rigid and rectified and the liner is a polyurethane geltype which is accurately described using non-linear (Mooney-Rivlin) material properties. The soft tissue of the residual limb is modelled as homogeneous, non-linear and hyperelastic and the bone structure within the residual limb is taken as rigid. The work gives an indication of how the stress induced by the process of donning the rigid socket is redistributed by the liner. Ultimately we hope to understand how the liner design might be modified to reduce discomfort. The ANSYS finite element code, version 5.6 is used.

An improved understanding of the natural resonances of moonpools contained within floating rigid-bodies: Theory and application to oscillating water column devices

DOE PAGES

Bull, Diana L.

2015-09-23

The fundamental interactions between waves, a floating rigid-body, and a moonpool that is selectively open to atmosphere or enclosed to purposefully induce pressure fluctuations are investigated. The moonpool hydrodynamic characteristics and the hydrodynamic coupling to the rigid-body are derived implicitly through reciprocity relations on an array of field points. By modeling the free surface of the moonpool in this manner, an explicit hydrodynamic coupling term is included in the equations of motion. This coupling results in the migration of the moonpool's natural resonance frequency from the piston frequency to a new frequency when enclosed in a floating rigid-body. Two geometriesmore » that highlight distinct aspects of marine vessels and oscillating water column (OWC) renewable energy devices are analyzed to reveal the coupled natural resonance migration. The power performance of these two OWCs in regular waves is also investigated. The air chamber is enclosed and a three-dimensional, linear, frequency domain performance model that links the rigid-body to the moonpool through a linear resistive control strategy is detailed. Furthermore, an analytic expression for the optimal linear resistive control values in regular waves is presented.« less

An improved understanding of the natural resonances of moonpools contained within floating rigid-bodies: Theory and application to oscillating water column devices

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

Bull, Diana L.

The fundamental interactions between waves, a floating rigid-body, and a moonpool that is selectively open to atmosphere or enclosed to purposefully induce pressure fluctuations are investigated. The moonpool hydrodynamic characteristics and the hydrodynamic coupling to the rigid-body are derived implicitly through reciprocity relations on an array of field points. By modeling the free surface of the moonpool in this manner, an explicit hydrodynamic coupling term is included in the equations of motion. This coupling results in the migration of the moonpool's natural resonance frequency from the piston frequency to a new frequency when enclosed in a floating rigid-body. Two geometriesmore » that highlight distinct aspects of marine vessels and oscillating water column (OWC) renewable energy devices are analyzed to reveal the coupled natural resonance migration. The power performance of these two OWCs in regular waves is also investigated. The air chamber is enclosed and a three-dimensional, linear, frequency domain performance model that links the rigid-body to the moonpool through a linear resistive control strategy is detailed. Furthermore, an analytic expression for the optimal linear resistive control values in regular waves is presented.« less

The tracer diffusion coefficient of soft nanoparticles in a linear polymer matrix

DOE PAGES

Imel, Adam E.; Rostom, Sahar; Holley, Wade; ...

2017-03-09

The diffusion properties of nanoparticles in polymer nanocomposites are largely unknown and are often difficult to determine experimentally. To address this shortcoming, we have developed a novel method to determine the tracer diffusion coefficient of soft polystyrene nanoparticles in a linear polystyrene matrix. Monitoring the interdiffusion of soft nanoparticles into a linear polystyrene matrix provides the mutual diffusion coefficient of this system, from which the tracer diffusion coefficient of the soft nanoparticle can be determined using the slow mode theory. Utilizing this protocol, the role of nanoparticle molecular weight and rigidity on its tracer diffusion coefficient is provided. These resultsmore » demonstrate that the diffusive behavior of these soft nanoparticles differ from that of star polymers, which is surprising since our recent studies suggest that the nanoparticle interacts with a linear polymer similarly to that of a star polymer. It appears that these deformable nanoparticles mostly closely mimic the diffusive behavior of fractal macromolecular architectures or microgels, where the transport of the nanoparticle relies on the cooperative motion of neighboring linear chains. Finally, the less cross-linked, and thus more deformable, nanoparticles diffuse faster than the more highly crosslinked nanoparticles, presumably because the increased deformability allows the nanoparticle to distort and fit into available space.« less

Users manual for linear Time-Varying Helicopter Simulation (Program TVHIS)

NASA Technical Reports Server (NTRS)

Burns, M. R.

1979-01-01

A linear time-varying helicopter simulation program (TVHIS) is described. The program is designed as a realistic yet efficient helicopter simulation. It is based on a linear time-varying helicopter model which includes rotor, actuator, and sensor models, as well as a simulation of flight computer logic. The TVHIS can generate a mean trajectory simulation along a nominal trajectory, or propagate covariance of helicopter states, including rigid-body, turbulence, control command, controller states, and rigid-body state estimates.

Hydrodynamics of suspensions of passive and active rigid particles: a rigid multiblob approach

DOE PAGES

Usabiaga, Florencio Balboa; Kallemov, Bakytzhan; Delmotte, Blaise; ...

2016-01-12

We develop a rigid multiblob method for numerically solving the mobility problem for suspensions of passive and active rigid particles of complex shape in Stokes flow in unconfined, partially confined, and fully confined geometries. As in a number of existing methods, we discretize rigid bodies using a collection of minimally resolved spherical blobs constrained to move as a rigid body, to arrive at a potentially large linear system of equations for the unknown Lagrange multipliers and rigid-body motions. Here we develop a block-diagonal preconditioner for this linear system and show that a standard Krylov solver converges in a modest numbermore » of iterations that is essentially independent of the number of particles. Key to the efficiency of the method is a technique for fast computation of the product of the blob-blob mobility matrix and a vector. For unbounded suspensions, we rely on existing analytical expressions for the Rotne-Prager-Yamakawa tensor combined with a fast multipole method (FMM) to obtain linear scaling in the number of particles. For suspensions sedimented against a single no-slip boundary, we use a direct summation on a graphical processing unit (GPU), which gives quadratic asymptotic scaling with the number of particles. For fully confined domains, such as periodic suspensions or suspensions confined in slit and square channels, we extend a recently developed rigid-body immersed boundary method by B. Kallemov, A. P. S. Bhalla, B. E. Griffith, and A. Donev (Commun. Appl. Math. Comput. Sci. 11 (2016), no. 1, 79-141) to suspensions of freely moving passive or active rigid particles at zero Reynolds number. We demonstrate that the iterative solver for the coupled fluid and rigid-body equations converges in a bounded number of iterations regardless of the system size. In our approach, each iteration only requires a few cycles of a geometric multigrid solver for the Poisson equation, and an application of the block-diagonal preconditioner, leading to linear scaling with the number of particles. We optimize a number of parameters in the iterative solvers and apply our method to a variety of benchmark problems to carefully assess the accuracy of the rigid multiblob approach as a function of the resolution. We also model the dynamics of colloidal particles studied in recent experiments, such as passive boomerangs in a slit channel, as well as a pair of non-Brownian active nanorods sedimented against a wall.« less

Self-assembly and glass-formation in a lattice model of telechelic polymer melts: Influence of stiffness of the sticky bonds

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

2016-06-07

Telechelic polymers are chain macromolecules that may self-assemble through the association of their two mono-functional end groups (called “stickers”). A deep understanding of the relation between microscopic molecular details and the macroscopic physical properties of telechelic polymers is important in guiding the rational design of telechelic polymer materials with desired properties. The lattice cluster theory (LCT) for strongly interacting, self-assembling telechelic polymers provides a theoretical tool that enables establishing the connections between important microscopic molecular details of self-assembling polymers and their bulk thermodynamics. The original LCT for self-assembly of telechelic polymers considers a model of fully flexible linear chains [J.more » Dudowicz and K. F. Freed, J. Chem. Phys. 136, 064902 (2012)], while our recent work introduces a significant improvement to the LCT by including a description of chain semiflexibility for the bonds within each individual telechelic chain [W.-S. Xu and K. F. Freed, J. Chem. Phys. 143, 024901 (2015)], but the physically associative (or called “sticky”) bonds between the ends of the telechelics are left as fully flexible. Motivated by the ubiquitous presence of steric constraints on the association of real telechelic polymers that impart an additional degree of bond stiffness (or rigidity), the present paper further extends the LCT to permit the sticky bonds to be semiflexible but to have a stiffness differing from that within each telechelic chain. An analytical expression for the Helmholtz free energy is provided for this model of linear telechelic polymer melts, and illustrative calculations demonstrate the significant influence of the stiffness of the sticky bonds on the self-assembly and thermodynamics of telechelic polymers. A brief discussion is also provided for the impact of self-assembly on glass-formation by combining the LCT description for this extended model of telechelic polymers with the Adam-Gibbs relation between the structural relaxation time and the configurational entropy.« less

Newtonian Analysis of a Folded Chain Drop

ERIC Educational Resources Information Center

Mungan, Carl E.

2018-01-01

Consider a chain of length L that hangs in a U shape with end A fixed to a rigid support and free end E released from rest starting from the same initial height (call it y = 0) as A. Figure 1 sketches the chain after end E has fallen a distance y. Points O and A are assumed to be close enough to each other and the chain flexible enough that the…

Contact mechanics for coated spheres that includes the transition from weak to strong adhesion

DOE PAGES

Reedy, Earl David

2007-09-01

Recently published results for a rigid spherical indenter contacting a thin, linear elastic coating on a rigid planar substrate have been extended to include the case of two contacting spheres, where each sphere is rigid and coated with a thin, linear elastic material. This is done by using an appropriately chosen effective radius and coating modulus. Finally, the earlier work has also been extended to provide analytical results that span the transition between the previously derived Derjaguin–Müller–Toporov (DMT)-like (work of adhesion/coating-modulus ratio is small) and Johnson–Kendall–Roberts (JKR)-like (work of adhesion/coating-modulus ratio is large) limits.

Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility.

PubMed

Drake, Justin A; Harris, Robert C; Pettitt, B Montgomery

2016-08-23

Oligoglycine is a backbone mimic for all proteins and is prevalent in the sequences of intrinsically disordered proteins. We have computed the absolute chemical potential of glycine oligomers at infinite dilution by simulation with the CHARMM36 and Amber ff12SB force fields. We performed a thermodynamic decomposition of the solvation free energy (ΔG(sol)) of Gly2-5 into enthalpic (ΔH(sol)) and entropic (ΔS(sol)) components as well as their van der Waals and electrostatic contributions. Gly2-5 was either constrained to a rigid/extended conformation or allowed to be completely flexible during simulations to assess the effects of flexibility on these thermodynamic quantities. For both rigid and flexible oligoglycine models, the decrease in ΔG(sol) with chain length is enthalpically driven with only weak entropic compensation. However, the apparent rates of decrease of ΔG(sol), ΔH(sol), ΔS(sol), and their elec and vdw components differ for the rigid and flexible models. Thus, we find solvation entropy does not drive aggregation for this system and may not explain the collapse of long oligoglycines. Additionally, both force fields yield very similar thermodynamic scaling relationships with respect to chain length despite both force fields generating different conformational ensembles of various oligoglycine chains. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Adaptive binding and selection of compressed 1,ω-diammonium-alkanes via molecular encapsulation in water† †Electronic supplementary information (ESI) available. CCDC 1040388–1040390. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4sc03945a Click here for additional data file. Click here for additional data file.

PubMed Central

Dumitrescu, Dan; Legrand, Yves-Marie; Petit, Eddy; van der Lee, Arie

2015-01-01

Guest molecules confined inside hollow molecular assemblies and thus protected from their environment can show unexpected structural behavior or special reactivity compared to their behavior in a bulk, unprotected environment. A special case is the coiling behavior of variable-length alkane chains in rigid hydrogen-bonded molecular cages. It has been found before that coiling may occur in such circumstances, but no experimental evidence concerning the exact conformation of the chains has yet been presented. We reveal in this study the self-assembly of a molecular cage in water and the crystalline state from three distinct components in which linear 1,ω-diammonium-alkanes chains are confined with different degrees of compression. The exact coiling behavior is determined from atomic resolution X-ray diffraction showing crenel-like conformations in the compressed state. Chemical selection can be obtained from mixtures of alkane chains via the encapsulation of kinetically stable conformations observed during the encapsulation of pure components. Moreover, it was found that uncompressed and compressed chains can be competitively trapped inside the capsule. These findings may provide insight in areas to a better understanding of biological processes, such as the fatty acid metabolism. PMID:29142675

Liquid crystalline phase behavior in systems of hard-sphere chains

NASA Astrophysics Data System (ADS)

Williamson, Dave C.; Jackson, George

1998-06-01

A study of the liquid crystalline phase transitions in a system of hard-sphere chains is presented. The chains comprise m=7 tangentially bonded hard-sphere segments in a linear conformation (LHSC). The isothermal-isobaric Monte Carlo simulation technique is used to obtain the equation of state of the system both by compressing the isotropic (I) liquid and by expanding the solid (K). As well as the usual isotropic and solid phases, nematic and smectic-A liquid crystalline states are seen. A large degree of hysteresis is found in the neighborhood of the I-N transition. The results for the rigid LHSC system were compared with existing data for the corresponding semiflexible hard-sphere chains (FHSC): the flexibility has a large destabilizing effect on the nematic phase and consequently it postpones the I-N transition. The results of the simulations are also compared with rescaled Onsager theories for the I-N transition. It is rather surprising to find that the Parsons approach, which has been so successful for other hard-core models such as spherocylinders and ellipsoids, gives very poor results. The related approach of Vega and Lago gives a good description of the I-N phase transition. The procedure of Vega and Lago, as with all two-body resummations of the Onsager theory, only gives a qualitative description of the nematic order.

Electrostatic bending response of a charged helix

NASA Astrophysics Data System (ADS)

Zampetaki, A. V.; Stockhofe, J.; Schmelcher, P.

2018-04-01

We explore the electrostatic bending response of a chain of charged particles confined on a finite helical filament. We analyze how the energy difference Δ E between the bent and the unbent helical chain scales with the length of the helical segment and the radius of curvature and identify features that are not captured by the standard notion of the bending rigidity, normally used as a measure of bending tendency in the linear response regime. Using Δ E to characterize the bending response of the helical chain we identify two regimes with qualitatively different bending behaviors for the ground state configuration: the regime of small and the regime of large radius-to-pitch ratio, respectively. Within the former regime, Δ E changes smoothly with the variation of the system parameters. Of particular interest are its oscillations with the number of charged particles encountered for commensurate fillings which yield length-dependent oscillations in the preferred bending direction of the helical chain. We show that the origin of these oscillations is the nonuniformity of the charge distribution caused by the long-range character of the Coulomb interactions and the finite length of the helix. In the second regime of large values of the radius-to-pitch ratio, sudden changes in the ground state structure of the charges occur as the system parameters vary, leading to complex and discontinuous variations in the ground state bending response Δ E .

New Factorization Techniques and Parallel (log N) Algorithms for Forward Dynamics Solution of Single Closed-Chain Robot Manipulators

NASA Technical Reports Server (NTRS)

Fijany, Amir

1993-01-01

In this paper parallel 0(log N) algorithms for dynamic simulation of single closed-chain rigid multibody system as specialized to the case of a robot manipulatoar in contact with the environment are developed.

SRS Computer Animation and Drive Train System

NASA Technical Reports Server (NTRS)

Arthun, Daniel; Schachner, Christian

2001-01-01

The spinning rocket simulator (SRS) is an ongoing project at Oral Roberts University. The goal of the SRS is to gather crucial data concerning a spinning rocket under thrust for the purpose of analysis and correction of the coning motion experienced by this type of spacecraft maneuver. The computer animation simulates a virtual, scale model of the component of the SRS that represents the spacecraft itself. This component is known as the (VSM), or virtual spacecraft model. During actual physical simulation, this component of the SRS will experience a coning. The goal of the animation is to cone the VSM within that range to accurately represent the motion of the actual simulator. The drive system of the SRS is the apparatus that turns the actual simulator. It consists of a drive motor, motor mount and chain to power the simulator into motion. The motor mount is adjustable and rigid for high torque application. A digital stepper motor controller actuates the main drive motor for linear acceleration. The chain transfers power from the motor to the simulator via sprockets on both ends.

Effect of tethering on the surface dynamics of a thin polymer melt layer

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

Uğur, Gökçe; Akgun, Bulent; Jiang, Zhang

The surface height fluctuations of a layer of low molecular weight (2.2k) untethered perdeuterated polystyrene (dPS) chains adjacent to a densely grafted polystyrene brush are slowed dramatically. Due to the interpenetration of the brush with the layer of “untethered chains” a hydrodynamic continuum theory can only describe the fluctuations when the effective thickness of the film is taken to be that which remains above the swollen brush. Furthermore, the portion of the film of initially untethered chains that interpenetrates with the brush becomes so viscous as to effectively play the role of a rigid substrate. They provide a route formore » tailoring polymer layer surface properties such as wetting, adhesion and friction, since these hybrid samples contain a covalently tethered layer at the bottom, does not readily dewet, and are more robust than thin layers of untethered short chains on rigid substrates.« less

Effect of tethering on the surface dynamics of a thin polymer melt layer

DOE PAGES

Uğur, Gökçe; Akgun, Bulent; Jiang, Zhang; ...

2016-05-13

The surface height fluctuations of a layer of low molecular weight (2.2k) untethered perdeuterated polystyrene (dPS) chains adjacent to a densely grafted polystyrene brush are slowed dramatically. Due to the interpenetration of the brush with the layer of “untethered chains” a hydrodynamic continuum theory can only describe the fluctuations when the effective thickness of the film is taken to be that which remains above the swollen brush. Furthermore, the portion of the film of initially untethered chains that interpenetrates with the brush becomes so viscous as to effectively play the role of a rigid substrate. They provide a route formore » tailoring polymer layer surface properties such as wetting, adhesion and friction, since these hybrid samples contain a covalently tethered layer at the bottom, does not readily dewet, and are more robust than thin layers of untethered short chains on rigid substrates.« less

Conformational rigidity in a lattice model of proteins.

PubMed

Collet, Olivier

2003-06-01

It is shown in this paper that some simulations of protein folding in lattice models, which use an incorrect implementation of the Monte Carlo algorithm, do not converge towards thermal equilibrium. I developed a rigorous treatment for protein folding simulation on a lattice model relying on the introduction of a parameter standing for the rigidity of the conformations. Its properties are discussed and its role during the folding process is elucidated. The calculation of thermal properties of small chains living on a two-dimensional lattice is performed and a Bortz-Kalos-Lebowitz scheme is implemented in the presented method in order to study kinetics of chains at very low temperature. The coefficients of the Arrhenius law obtained with this algorithm are found to be in excellent agreement with the value of the main potential barrier of the system. Finally, a scenario of the mechanisms, including the rigidity parameters, that guide a protein towards its native structure, at medium temperature, is given.

Synthesis of Lipid Based Polyols from 1-butene Metathesized Palm Oil for Use in Polyurethane Foam Applications

NASA Astrophysics Data System (ADS)

Sasidharan Pillai, Prasanth Kumar

This thesis explores the use of 1-butene cross metathesized palm oil (PMTAG) as a feedstock for preparation of polyols which can be used to prepare rigid and flexible polyurethane foams. PMTAG is advantageous over its precursor feedstock, palm oil, for synthesizing polyols, especially for the preparation of rigid foams, because of the reduction of dangling chain effects associated with the omega unsaturated fatty acids. 1-butene cross metathesis results in shortening of the unsaturated fatty acid moieties, with approximately half of the unsaturated fatty acids assuming terminal double bonds. It was shown that the associated terminal OH groups introduced through epoxidation and hydroxylation result in rigid foams with a compressive strength approximately 2.5 times higher than that of rigid foams from palm and soybean oil polyols. Up to 1.5 times improvement in the compressive strength value of the rigid foams from the PMTAG polyol was further obtained following dry and/or solvent assisted fractionation of PMTAG in order to reduce the dangling chain effects associated with the saturated components of the PMTAG. Flexible foams with excellent recovery was achieved from the polyols of PMTAG and the high olein fraction of PMTAG indicating that these bio-derived polyurethane foams may be suitable for flexible foam applications. PMTAG polyols with controlled OH values prepared via an optimized green solvent free synthetic strategy provided flexible foams with lower compressive strength and higher recovery; i.e., better flexible foam potential compared to the PMTAG derived foams with non-controlled OH values. Overall, this study has revealed that the dangling chain issues of vegetable oils can be addressed in part using appropriate chemical and physical modification techniques such as cross metathesis and fractionation, respectively. In fact, the rigidity and the compressive strength of the polyurethane foams were in very close agreement with the percentage of terminal hydroxyl and OH value of the polyol. The results obtained from the study can be used to convert PMTAG like materials into industrially valuable materials.

Untangleing the effects of chain rigidity on the structure and dynamics of strongly adsorbed polymer melts

DOE PAGES

Carrillo, Jan-Michael Y.; Cheng, Shiwang; Kumar, Rajeev; ...

2015-06-11

Here, we present a detailed analysis of coarse-grained molecular dynamics simulations of semiflexible polymer melts in contact with a strongly adsorbing substrate. We have characterized the segments in the interfacial layer by counting the number of trains, loops, tails and unadsorbed segments. For more rigid chains, a tail and an adsorbed segment (a train) dominate while loops are more prevalent in more flexible chains. The tails exhibit a non-uniformly stretched conformation akin to the polydispersed pseudobrush envisioned by Guiselin. To probe the dynamics of the segments we computed the layer z-resolved intermediate coherent collective dynamics structure factor, S(q, t, z),more » mean-square displacement of segments, and the 2nd Legendre polynomial of the time-autocorrelation of unit bond vectors, 2[n i(t,z)•n i(0,z)]>. Our results show that segmental dynamics is slower for stiffer chains and there is a strong correlation between the structure and dynamics in the interfacial layer. There is no glassy layer, and the slowing down in dynamics of stiffer chains in the adsorbed region can be attributed to the densification and the more persistent layering of segments.« less

Supramolecular structure formation of Langmuir-Blodgett films of comblike precursor and polyimide

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

Goloudina, S. I., E-mail: goloudina@mail.ru; Luchinin, V. V.; Rozanov, V. V.

2013-03-15

The surface structure of Langmuir-Blodgett films of a comblike polyimide precursor-a rigid-chain polyamic acid alkylamine salt bearing multichains of tertiary amine-and films of the corresponding polyimide were studied by atomic force microscopy (AFM). An analysis of the images of the surface of three-layer films revealed a domain structure. It was found that the Langmuir-Blodgett film formation of the precursor occurs as a result of the layer-by-layer deposition of two-dimensional domains (composed of polyamic acid salt molecules on the water surface) onto a substrate. The formation of domains in a monolayer is associated with the chemical structure of the precursor, tomore » be more precise, with the rigidity of the main chain and the presence of closely spaced aliphatic side chains in the polymer chain, whose total cross-section area is close to the surface area of the projection onto the plane of the repeating unit of the main chain. Polyimide films inherit the domain structure of the precursor films; the inhomogeneity of the film thickness substantially decreases, whereas the domain size and character of their distribution in the film remain unchanged.« less

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

Modular design attitude control system

NASA Technical Reports Server (NTRS)

Chichester, F. D.

1984-01-01

A sequence of single axismodels and a series of reduced state linear observers of minimum order are used to reconstruct inaccessible variables pertaining to the modular attitude control of a rigid body flexible suspension model of a flexible spacecraft. The single axis models consist of two, three, four, and five rigid bodies, each interconnected by a flexible shaft passing through the mass centers of the bodies. Modal damping is added to each model. Reduced state linear observers are developed for synthesizing the inaccessible modal state variables for each modal model.

Investigation of Liquid Sloshing in Spin-Stabilized Satellites.

DTIC Science & Technology

1993-01-31

deformation of the spinning structure in addition to the rigid body motion . A Lagrangian approach was used to develop the equations of motion which include...nonlinear relationships for the unknown rigid body motions and linear terms for the relatively small elastic deformations of the members. Appendix F...the rigid body motion of the test assembly. A pendulum analogy was used to model the sloshing liquid in that early program. Several numerical

Weak completions, bornologies and rigid cohomology

NASA Astrophysics Data System (ADS)

Cortiñas, Guillermo; Cuntz, Joachim; Meyer, Ralf; Tamme, Georg

2018-07-01

Let V be a complete discrete valuation ring with residue field k of positive characteristic and with fraction field K of characteristic 0. We clarify the analysis behind the Monsky-Washnitzer completion of a commutative V-algebra using completions of bornological V-algebras. This leads us to a functorial chain complex for a finitely generated commutative algebra over the residue field k that computes its rigid cohomology in the sense of Berthelot.

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

NASA Astrophysics Data System (ADS)

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

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

General rigid motion correction for computed tomography imaging based on locally linear embedding

NASA Astrophysics Data System (ADS)

Chen, Mianyi; He, Peng; Feng, Peng; Liu, Baodong; Yang, Qingsong; Wei, Biao; Wang, Ge

2018-02-01

The patient motion can damage the quality of computed tomography images, which are typically acquired in cone-beam geometry. The rigid patient motion is characterized by six geometric parameters and are more challenging to correct than in fan-beam geometry. We extend our previous rigid patient motion correction method based on the principle of locally linear embedding (LLE) from fan-beam to cone-beam geometry and accelerate the computational procedure with the graphics processing unit (GPU)-based all scale tomographic reconstruction Antwerp toolbox. The major merit of our method is that we need neither fiducial markers nor motion-tracking devices. The numerical and experimental studies show that the LLE-based patient motion correction is capable of calibrating the six parameters of the patient motion simultaneously, reducing patient motion artifacts significantly.

The effect of chain rigidity on the interfacial layer thickness and dynamics of polymer nanocomposites

NASA Astrophysics Data System (ADS)

Cheng, Shiwang; Carrillo, Jan-Michael Y.; Carroll, Bobby; Sumpter, Bobby G.; Sokolov, Alexei P.

There are growing experimental evidences showing the existence of an interfacial layer that has a finite thickness with slowing down dynamics in polymer nanocomposites (PNCs). Moreover, it is believed that the interfacial layer plays a significant role on various macroscopic properties of PNCs. A thicker interfacial layer is found to have more pronounced effect on the macroscopic properties such as the mechanical enhancement. However, it is not clear what molecular parameter controls the interfacial layer thickness. Inspired by our recent computer simulations that showed the chain rigidity correlated well with the interfacial layer thickness, we performed systematic experimental studies on different polymer nanocomposites by varying the chain stiffness. Combining small-angle X-ray scattering, broadband dielectric spectroscopy and temperature modulated differential scanning calorimetry, we find a good correlation between the polymer Kuhn length and the thickness of the interfacial layer, confirming the earlier computer simulations results. Our findings provide a direct guidance for the design of new PNCs with desired properties.

Observation of hairpin defects in a nematic main-chain polyester

NASA Astrophysics Data System (ADS)

Li, M. H.; Brûlet, A.; Davidson, P.; Keller, P.; Cotton, J. P.

1993-04-01

The conformation of a main-chain liquid crystalline polyester in its oriented nematic phase has been determined by small-angle neutron scattering. The data are fitted by a model of rigid cylinder with orientational fluctuations. For a low degree of polymerization (~9) the chain is almost completely elongated in the direction of the nematic field. For a polymer 3 times longer, the existence of two hairpins is shown at high temperature; this number decreases with decreasing temperature.

How does symmetry impact the flexibility of proteins?

PubMed

Schulze, Bernd; Sljoka, Adnan; Whiteley, Walter

2014-02-13

It is well known that (i) the flexibility and rigidity of proteins are central to their function, (ii) a number of oligomers with several copies of individual protein chains assemble with symmetry in the native state and (iii) added symmetry sometimes leads to added flexibility in structures. We observe that the most common symmetry classes of protein oligomers are also the symmetry classes that lead to increased flexibility in certain three-dimensional structures-and investigate the possible significance of this coincidence. This builds on the well-developed theory of generic rigidity of body-bar frameworks, which permits an analysis of the rigidity and flexibility of molecular structures such as proteins via fast combinatorial algorithms. In particular, we outline some very simple counting rules and possible algorithmic extensions that allow us to predict continuous symmetry-preserving motions in body-bar frameworks that possess non-trivial point-group symmetry. For simplicity, we focus on dimers, which typically assemble with twofold rotational axes, and often have allosteric function that requires motions to link distant sites on the two protein chains.

How does symmetry impact the flexibility of proteins?

PubMed Central

Schulze, Bernd; Sljoka, Adnan; Whiteley, Walter

2014-01-01

It is well known that (i) the flexibility and rigidity of proteins are central to their function, (ii) a number of oligomers with several copies of individual protein chains assemble with symmetry in the native state and (iii) added symmetry sometimes leads to added flexibility in structures. We observe that the most common symmetry classes of protein oligomers are also the symmetry classes that lead to increased flexibility in certain three-dimensional structures—and investigate the possible significance of this coincidence. This builds on the well-developed theory of generic rigidity of body–bar frameworks, which permits an analysis of the rigidity and flexibility of molecular structures such as proteins via fast combinatorial algorithms. In particular, we outline some very simple counting rules and possible algorithmic extensions that allow us to predict continuous symmetry-preserving motions in body–bar frameworks that possess non-trivial point-group symmetry. For simplicity, we focus on dimers, which typically assemble with twofold rotational axes, and often have allosteric function that requires motions to link distant sites on the two protein chains. PMID:24379431

Supramolecular Control over the Interparticle Distance in Gold Nanoparticle Arrays by Cyclodextrin Polyrotaxanes

PubMed Central

Paulo Coelho, Joao; Osío Barcina, José; Aicart, Emilio; Tardajos, Gloria; Cruz-Gil, Pablo; Salgado, Cástor; Díaz-Núñez, Pablo

2018-01-01

Amphiphilic nonionic ligands, synthesized with a fixed hydrophobic moiety formed by a thiolated alkyl chain and an aromatic ring, and with a hydrophilic tail composed of a variable number of oxyethylene units, were used to functionalize spherical gold nanoparticles (AuNPs) in water. Steady-state and time-resolved fluorescence measurements of the AuNPs in the presence of α-cyclodextrin (α-CD) revealed the formation of supramolecular complexes between the ligand and macrocycle at the surface of the nanocrystals. The addition of α-CD induced the formation of inclusion complexes with a high apparent binding constant that decreased with the increasing oxyethylene chain length. The formation of polyrotaxanes at the surface of AuNPs, in which many α-CDs are trapped as hosts on the long and linear ligands, was demonstrated by the formation of large and homogeneous arrays of self-assembled AuNPs with hexagonal close packing, where the interparticle distance increased with the length of the oxyethylene chain. The estimated number of α-CDs per polyrotaxane suggests a high rigidization of the ligand upon complexation, allowing for nearly perfect control of the interparticle distance in the arrays. This degree of supramolecular control was extended to arrays formed by AuNPs stabilized with polyethylene glycol and even to binary arrays. Electromagnetic simulations showed that the enhancement and distribution of the electric field can be finely controlled in these plasmonic arrays. PMID:29547539

Hybrid photoluminescent materials containing a benzobisthiazole core for liquid crystal and gel applications.

PubMed

Díaz, E; Elgueta, E; Sanchez, S A; Barberá, J; Vergara, J; Parra, M; Dahrouch, M

2017-03-01

Tetra- and hexacatenar amide compounds containing a linear centrosymmetric benzobisthiazole core were synthesized with good yields. These compounds were characterized and their structures confirmed by elemental analysis, and FT-IR, Maldi mass and NMR spectroscopy. All compounds exhibited excellent thermal stability up to 330 °C. The tetracatenar series containing a double substitution in the meta positions did not show mesomorphic behaviour, whereas the hexacatenar and tetracatenar series having a double substitution in the meta and para positions showed liquid crystal properties with optical textures typical of columnar mesophases corroborated by POM analysis. The mesomorphic properties were dependent on the length, number and position of alkoxy chains attached at the end of the rigid core. XRD studies of the hexacatenar series showed the hexagonal columnar structure of the mesophases. Photoluminescence properties in solution were observed in the visible region, with good quantum yields. In the solid state, these compounds behave as blue emitters and they are able to change colour with acid or base addition. The hexacatenar benzobisthiazole compound with an alkoxy chain of 14 carbons presented properties of a supergelator in chloroform, leading to the formation of a fluorescent organogel material with fluorescence emission in the blue region.

Political conservatism, rigidity, and dogmatism in American foreign policy officials: the 1966 Mennis data.

PubMed

Kemmelmeier, Markus

2007-01-01

Researchers have established a relationship between political orientation and cognitive styles (A. Chirumbolo, 2002; J. T. Jost, J. Glaser, A. W. Kruglanski, & F. Sulloway, 2003a, 2003b; M. Kemmelmeier, 1997). In this article, the author examined whether this finding is true in the political elite, whether the relationship is linear or curvilinear, and whether interest in politics moderates the relationship between political orientation and cognitive styles. He used a 1966 sample of American foreign policy officials (N = 95) to examine the relationship between self-described conservatism and party identification and individual differences in rigidity and dogmatism. Rigidity was related to self-described conservatism, but this relationship was only significant among participants high in political interest, whereas dogmatism was unconditionally related to party identification. All relationships were linear and did not contain a curvilinear component.

Chiropractic biophysics technique: a linear algebra approach to posture in chiropractic.

PubMed

Harrison, D D; Janik, T J; Harrison, G R; Troyanovich, S; Harrison, D E; Harrison, S O

1996-10-01

This paper discusses linear algebra as applied to human posture in chiropractic, specifically chiropractic biophysics technique (CBP). Rotations, reflections and translations are geometric functions studied in vector spaces in linear algebra. These mathematical functions are termed rigid body transformations and are applied to segmental spinal movement in the literature. Review of the literature indicates that these linear algebra concepts have been used to describe vertebral motion. However, these rigid body movers are presented here as applying to the global postural movements of the head, thoracic cage and pelvis. The unique inverse functions of rotations, reflections and translations provide a theoretical basis for making postural corrections in neutral static resting posture. Chiropractic biophysics technique (CBP) uses these concepts in examination procedures, manual spinal manipulation, instrument assisted spinal manipulation, postural exercises, extension traction and clinical outcome measures.

Structure of rigid polymers confined to nanoparticles: Molecular dynamics simulations insight

DOE PAGES

Maskey, Sabina; Lane, J. Matthew D.; Perahia, Dvora; ...

2016-02-04

Nanoparticles (NPs) grafted with organic layers form hybrids able to retain their unique properties through integration into the mesoscopic scale. The organic layer structure and response often determine the functionality of the hybrids on the mesoscopic length scale. Using molecular dynamics (MD) simulations, we probe the conformation of luminescent rigid polymers, dialkyl poly(p-phenylene ethynylene)s (PPE), end-grafted onto a silica nanoparticle in different solvents as the molecular weights and polymer coverages are varied. We find that, in contrast to NP-grafted flexible polymers, the chains are fully extended independent of the solvent. In toluene and decane, which are good solvents, the graftedmore » PPEs chains assume a similar conformation to that observed in dilute solutions. In water, which is a poor solvent for the PPEs, the polymer chains form one large cluster but remain extended. The radial distribution of the chains around the core of the nanoparticle is homogeneous in good solvents, whereas in poor solvents clusters are formed independent of molecular weights and coverages. As a result, the clustering is distinctively different from the response of grafted flexible and semiflexible polymers.« less

A probabilistic model for detecting rigid domains in protein structures.

PubMed

Nguyen, Thach; Habeck, Michael

2016-09-01

Large-scale conformational changes in proteins are implicated in many important biological functions. These structural transitions can often be rationalized in terms of relative movements of rigid domains. There is a need for objective and automated methods that identify rigid domains in sets of protein structures showing alternative conformational states. We present a probabilistic model for detecting rigid-body movements in protein structures. Our model aims to approximate alternative conformational states by a few structural parts that are rigidly transformed under the action of a rotation and a translation. By using Bayesian inference and Markov chain Monte Carlo sampling, we estimate all parameters of the model, including a segmentation of the protein into rigid domains, the structures of the domains themselves, and the rigid transformations that generate the observed structures. We find that our Gibbs sampling algorithm can also estimate the optimal number of rigid domains with high efficiency and accuracy. We assess the power of our method on several thousand entries of the DynDom database and discuss applications to various complex biomolecular systems. The Python source code for protein ensemble analysis is available at: https://github.com/thachnguyen/motion_detection : mhabeck@gwdg.de. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Syntheses of some α-cyclic tripeptides as potential inhibitors for HMG-CoA Reductase.

PubMed

Chakraborty, Subrata; Lin, Shih-Hung; Shiuan, David; Tai, Dar-Fu

2015-08-01

α-Cyclic tripeptides (CtPs) are the most rigid members of the cyclic peptide family. However, due to their synthetic difficulty, biological activity has remained undisclosed. The incorporation of side-chain-protected natural amino acids into functional CtPs was performed to explore the potential biological functions. Several novel CtPs that consist of protected serine (S(Bn)) and/or glutamate (E(OBn)) were prepared from corresponding linear tripeptides by chemical synthesis. There is a strong possibility for CtPs that contain 3 phenyl groups to correlate with atorvastatin structure. The binding effects in human HMG-CoA reductase (hHMGR) activities were first evaluated by molecular docking. High docking scores were received with these CtPs for enzyme. Therefore, enzymatic assays were carried out and the compound cyclo(S(Bn))3 was indeed able to moderately inhibit hHMGR (IC50 = 110 μM).

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

NASA Technical Reports Server (NTRS)

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

1974-01-01

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

Sliding friction between polymer surfaces: A molecular interpretation

NASA Astrophysics Data System (ADS)

Allegra, Giuseppe; Raos, Guido

2006-04-01

For two contacting rigid bodies, the friction force F is proportional to the normal load and independent of the macroscopic contact area and relative velocity V (Amonton's law). With two mutually sliding polymer samples, the surface irregularities transmit deformation to the underlying material. Energy loss along the deformation cycles is responsible for the friction force, which now appears to depend strongly on V [see, e.g., N. Maeda et al., Science 297, 379 (2002)]. We base our theoretical interpretation on the assumption that polymer chains are mainly subjected to oscillatory "reptation" along their "tubes." At high deformation frequencies—i.e., with a large sliding velocity V—the internal viscosity due to the rotational energy barriers around chain bonds hinders intramolecular mobility. As a result, energy dissipation and the correlated friction force strongly diminish at large V. Derived from a linear differential equation for chain dynamics, our results are basically consistent with the experimental data by Maeda et al. [Science 297, 379 (2002)] on modified polystyrene. Although the bulk polymer is below Tg, we regard the first few chain layers below the surface to be in the liquid state. In particular, the observed maximum of F vs V is consistent with physically reasonable values of the molecular parameters. As a general result, the ratio F /V is a steadily decreasing function of V, tending to V-2 for large velocities. We evaluate a much smaller friction for a cross-linked polymer under the assumption that the junctions are effectively immobile, also in agreement with the experimental results of Maeda et al. [Science 297, 379 (2002)].

Precise Side-Chain Engineering of Thienylenevinylene-Benzotriazole-Based Conjugated Polymers with Coplanar Backbone for Organic Field Effect Transistors and CMOS-like Inverters.

PubMed

Lee, Min-Hye; Kim, Juhwan; Kang, Minji; Kim, Jihong; Kang, Boseok; Hwang, Hansu; Cho, Kilwon; Kim, Dong-Yu

2017-01-25

Two donor-acceptor (D-A) alternating conjugated polymers based on thienylenevinylene-benzotriazole (TV-BTz), PTV6B with a linear side chain and PTVEhB with a branched side chain, were synthesized and characterized for organic field effect transistors (OFETs) and complementary metal-oxide-semiconductor (CMOS)-like inverters. According to density functional theory (DFT), polymers based on TV-BTz exhibit a coplanar and rigid structure with no significant twists, which could cause to an increase in charge-carrier mobility in OFETs. Alternating alkyl side chains of the polymers impacted neither the band gap nor the energy level. However, it significantly affected the morphology and crystallinity when the polymer films were thermally annealed. To investigate the effect of thermal annealing on the morphology and crystallinity, we characterized the polymer films using atomic force microscopy (AFM) and 2D-grazing incidence X-ray diffraction (2D-GIWAXD). Fibrillary morphologies with larger domains and increased crystallinity were observed in the polymer films after thermal annealing. These polymers exhibited improved charge-carrier mobilities in annealed films at 200 °C and demonstrated optimal OFET device performance with p-type transport characteristics with charge-carrier mobilities of 1.51 cm 2 /(V s) (PTV6B) and 2.58 cm 2 /(V s) (PTVEhB). Furthermore, CMOS-like inorganic (ZnO)-organic (PTVEhB) hybrid bilayer inverter showed that the inverting voltage (V inv ) was positioned near the ideal switching point at half (1/2) of supplied voltage (V DD ) due to fairly balanced p- and n-channels.

On the monoaxial stabilization of a rigid body under vanishing restoring torque

NASA Astrophysics Data System (ADS)

Aleksandrov, A. Yu.; Aleksandrova, E. B.; Tikhonov, A. A.

2018-05-01

The problem of monoaxial stabilization of a rigid body is studied. It is assumed that a linear time-invariant dissipative torque and a time-varying restoring torque vanishing as time increases act on the body. Both the case of linear restoring torque and that of essentially nonlinear one are considered. With the aid of the decomposition method, conditions are obtained under which we can guarantee the asymptotic stability of an equilibrium position of the body despite the vanishing of the restoring torque. A numerical simulation is provided to demonstrate the effectiveness of our theoretical results.

On vibrational imperfection sensitivity of Augusti's model structure in the vicinity of a non-linear static state

NASA Technical Reports Server (NTRS)

Elishakoff, Isaac; Marcus, S.; Starnes, J. H., JR.

1998-01-01

In this paper we present a closed-form solution for vibrational imperfection sensitivity the effect of small imperfections on the vibrational frequencies of perturbed motion around the static equilibrium state of Augusti's model Structure (a rigid link, pinned at one end to a rigid foundation and supported at the other by a linear extensional spring that retains its horizontality, as the system deflects). We also treat a modified version of that model with attendant slightly different dynamics. It is demonstrated that the vibrational frequencies decreases as the initial imperfections increase.

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

Buoyancy prime mover

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

Everett, T.D.

1982-12-14

A buoyancy prime mover that converts the potential energy of a gas buoyant within a liquid into rotating mechanical energy comprises a plurality of rigid or collapsible buckets joined by one or more chains with rotatable sprockets and shafts to form a continuous loop so that when the buoyant gas is trapped within the buckets, the buckets rise through the liquid and rotate the chain and sprockets to generate power.

Hybrid lattice gas simulations of flow through porous media

NASA Astrophysics Data System (ADS)

Becklehimer, Jeffrey Lynn

1997-10-01

This study introduces a suite of models designed to investigate transport phenomena in simulated porous media such as rigid or quenched sediment and clay-like deformable environments. This is achieved by using a variety of techniques that are borrowed from the field of statistical physics. These techniques include percolation, lattice gas, and cellular automata. A percolation-based model is used to study a porous medium by using rods and chains of various shapes and sizes to model the porous media formed by sediments. This is further extended to model clay-like deformable media by interacting heavy sediment particles. An interacting lattice gas computer simulation model based on the Metropolis algorithm is used to study the transport properties of fluid particles and permeability of a porous sediment. Finally, a hybrid lattice gas model is introduced by combining the Metropolis Monte Carlo method with a direct simulation which involves the collision rules as in cellular automata. This model is then used to study shock propagation in a fluid filled porous medium. This study is then extended to study shock propagation through in a fluid filled elastic porous medium. Several interesting and new results were obtained. These results show that for rigid chain percolation the percolation threshold shows a dependence on the chain length of pc~ Lc-1/2 and the jamming coverage decreases with the chain length as Lc- 1/3. For the random SAW-like chains the percolation threshold decays with the chain length as Lc- 0.01 and the jamming coverage as Lc-1/3. The fluid flow model shows that permeability depends nonmonotonically on the concentration of the fluid. For some fluids at a fixed porosity, the permeability increases on increasing the bias until a certain value Bc above which it decreases. Also, it was found that a shock propagates in a drift-like fashion when in a rigid porous medium when the porosity is high; low porosity damps out the shock front very quickly. For a shock propagating in a clay-like porous medium an unusually super-fast power-law behavior is observed for the RMS displacements of the fluid and clay particles.

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

PubMed

Pergamenshchik, V M; Vozniak, A B

2017-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-01-01

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

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.

Homogenized rigid body and spring-mass (HRBSM) model for the pushover analysis of out-of-plane loaded unreinforced and FRP reinforced walls

NASA Astrophysics Data System (ADS)

Bertolesi, Elisa; Milani, Gabriele

2017-07-01

The present paper is devoted to the discussion of a series of unreinforced and FRP retrofitted panels analyzed adopting the Rigid Body and Spring-Mass (HRBSM) model developed by the authors. To this scope, a total of four out of plane loaded masonry walls tested up to failure are considered. At a structural level, the non-linear analyses are conducted replacing the homogenized orthotropic continuum with a rigid element and non-linear spring assemblage by means of which out of plane mechanisms are allowed. FRP retrofitting is modeled adopting two noded truss elements whose mechanical properties are selected in order to describe possible debonding phenomenon or tensile rupture of the strengthening. The outcome provided numerically are compared to the experimental results showing a satisfactory agreement in terms of global pressure-deflection curves and failure mechanisms.

Encountered-Type Haptic Interface for Representation of Shape and Rigidity of 3D Virtual Objects.

PubMed

Takizawa, Naoki; Yano, Hiroaki; Iwata, Hiroo; Oshiro, Yukio; Ohkohchi, Nobuhiro

2017-01-01

This paper describes the development of an encountered-type haptic interface that can generate the physical characteristics, such as shape and rigidity, of three-dimensional (3D) virtual objects using an array of newly developed non-expandable balloons. To alter the rigidity of each non-expandable balloon, the volume of air in it is controlled through a linear actuator and a pressure sensor based on Hooke's law. Furthermore, to change the volume of each balloon, its exposed surface area is controlled by using another linear actuator with a trumpet-shaped tube. A position control mechanism is constructed to display virtual objects using the balloons. The 3D position of each balloon is controlled using a flexible tube and a string. The performance of the system is tested and the results confirm the effectiveness of the proposed principle and interface.

Influence of cross-linkers on the cohesive and adhesive self-healing ability of polysulfide-based thermosets.

PubMed

Lafont, U; van Zeijl, H; van der Zwaag, S

2012-11-01

Synthetic systems with intrinsic self-repairing or self-healing abilities have emerged during the past decade. In this work, the influence of the cross-linker and chain rigidity on the healing ability of thermoset rubbers containing disulfide bonds have been investigated. The produced materials exhibit adhesive and cohesive self-healing properties. The recovery of these two functionalities upon the thermally triggered healing events has shown to be highly dependent on the network cross-link density and chain rigidity. As a result, depending on the rubber thermoset intrinsic physical properties, the thermal mending leading to full cohesive recovery can be achieved in 20-300 min at a modest healing temperature of 65 °C. The adhesive strength ranges from 0.2 to 0.5 MPa and is fully recovered even after multiple failure events.

Enhancement in Elastic Bending Rigidity of Polymer Loaded Reverse Microemulsions.

PubMed

Geethu, P M; Yadav, Indresh; Aswal, Vinod K; Satapathy, Dillip K

2017-11-14

Elastic bending rigidity of the surfactant shell is a crucial parameter which determines the phase behavior and stability of microemulsion droplets. For water-in-oil reverse microemulsions stabilized by AOT (sodium 1,4-bis(2-ethylhexoxy)-1,4-dioxobutane-2-sulfonate) surfactant, the elastic bending rigidity is close to thermal energy at room temperature (k B T) and can be modified by the presence of hydrophilic polymers. Here, we explore the influence of two polymers polyethylene glycol (PEG) and polyvinylpyrrolidone (PVP), both having nearly same size (radius of gyration, R g ) but different dipole moment, on elastic bending rigidity of water-AOT-n-decane reverse microemulsions via estimating the percolation temperatures (T P ) and droplet radii using dielectric relaxation spectroscopy (DRS) and small-angle neutron scattering (SANS) techniques. Notably, an increase in T P is observed on introducing PEG and PVP polymers and is attributed to the adsorption of polymer chains onto the surfactant monolayer. The stability of the droplet phase of microemulsion after the incorporation of PEG and PVP polymers is confirmed by contrast matching SANS experiments. An enhancement in elastic bending rigidity of AOT surfactant shell amounting to ∼46% is observed upon incorporation of PVP into the droplet core, whereas for PEG addition, a smaller increase of about 17% is recorded. We conjecture that the considerable increase in elastic bending rigidity of the surfactant monolayer upon introducing PVP is because of the strong ion-dipole interaction between anionic AOT and dipoles present along the PVP polymer chains. Scaling exponents extracted from the temperature dependent electrical conductivity measurements and the frequency dependent scaling of conductivity at percolation indicate the dynamic nature of percolation for both pure and polymer loaded reverse microemulsions. The decrease in activation energy of percolation upon incorporating PEG and PVP polymer molecules also reflects the increased stability of microemulsion droplets against thermal fluctuations.

A biomechanical testing system to determine micromotion between hip implant and femur accounting for deformation of the hip implant: Assessment of the influence of rigid body assumptions on micromotions measurements.

PubMed

Leuridan, Steven; Goossens, Quentin; Roosen, Jorg; Pastrav, Leonard; Denis, Kathleen; Mulier, Michiel; Desmet, Wim; Vander Sloten, Jos

2017-02-01

Accurate pre-clinical evaluation of the initial stability of new cementless hip stems using in vitro micromotion measurements is an important step in the design process to assess the new stem's potential. Several measuring systems, linear variable displacement transducer-based and other, require assuming bone or implant to be rigid to obtain micromotion values or to calculate derived quantities such as relative implant tilting. An alternative linear variable displacement transducer-based measuring system not requiring a rigid body assumption was developed in this study. The system combined advantages of local unidirectional and frame-and-bracket micromotion measuring concepts. The influence and possible errors that would be made by adopting a rigid body assumption were quantified. Furthermore, as the system allowed emulating local unidirectional and frame-and-bracket systems, the influence of adopting rigid body assumptions were also analyzed for both concepts. Synthetic and embalmed bone models were tested in combination with primary and revision implants. Single-legged stance phase loading was applied to the implant - bone constructs. Adopting a rigid body assumption resulted in an overestimation of mediolateral micromotion of up to 49.7μm at more distal measuring locations. Maximal average relative rotational motion was overestimated by 0.12° around the anteroposterior axis. Frontal and sagittal tilting calculations based on a unidirectional measuring concept underestimated the true tilting by an order of magnitude. Non-rigid behavior is a factor that should not be dismissed in micromotion stability evaluations of primary and revision femoral implants. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nonlinear vibration of an axially loaded beam carrying rigid bodies

NASA Astrophysics Data System (ADS)

Barry, O.

2016-12-01

This paper investigates the nonlinear vibration due to mid-plane stretching of an axially loaded simply supported beam carrying multiple rigid masses. Explicit expressions and closed form solutions of both linear and nonlinear analysis of the present vibration problem are presented for the first time. The validity of the analytical model is demonstrated using finite element analysis and via comparison with the result in the literature. Parametric studies are conducted to examine how the nonlinear frequency and frequency response curve are affected by tension, rotational inertia, and number of intermediate rigid bodies.

Compact Vibration Damper

NASA Technical Reports Server (NTRS)

Ivanco, Thomas G. (Inventor)

2014-01-01

A vibration damper includes a rigid base with a mass coupled thereto for linear movement thereon. Springs coupled to the mass compress in response to the linear movement along either of two opposing directions. A converter coupled to the mass converts the linear movement to a corresponding rotational movement. A rotary damper coupled to the converter damps the rotational movement.

Derivation and definition of a linear aircraft model

NASA Technical Reports Server (NTRS)

Duke, Eugene L.; Antoniewicz, Robert F.; Krambeer, Keith D.

1988-01-01

A linear aircraft model for a rigid aircraft of constant mass flying over a flat, nonrotating earth is derived and defined. The derivation makes no assumptions of reference trajectory or vehicle symmetry. The linear system equations are derived and evaluated along a general trajectory and include both aircraft dynamics and observation variables.

Structure Analysis of Jungle-Gym-Type Gels by Brownian Dynamics Simulation

NASA Astrophysics Data System (ADS)

Ohta, Noriyoshi; Ono, Kohki; Takasu, Masako; Furukawa, Hidemitsu

2008-02-01

We investigated the structure and the formation process of two kinds of gels by Brownian dynamics simulation. The effect of flexibility of main chain oligomer was studied. From our results, hard gel with rigid main chain forms more homogeneous network structure than soft gel with flexible main chain. In soft gel, many small loops are formed, and clusters tend to shrink. This heterogeneous network structure may be caused by microgels. In the low density case, soft gel shows more heterogeneity than the high density case.

Recursive mass matrix factorization and inversion: An operator approach to open- and closed-chain multibody dynamics

NASA Technical Reports Server (NTRS)

Rodriguez, G.; Kreutz, K.

1988-01-01

This report advances a linear operator approach for analyzing the dynamics of systems of joint-connected rigid bodies.It is established that the mass matrix M for such a system can be factored as M=(I+H phi L)D(I+H phi L) sup T. This yields an immediate inversion M sup -1=(I-H psi L) sup T D sup -1 (I-H psi L), where H and phi are given by known link geometric parameters, and L, psi and D are obtained recursively by a spatial discrete-step Kalman filter and by the corresponding Riccati equation associated with this filter. The factors (I+H phi L) and (I-H psi L) are lower triangular matrices which are inverses of each other, and D is a diagonal matrix. This factorization and inversion of the mass matrix leads to recursive algortihms for forward dynamics based on spatially recursive filtering and smoothing. The primary motivation for advancing the operator approach is to provide a better means to formulate, analyze and understand spatial recursions in multibody dynamics. This is achieved because the linear operator notation allows manipulation of the equations of motion using a very high-level analytical framework (a spatial operator algebra) that is easy to understand and use. Detailed lower-level recursive algorithms can readily be obtained for inspection from the expressions involving spatial operators. The report consists of two main sections. In Part 1, the problem of serial chain manipulators is analyzed and solved. Extensions to a closed-chain system formed by multiple manipulators moving a common task object are contained in Part 2. To retain ease of exposition in the report, only these two types of multibody systems are considered. However, the same methods can be easily applied to arbitrary multibody systems formed by a collection of joint-connected regid bodies.

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

Gaussian Curvature as an Identifier of Shell Rigidity

NASA Astrophysics Data System (ADS)

Harutyunyan, Davit

2017-11-01

In the paper we deal with shells with non-zero Gaussian curvature. We derive sharp Korn's first (linear geometric rigidity estimate) and second inequalities on that kind of shell for zero or periodic Dirichlet, Neumann, and Robin type boundary conditions. We prove that if the Gaussian curvature is positive, then the optimal constant in the first Korn inequality scales like h, and if the Gaussian curvature is negative, then the Korn constant scales like h 4/3, where h is the thickness of the shell. These results have a classical flavour in continuum mechanics, in particular shell theory. The Korn first inequalities are the linear version of the famous geometric rigidity estimate by Friesecke et al. for plates in Arch Ration Mech Anal 180(2):183-236, 2006 (where they show that the Korn constant in the nonlinear Korn's first inequality scales like h 2), extended to shells with nonzero curvature. We also recover the uniform Korn-Poincaré inequality proven for "boundary-less" shells by Lewicka and Müller in Annales de l'Institute Henri Poincare (C) Non Linear Anal 28(3):443-469, 2011 in the setting of our problem. The new estimates can also be applied to find the scaling law for the critical buckling load of the shell under in-plane loads as well as to derive energy scaling laws in the pre-buckled regime. The exponents 1 and 4/3 in the present work appear for the first time in any sharp geometric rigidity estimate.

Nonlinear dynamics of a support-excited flexible rotor with hydrodynamic journal bearings

NASA Astrophysics Data System (ADS)

Dakel, Mzaki; Baguet, Sébastien; Dufour, Régis

2014-05-01

The major purpose of this study is to predict the dynamic behavior of an on-board rotor mounted on hydrodynamic journal bearings in the presence of rigid support movements, the target application being turbochargers of vehicles or rotating machines subject to seismic excitation. The proposed on-board rotor model is based on Timoshenko beam finite elements. The dynamic modeling takes into account the geometric asymmetry of shaft and/or rigid disk as well as the six deterministic translations and rotations of the rotor rigid support. Depending on the type of analysis used for the bearing, the fluid film forces computed with the Reynolds equation are linear/nonlinear. Thus the application of Lagrange's equations yields the linear/nonlinear equations of motion of the rotating rotor in bending with respect to the moving rigid support which represents a non-inertial frame of reference. These equations are solved using the implicit Newmark time-step integration scheme. Due to the geometric asymmetry of the rotor and to the rotational motions of the support, the equations of motion include time-varying parametric terms which can lead to lateral dynamic instability. The influence of sinusoidal rotational or translational motions of the support, the accuracy of the linear 8-coefficient bearing model and the interest of the nonlinear model for a hydrodynamic journal bearing are examined and discussed by means of stability charts, orbits of the rotor, time history responses, fast Fourier transforms, bifurcation diagrams as well as Poincaré maps.

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.

Template-Based 3D Reconstruction of Non-rigid Deformable Object from Monocular Video

NASA Astrophysics Data System (ADS)

Liu, Yang; Peng, Xiaodong; Zhou, Wugen; Liu, Bo; Gerndt, Andreas

2018-06-01

In this paper, we propose a template-based 3D surface reconstruction system of non-rigid deformable objects from monocular video sequence. Firstly, we generate a semi-dense template of the target object with structure from motion method using a subsequence video. This video can be captured by rigid moving camera orienting the static target object or by a static camera observing the rigid moving target object. Then, with the reference template mesh as input and based on the framework of classical template-based methods, we solve an energy minimization problem to get the correspondence between the template and every frame to get the time-varying mesh to present the deformation of objects. The energy terms combine photometric cost, temporal and spatial smoothness cost as well as as-rigid-as-possible cost which can enable elastic deformation. In this paper, an easy and controllable solution to generate the semi-dense template for complex objects is presented. Besides, we use an effective iterative Schur based linear solver for the energy minimization problem. The experimental evaluation presents qualitative deformation objects reconstruction results with real sequences. Compare against the results with other templates as input, the reconstructions based on our template have more accurate and detailed results for certain regions. The experimental results show that the linear solver we used performs better efficiency compared to traditional conjugate gradient based solver.

Non-rigid Motion Correction in 3D Using Autofocusing with Localized Linear Translations

PubMed Central

Cheng, Joseph Y.; Alley, Marcus T.; Cunningham, Charles H.; Vasanawala, Shreyas S.; Pauly, John M.; Lustig, Michael

2012-01-01

MR scans are sensitive to motion effects due to the scan duration. To properly suppress artifacts from non-rigid body motion, complex models with elements such as translation, rotation, shear, and scaling have been incorporated into the reconstruction pipeline. However, these techniques are computationally intensive and difficult to implement for online reconstruction. On a sufficiently small spatial scale, the different types of motion can be well-approximated as simple linear translations. This formulation allows for a practical autofocusing algorithm that locally minimizes a given motion metric – more specifically, the proposed localized gradient-entropy metric. To reduce the vast search space for an optimal solution, possible motion paths are limited to the motion measured from multi-channel navigator data. The novel navigation strategy is based on the so-called “Butterfly” navigators which are modifications to the spin-warp sequence that provide intrinsic translational motion information with negligible overhead. With a 32-channel abdominal coil, sufficient number of motion measurements were found to approximate possible linear motion paths for every image voxel. The correction scheme was applied to free-breathing abdominal patient studies. In these scans, a reduction in artifacts from complex, non-rigid motion was observed. PMID:22307933

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

The dynamics and control of large-flexible space structures, part 10

NASA Technical Reports Server (NTRS)

Bainum, Peter M.; Reddy, A. S. S. R.

1988-01-01

A mathematical model is developed to predict the dynamics of the proposed orbiting Spacecraft Control Laboratory Experiment (SCOLE) during the station keeping phase. The equations of motion are derived using a Newton-Euler formulation. The model includes the effects of gravity, flexibility, and orbital dynamics. The control is assumed to be provided to the system through the Shuttle's three torquers, and through six actuators located by pairs at two points on the mast and at the mass center of the reflector. The modal shape functions are derived using the fourth order beam equation. The generic mode equations are derived to account for the effects of the control forces on the modal shape and frequencies. The equations are linearized about a nominal equilibrium position. The linear regulator theory is used to derive control laws for both the linear model of the rigidized SCOLE as well as that of the actual SCOLE including the first four flexible modes. The control strategy previously derived for the linear model of the rigidized SCOLE is applied to the nonlinear model of the same configuration of the system and preliminary single axis slewing maneuvers conducted. The results obtained confirm the applicability of the intuitive and appealing two-stage control strategy which would slew the SCOLE system, as if rigid to its desired position and then concentrate on damping out the residual flexible motions.

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”.

Three isostructural one-dimensional Ln(III) chains with distorted cubane motifs showing dual fluorescence and slow magnetic relaxation/magnetocaloric effect.

PubMed

Li, Yan; Yu, Jia-Wen; Liu, Zhong-Yi; Yang, En-Cui; Zhao, Xiao-Jun

2015-01-05

Three new homometallic lanthanide complexes with mixed carboxylate-modified rigid ligands, [Ln(μ3-OH)(na)(pyzc)]n (na(-) = 1-naphtholate, pyzc(-) = 2-pyrazinecarboxylate, Ln = Dy (1), Yb (2), and Gd (3)), were solvothermally synthesized, and their structures and magnetic as well as photophysical properties were completely investigated. Complexes 1-3 are crystallographically isostructural, exhibiting linear chains with four bidentate bridging μ-COO(-) moieties encapsulated cubic {Ln4(μ3-OH)4}(8+) clusters repeatedly extended by 4-fold chelating-bridging-pyzc(-) connectors. Magnetically, the former two complexes with highly anisotropic Dy(III) and weak anisotropic Yb(III) ions in the distorted NO7 triangular dodecahedron coordination environment display field-induced slow relaxation of magnetization. Fitting the dynamic magnetic data to the Arrhenius law gives energy barrier ΔE/kB = 39.6 K and pre-exponential factor τo = 1.52 × 10(-8) s for 1 and ΔE/kB = 14.1 K and τo = 2.13 × 10(-7) s for 2. By contrast, complex 3 with isotropic Gd(III) ion and weak intracluster antiferromagnetic coupling shows a significant cryogenic magnetocaloric effect, with a maximum -ΔSm value of 30.0 J kg(-1) K(-1) at 2.5 K and 70 kOe. Additionally, the chromophoric na(-) and pyzc(-) ligands can serve as antenna groups, selectively sensitizing the Dy(III)- and Yb(III)-based luminescence of 1 and 2 in the UV-visible region by an intramolecular energy transfer process. Thus, complexes 1-3, incorporating field-induced slow magnetic magnetization and interesting luminescence together, can be used as composite magneto-optical materials. More importantly, these interesting results further demonstrate that the mixed-ligand system with rigid carboxylate-functionalized chromophores can be excellent candidates for the preparations of new bifunctional magneto-optical materials.

Linearized mathematical models for De Havilland Canada "Buffalo & Twin Otter" STOL transports.

DOT National Transportation Integrated Search

1971-06-01

Linearized six degree of freedom rigid body aircraft equations of motion are presented in a stability axes system. Values of stability derivatives are estimated for two representative STOL aircraft - the DeHavilland of Canada 'Buffalo' and 'Twin Otte...

The effect of the rigidity of perfluoropolyether surfactant on its behavior at the water/supercritical carbon dioxide interface.

PubMed

Lu, Lanyuan; Berkowitz, Max L

2005-11-24

We performed a series of molecular dynamics simulations to study the PFPE (perfluoropolyether) and PE (polyether) surfactant monolayers at the water/supercritical carbon dioxide interface. Molecular differences between fluorocarbon surfactant PFPE and its hydrocarbon analogue PE were analyzed. We observed that values of intramolecular bonded interaction parameters which are related to chain rigidity determine the monolayer surface pressure. We show that "good" and "bad" properties of PFPE/PE surfactants are connected to conformational entropy. These results are consistent with our previous micellar simulations.

Molecular dynamics study of the diffusivity of a hydrophobic drug Cucurbitacin B in pseudo-poly(ethylene oxide-b-caprolactone) micelle environments.

PubMed

Razavilar, Negin; Choi, Phillip

2014-07-08

Isobaric-isothermal molecular dynamics simulation was used to study the diffusion of a hydrophobic drug Cucurbitacin B (CuB) in pseudomicelle environments consisting of poly(ethylene oxide-b-caprolactone) (PEO-b-PCL) swollen by various amounts of water. Two PEO-b-PCL configurations, linear and branched, with the same total molecular weight were used. For the branched configuration, the block copolymer contained one linear block of PEO with the same molecular weight as that of the PEO block used in the linear configuration but with one end connecting to three PCL blocks with the same chain length, hereafter denoted PEO-b-3PCL. Regardless of the configuration, the simulation results showed that the diffusivity of CuB was insensitive to the water concentration up to ∼8 wt % while that of water decreased with an increasing water concentration. The diffusivity of CuB (10(-8) cm(2)/s) was 3 orders of magnitude lower than that of water (10(-5) cm(2)/s). This is attributed to the fact that CuB relied on the wiggling motion of the block copolymers to diffuse while water molecules diffused via a hopping mechanism. The rates at which CuB and water diffused into PEO-b-PCL were twice those in PEO-b-3PCL because the chain mobility and the degree of swelling are higher and there are fewer intermolecular hydrogen bonds in the case of PEO-b-PCL. The velocity autocorrelation functions of CuB show that the free volume holes formed by PEO-b-3PCL are more rigid than those formed by PEO-b-PCL, making CuB exhibit higher-frequency collision motion in PEO-b-3PCL than in PEO-b-PCL, and the difference in frequency is insensitive to water concentration.

Enhanced Cellular Uptake of Short Polyarginine Peptides through Fatty Acylation and Cyclization

PubMed Central

2015-01-01

Many of the reported arginine-rich cell-penetrating peptides (CPPs) for the enhanced delivery of drugs are linear peptides composed of more than seven arginine residues to retain the cell penetration properties. Herein, we synthesized a class of nine polyarginine peptides containing 5 and 6 arginines, namely, R5 and R6. We further explored the effect of acylation with long chain fatty acids (i.e., octanoic acid, dodecanoic acid, and hexadecanoic acid) and cyclization on the cell penetrating properties of the peptides. The fluorescence-labeled acylated cyclic peptide dodecanoyl-[R5] and linear peptide dodecanoyl-(R5) showed approximately 13.7- and 10.2-fold higher cellular uptake than that of control 5,6-carboxyfluorescein, respectively. The mechanism of the peptide internalization into cells was found to be energy-dependent endocytosis. Dodecanoyl-[R5] and dodecanoyl-[R6] enhanced the intracellular uptake of a fluorescence-labeled cell-impermeable negatively charged phosphopeptide (F′-GpYEEI) in human ovarian cancer cells (SK-OV-3) by 3.4-fold and 5.5-fold, respectively, as shown by flow cytometry. The cellular uptake of F′-GpYEEI in the presence of hexadecanoyl-[R5] was 9.3- and 6.0-fold higher than that in the presence of octanoyl-[R5] and dodecanoyl-[R5], respectively. Dodecanoyl-[R5] enhanced the cellular uptake of the phosphopeptide by 1.4–2.5-fold higher than the corresponding linear peptide dodecanoyl-(R5) and those of representative CPPs, such as hepta-arginine (CR7) and TAT peptide. These results showed that a combination of acylation by long chain fatty acids and cyclization on short arginine-containing peptides can improve their cell-penetrating property, possibly through efficient interaction of rigid positively charged R and hydrophobic dodecanoyl moiety with the corresponding residues in the cell membrane phospholipids. PMID:24978295

Structure and thermodynamics of core-softened models for alcohols

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

Munaò, Gianmarco, E-mail: gmunao@unime.it; Urbic, Tomaz

The phase behavior and the fluid structure of coarse-grain models for alcohols are studied by means of reference interaction site model (RISM) theory and Monte Carlo simulations. Specifically, we model ethanol and 1-propanol as linear rigid chains constituted by three (trimers) and four (tetramers) partially fused spheres, respectively. Thermodynamic properties of these models are examined in the RISM context, by employing closed formulæ for the calculation of free energy and pressure. Gas-liquid coexistence curves for trimers and tetramers are reported and compared with already existing data for a dimer model of methanol. Critical temperatures slightly increase with the number ofmore » CH{sub 2} groups in the chain, while critical pressures and densities decrease. Such a behavior qualitatively reproduces the trend observed in experiments on methanol, ethanol, and 1-propanol and suggests that our coarse-grain models, despite their simplicity, can reproduce the essential features of the phase behavior of such alcohols. The fluid structure of these models is investigated by computing radial distribution function g{sub ij}(r) and static structure factor S{sub ij}(k); the latter shows the presence of a low−k peak at intermediate-high packing fractions and low temperatures, suggesting the presence of aggregates for both trimers and tetramers.« less

Interplay between alkyl chain asymmetry and cholesterol addition in the rigid ion pair amphiphile bilayer systems

NASA Astrophysics Data System (ADS)

Huang, Fong-yin; Chiu, Chi-cheng

2017-01-01

Ion pair amphiphile (IPA), a molecular complex composed of a pair of cationic and anionic surfactants, has been proposed as a novel phospholipid substitute. Controlling the physical stability of IPA vesicles is important for its application developments such as cosmetic and drug deliveries. To investigate the effects of IPA alkyl chain combinations and the cholesterol additive on the structural and mechanical properties of IPA vesicular bilayers, we conducted a series of molecular dynamics studies on the hexadecyltrimethylammonium-dodecylsulfate (HTMA-DS) and dodecyltrimethylammonium-hexadecylsulfate (DTMA-HS) IPA bilayers with cholesterol. We found that both IPA bilayers are in the gel phase at 298 K, consistent with experimental observations. Compared with the HTMA-DS system, the DTMA-HS bilayer has more disordered alkyl chains in the hydrophobic region. When adding cholesterol, it induces alkyl chain ordering around its rigid sterol ring. Yet, cholesterol increases the molecular areas for all species and disturbs the molecular packing near the hydrophilic region and the bilayer core. Cholesterol also promotes the alkyl chain mismatch between the IPA moieties, especially for the DTMA-HS bilayer. The combined effects lead to non-monotonically enhancement of the membrane mechanical moduli for both IPA-cholesterol systems. Furthermore, cholesterol can form H-bonds with the alkylsulfate and thus enhance the contribution of alkylsulfate to the overall mechanical moduli. Combined results provide valuable molecular insights into the roles of each IPA component and the cholesterol on modulating the IPA bilayer properties.

3D printed soft parallel actuator

NASA Astrophysics Data System (ADS)

Zolfagharian, Ali; Kouzani, Abbas Z.; Khoo, Sui Yang; Noshadi, Amin; Kaynak, Akif

2018-04-01

This paper presents a 3-dimensional (3D) printed soft parallel contactless actuator for the first time. The actuator involves an electro-responsive parallel mechanism made of two segments namely active chain and passive chain both 3D printed. The active chain is attached to the ground from one end and constitutes two actuator links made of responsive hydrogel. The passive chain, on the other hand, is attached to the active chain from one end and consists of two rigid links made of polymer. The actuator links are printed using an extrusion-based 3D-Bioplotter with polyelectrolyte hydrogel as printer ink. The rigid links are also printed by a 3D fused deposition modelling (FDM) printer with acrylonitrile butadiene styrene (ABS) as print material. The kinematics model of the soft parallel actuator is derived via transformation matrices notations to simulate and determine the workspace of the actuator. The printed soft parallel actuator is then immersed into NaOH solution with specific voltage applied to it via two contactless electrodes. The experimental data is then collected and used to develop a parametric model to estimate the end-effector position and regulate kinematics model in response to specific input voltage over time. It is observed that the electroactive actuator demonstrates expected behaviour according to the simulation of its kinematics model. The use of 3D printing for the fabrication of parallel soft actuators opens a new chapter in manufacturing sophisticated soft actuators with high dexterity and mechanical robustness for biomedical applications such as cell manipulation and drug release.

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.

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

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.

Unusual early-onset Huntingtons disease.

PubMed

Vargas, Antonio P; Carod-Artal, Francisco J; Bomfim, Denise; Vázquez-Cabrera, Carolina; Dantas-Barbosa, Carmela

2003-06-01

Huntington's disease is an autosomal dominant progressive neurodegenerative disorder characterized by involuntary movements, cognitive decline, and behavioral disorders leading to functional disability. In contrast to patients with adult onset, in which chorea is the major motor abnormality, children often present with spasticity, rigidity, and significant intellectual decline associated with a more rapidly progressive course. An unusual early-onset Huntington's disease case of an 11-year-old boy with severe hypokinetic/rigid syndrome appearing at the age of 2.5 years is presented. Clinical diagnosis was confirmed by polymerase chain reaction study of the expanded IT-15 allele with a compatible size of 102 cytosine-adenosine-guanosine repeats L-Dopa mildly ameliorated rigidity, bradykinesia, and dystonia. We conclude that Huntington's disease should be included in the differential diagnoses of regressive syndromes of early childhood.

The effect of lipid monolayer in-plane rigidity on in vivo microbubble circulation persistence

PubMed Central

Garg, Sumit; Thomas, Alex A.; Borden, Mark A.

2013-01-01

The goal of this study was to increase in vivo microbubble circulation persistence for applications in medical imaging and targeted drug delivery. Our approach was to investigate the effect of lipid monolayer in-plane rigidity to reduce the rate of microbubble dissolution, while holding constant the microbubble size, concentration and surface architecture. We first estimated the impact of acyl chain length of the main diacyl phosphatidyl-choline (PC) lipid and inter-lipid distance on the cohesive surface energy and, based on these results, we hypothesized that microbubble stability and in vivo ultrasound contrast persistence would increase monotonically with increasing acyl chain length. We therefore measured microbubble in vitro stability to dilution with and without ultrasound exposure, as well as in vivo ultrasound contrast persistence. All measurements showed a sharp rise in stability between DPPC (C16:0) and DSPC (C18:0), which correlates to the wrinkling transition, which signals the onset of significant surface shear and gas permeation resistance, observed in prior single-bubble dissolution studies. Further evidence for the effect of the wrinkling transition came from an in vitro and in vivo stability comparison of microbubbles coated with pure DPPC with those of lung surfactant extract. Microbubble stability against dilution without ultrasound and in vivo ultrasound contrast persistence showed a monotonic increase with acyl chain length from DSPC to DBPC (C22:0). However, we also observed that stability dropped precipitously for all measurements on further increasing lipid acyl chain length from DBPC to DLiPC (C24:0). This result suggests that hydrophobic mismatch between the main PC lipid and the lipopolymer emulsifier, DSPE-PEG5000, may drive a less stable surface microstructure. Overall, these results support our general hypothesis of the role of in-plane rigidity for increasing the lifetime of microbubble circulation. PMID:23787108

Molecular dynamics study of the structural and dynamic characteristics of the polyextremophilic short-chain dehydrogenase from the Thermococcus sibiricus archaeon and its homologues

NASA Astrophysics Data System (ADS)

Popinako, Anna V.; Antonov, Mikhail Yu.; Bezsudnova, Ekaterina Yu.; Prokopiev, Georgiy A.; Popov, Vladimir O.

2017-11-01

The study of structural adaptations of proteins from polyextremophilic organisms using computational molecular dynamics method is appealing because the obtained knowledge can be applied to construction of synthetic proteins with high activity and stability in polyextreme media which is useful for many industrial applications. To investigate molecular adaptations to high temperature, we have focused on a superthermostable short-chain dehydrogenase TsAdh319 from the Thermococcus sibiricus polyextremophilic archaeon and its closest structural homologues. Molecular dynamics method is widely used for molecular structure refinement, investigation of biological macromolecules motion, and, consequently, for interpreting the results of certain biophysical experiments. We performed molecular dynamics simulations of the proteins at different temperatures. Comparison of root mean square fluctuations (RMSF) of the atoms in thermophilic alcohol dehydrogenases (ADHs) at 300 K and 358 K revealed the existence of stable residues at 358 K. These residues surround the active site and form a "nucleus of rigidity" in thermophilic ADHs. The results of our studies suggest that the existence of the "nucleus of rigidity" is crucial for the stability of TsAdh319. Absence of the "nucleus of rigidity" in non-thermally stable proteins causes fluctuations throughout the protein, especially on the surface, triggering the process of denaturation at high temperatures.

A new bistable electroactive polymer for prolonged cycle lifetime of refreshable Braille displays

NASA Astrophysics Data System (ADS)

Ren, Zhi; Niu, Xiaofan; Chen, Dustin; Hu, Wei; Pei, Qibing

2014-03-01

ABSTRACT: Bistable electroactive polymers (BSEP) amalgamating electrically induced large-strain actuation and shape memory effect present a unique opportunity for refreshable Braille displays. A new BSEP material with long-chain crosslinkers to achieve prolonged cycle lifetime of refreshable Braille displays is reported here. The modulus of the BSEP material decreases by more than three orders of magnitude from a rigid, plastic state to a rubbery state when heated above the polymer's glass transition temperature. In its rubbery state, the polymer film can be electrically actuated to buckle convexly when a high voltage is applied across a circular active area. Modifying the concentration of long-chain crosslinkers in the polymer allows not only for fine-tuning of the polymer's glass transition temperature and elasticity in the rubbery state, but also enhancement of the actuation stability. For a raised height of 0.4 mm by a Braille dot with a 1.3 mm diameter, actuation can be repeated over 2000 cycles at 70°C in the rubbery state. The actuated dome shape can be fixed by cooling the polymer below the glass transition temperature. This refreshable rigid-to-rigid actuation simultaneously provides large-strain actuation and large force support. Devices capable of displaying Braille characters over a page-size area consisting of 324 Braille cells have been fabricated.

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.

Effect of replacing polyol by organosolv and kraft lignin on the property and structure of rigid polyurethane foam.

PubMed

Pan, Xuejun; Saddler, Jack N

2013-01-28

Lignin is one of the three major components in plant cell walls, and it can be isolated (dissolved) from the cell wall in pretreatment or chemical pulping. However, there is a lack of high-value applications for lignin, and the commonest proposal for lignin is power and steam generation through combustion. Organosolv ethanol process is one of the effective pretreatment methods for woody biomass for cellulosic ethanol production, and kraft process is a dominant chemical pulping method in paper industry. In the present research, the lignins from organosolv pretreatment and kraft pulping were evaluated to replace polyol for producing rigid polyurethane foams (RPFs). Petroleum-based polyol was replaced with hardwood ethanol organosolv lignin (HEL) or hardwood kraft lignin (HKL) from 25% to 70% (molar percentage) in preparing rigid polyurethane foam. The prepared foams contained 12-36% (w/w) HEL or 9-28% (w/w) HKL. The density, compressive strength, and cellular structure of the prepared foams were investigated and compared. Chain extenders were used to improve the properties of the RPFs. It was found that lignin was chemically crosslinked not just physically trapped in the rigid polyurethane foams. The lignin-containing foams had comparable structure and strength up to 25-30% (w/w) HEL or 19-23% (w/w) HKL addition. The results indicated that HEL performed much better in RPFs and could replace more polyol at the same strength than HKL because the former had a better miscibility with the polyol than the latter. Chain extender such as butanediol could improve the strength of lignin-containing RPFs.

Simultaneous Enhancements of Conductivity and Stability for Anion Exchange Membranes (AEMs) through Precise Structure Design

PubMed Central

Ran, Jin; Wu, Liang; Wei, Bing; Chen, Yaoyao; Xu, Tongwen

2014-01-01

Polymeric materials as anion exchange membranes (AEMs) play an essential role in the field of energy and environment. The achievement of high performance AEMs by the precise manipulation of macromolecular architecture remains a daunting challenge. Herein, we firstly report a novel rod-coil graft copolymer AEM, possessing rigid hydrophobic main chains and soft hydrophilic graft chains. The low graft density, which can alleviate the adverse influences of ioinc graft chains on the main chains, was obtained by using the living polymerization technique. Consequently, the grafted ionic groups which result in the degradation of polymer backbone was decreased to a small degree. Moreover, the relatively long graft chains induced the nanophase separation between the hydrophobic polymer chains and hydrophilic graft chains, which creates a convinient pathway for high hydroxide ion mobility. Such an accurate molecular design simultaneously improves the hydroxide ion conductivity and alkaline stability as well as dimensional stability. PMID:25255843

Simultaneous Enhancements of Conductivity and Stability for Anion Exchange Membranes (AEMs) through Precise Structure Design

NASA Astrophysics Data System (ADS)

Ran, Jin; Wu, Liang; Wei, Bing; Chen, Yaoyao; Xu, Tongwen

2014-09-01

Polymeric materials as anion exchange membranes (AEMs) play an essential role in the field of energy and environment. The achievement of high performance AEMs by the precise manipulation of macromolecular architecture remains a daunting challenge. Herein, we firstly report a novel rod-coil graft copolymer AEM, possessing rigid hydrophobic main chains and soft hydrophilic graft chains. The low graft density, which can alleviate the adverse influences of ioinc graft chains on the main chains, was obtained by using the living polymerization technique. Consequently, the grafted ionic groups which result in the degradation of polymer backbone was decreased to a small degree. Moreover, the relatively long graft chains induced the nanophase separation between the hydrophobic polymer chains and hydrophilic graft chains, which creates a convinient pathway for high hydroxide ion mobility. Such an accurate molecular design simultaneously improves the hydroxide ion conductivity and alkaline stability as well as dimensional stability.

Structure-property relations in siloxane-based main chain liquid crystalline elastomers and related linear polymers

NASA Astrophysics Data System (ADS)

Ren, Wanting

2007-12-01

Soft materials have attracted much scientific and technical interest in recent years. In this thesis, attention has been placed on the underpinning relations between molecular structure and properties of one type of soft matter---main chain liquid crystalline elastomers (MCLCEs), which may have application as shape memory or as auxetic materials. In this work, a number of siloxane-based MCLCEs and their linear polymer analogues (MCLCEs) with chemical variations were synthesized and examined. Among these chemical variations, rigid p-phenylene transverse rod and flat-shaped anthraquinone (AQ) mesogenic monomers were specifically incorporated. Thermal and X-ray analysis found a smectic C phase in most of our MCLCEs, which was induced by the strong self-segregation of siloxane spacers, hydrocarbon spacers and mesogenic rods. The smectic C mesophase of the parent LCE was not grossly affected by terphenyl transverse rods. Mechanical studies of MCLCEs indicated the typical three-region stress-strain curve and a polydomain-to-monodomain transition. Strain recovery experiments of MCLCEs showed a significant dependence of strain retentions on the initial strains but not on the chemical variations, such as the crosslinker content and the lateral substituents on mesogenic rods. The MCLCE with p-phenylene transverse rod showed a highly ordered smectic A mesophase at room temperature with high stiffness. Mechanical properties of MCLCEs with AQ monomers exhibit a strong dependence on the specific combination of hydrocarbon spacer and siloxane spacer, which also strongly affect the formation of pi-pi stacking between AQ units. Poisson's ratio measurement over a wide strain range found distinct trends of Poisson's ratio as a function of the crosslinker content as well as terphenyl transverse rod loadings in its parent MCLCEs.

Design and analysis of linear cascade DNA hybridization chain reactions using DNA hairpins

NASA Astrophysics Data System (ADS)

Bui, Hieu; Garg, Sudhanshu; Miao, Vincent; Song, Tianqi; Mokhtar, Reem; Reif, John

2017-01-01

DNA self-assembly has been employed non-conventionally to construct nanoscale structures and dynamic nanoscale machines. The technique of hybridization chain reactions by triggered self-assembly has been shown to form various interesting nanoscale structures ranging from simple linear DNA oligomers to dendritic DNA structures. Inspired by earlier triggered self-assembly works, we present a system for controlled self-assembly of linear cascade DNA hybridization chain reactions using nine distinct DNA hairpins. NUPACK is employed to assist in designing DNA sequences and Matlab has been used to simulate DNA hairpin interactions. Gel electrophoresis and ensemble fluorescence reaction kinetics data indicate strong evidence of linear cascade DNA hybridization chain reactions. The half-time completion of the proposed linear cascade reactions indicates a linear dependency on the number of hairpins.

Strong liquid-crystalline polymeric compositions

DOEpatents

Dowell, Flonnie

1993-01-01

Strong liquid-crystalline polymeric (LCP) compositions of matter. LCP backbones are combined with liquid crystalline (LC) side chains in a manner which maximizes molecular ordering through interdigitation of the side chains, thereby yielding materials which are predicted to have superior mechanical properties over existing LCPs. The theoretical design of LCPs having such characteristics includes consideration of the spacing distance between side chains along the backbone, the need for rigid sections in the backbone and in the side chains, the degree of polymerization, the length of the side chains, the regularity of the spacing of the side chains along the backbone, the interdigitation of side chains in sub-molecular strips, the packing of the side chains on one or two sides of the backbone to which they are attached, the symmetry of the side chains, the points of attachment of the side chains to the backbone, the flexibility and size of the chemical group connecting each side chain to the backbone, the effect of semiflexible sections in the backbone and the side chains, and the choice of types of dipolar and/or hydrogen bonding forces in the backbones and the side chains for easy alignment.

Virtual rigid body: a new optical tracking paradigm in image-guided interventions

NASA Astrophysics Data System (ADS)

Cheng, Alexis; Lee, David S.; Deshmukh, Nishikant; Boctor, Emad M.

2015-03-01

Tracking technology is often necessary for image-guided surgical interventions. Optical tracking is one the options, but it suffers from line of sight and workspace limitations. Optical tracking is accomplished by attaching a rigid body marker, having a pattern for pose detection, onto a tool or device. A larger rigid body results in more accurate tracking, but at the same time large size limits its usage in a crowded surgical workspace. This work presents a prototype of a novel optical tracking method using a virtual rigid body (VRB). We define the VRB as a 3D rigid body marker in the form of pattern on a surface generated from a light source. Its pose can be recovered by observing the projected pattern with a stereo-camera system. The rigid body's size is no longer physically limited as we can manufacture small size light sources. Conventional optical tracking also requires line of sight to the rigid body. VRB overcomes these limitations by detecting a pattern projected onto the surface. We can project the pattern onto a region of interest, allowing the pattern to always be in the view of the optical tracker. This helps to decrease the occurrence of occlusions. This manuscript describes the method and results compared with conventional optical tracking in an experiment setup using known motions. The experiments are done using an optical tracker and a linear-stage, resulting in targeting errors of 0.38mm+/-0.28mm with our method compared to 0.23mm+/-0.22mm with conventional optical markers. Another experiment that replaced the linear stage with a robot arm resulted in rotational errors of 0.50+/-0.31° and 2.68+/-2.20° and the translation errors of 0.18+/-0.10 mm and 0.03+/-0.02 mm respectively.

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.

Experimental validation of flexible robot arm modeling and control

NASA Technical Reports Server (NTRS)

Ulsoy, A. Galip

1989-01-01

Flexibility is important for high speed, high precision operation of lightweight manipulators. Accurate dynamic modeling of flexible robot arms is needed. Previous work has mostly been based on linear elasticity with prescribed rigid body motions (i.e., no effect of flexible motion on rigid body motion). Little or no experimental validation of dynamic models for flexible arms is available. Experimental results are also limited for flexible arm control. Researchers include the effects of prismatic as well as revolute joints. They investigate the effect of full coupling between the rigid and flexible motions, and of axial shortening, and consider the control of flexible arms using only additional sensors.

Identification and control of structures in space

NASA Technical Reports Server (NTRS)

Meirovitch, L.; Quinn, R. D.; Norris, M. A.

1984-01-01

The derivation of the equations of motion for the Spacecraft Control Laboratory Experiment (SCOLE) is reported and the equations of motion of a similar structure orbiting the earth are also derived. The structure is assumed to undergo large rigid-body maneuvers and small elastic deformations. A perturbation approach is proposed whereby the quantities defining the rigid-body maneuver are assumed to be relatively large, with the elastic deformations and deviations from the rigid-body maneuver being relatively small. The perturbation equations have the form of linear equations with time-dependent coefficients. An active control technique can then be formulated to permit maneuvering of the spacecraft and simultaneously suppressing the elastic vibration.

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

Substrate rigidity regulates Ca2+ oscillation via RhoA pathway in stem cells

PubMed Central

Kim, Tae-Jin; Seong, Jihye; Ouyang, Mingxing; Sun, Jie; Lu, Shaoying; Hong, Jun Pyu; Wang, Ning; Wang, Yingxiao

2008-01-01

Substrate rigidity plays crucial roles in regulating cellular functions, such as cell spreading, traction forces, and stem cell differentiation. However, it is not clear how substrate rigidity influences early cell signaling events such as calcium in living cells. Using highly-sensitive Ca2+ biosensors based on fluorescence resonance energy transfer (FRET), we investigated the molecular mechanism by which substrate rigidity affects calcium signaling in human mesenchymal stem cells (HMSCs). Spontaneous Ca2+ oscillations were observed inside the cytoplasm and the endoplasmic reticulum (ER) using the FRET biosensors targeted at subcellular locations in cells plated on rigid dishes. Lowering the substrate stiffness to 1 kPa significantly inhibited both the magnitudes and frequencies of the cytoplasmic Ca2+ oscillation in comparison to stiffer or rigid substrate. This Ca2+ oscillation was shown to be dependent on ROCK, a downstream effector molecule of RhoA, but independent of actin filaments, microtubules, myosin light chain kinase, or myosin activity. Lysophosphatidic acid, which activates RhoA, also inhibited the frequency of the Ca2+ oscillation. Consistently, either a constitutive active mutant of RhoA (RhoA-V14) or a dominant negative mutant of RhoA (RhoA-N19) inhibited the Ca2+ oscillation. Further experiments revealed that HMSCs cultured on gels with low elastic moduli displayed low RhoA activities. Therefore, our results demonstrate that RhoA and its downstream molecule ROCK may mediate the substrate rigidity-regulated Ca2+ oscillation, which determines the physiological functions of HMSCs. PMID:18844232

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

Analytical expressions for the closure probability of a stiff wormlike chain for finite capture radius.

PubMed

Guérin, T

2017-08-01

Estimating the probability that two monomers of the same polymer chain are close together is a key ingredient to characterize intramolecular reactions and polymer looping. In the case of stiff wormlike polymers (rigid fluctuating elastic rods), for which end-to-end encounters are rare events, we derive an explicit analytical formula for the probability η(r_{c}) that the distance between the chain extremities is smaller than some capture radius r_{c}. The formula is asymptotically exact in the limit of stiff chains, and it leads to the identification of two distinct scaling regimes for the closure factor, originating from a strong variation of the fluctuations of the chain orientation at closure. Our theory is compatible with existing analytical results from the literature that cover the cases of a vanishing capture radius and of nearly fully extended chains.

Solving the Problem of Bending of Multiply Connected Plates with Elastic Inclusions

NASA Astrophysics Data System (ADS)

Kaloerov, S. A.; Koshkin, A. A.

2017-11-01

This paper describes a method for determining the strain state of a thin anisotropic plate with elastic arbitrarily arranged elliptical inclusions. Complex potentials are used to reduce the problem to determining functions of generalized complex variables, which, in turn, comes down to an overdetermined system of linear algebraic equations, solved by singular expansions. This paper presents the results of numerical calculations that helped establish the influence of rigidity of elastic inclusions, distances between inclusions, and their geometric characteristics on the bending moments occurring in the plate. It is found that the specific properties of distribution of moments near the apexes of linear elastic inclusions, characterized by moment intensity coefficients, occur only in the case of sufficiently rigid and elastic inclusions.

Vibration control of a manipulator tip on a flexible body

NASA Technical Reports Server (NTRS)

Xu, J.; Bainum, P. M.; Li, F.

1992-01-01

Vibration control of a rigid manipulator tip on a main flexible uniform beam is examined. It is proposed to add a compensator between the manipulator and the beam to rotate and extend/retrieve the manipulator during the control period. The 2D station-keeping maneuvers within the linear range without gravity and damping are considered. The compensatory open-loop control law, which depends on the amplitudes of the beam's flexible deformations at the connection joint, is synthesized using linear quadratic regulator techniques. After introducing the compensatory control into the system, system control is still stable, and the tip coordinates of the manipulator can be made to closely follow the rigid beam motion, which is assumed to be a desired motion.

Inertial and viscoelastic forces on rigid colloids in microfluidic channels.

PubMed

Howard, Michael P; Panagiotopoulos, Athanassios Z; Nikoubashman, Arash

2015-06-14

We perform hybrid molecular dynamics simulations to study the flow behavior of rigid colloids dispersed in a dilute polymer solution. The underlying Newtonian solvent and the ensuing hydrodynamic interactions are incorporated through multiparticle collision dynamics, while the constituent polymers are modeled as bead-spring chains, maintaining a description consistent with the colloidal nature of our system. We study the cross-stream migration of the solute particles in slit-like channels for various polymer lengths and colloid sizes and find a distinct focusing onto the channel center under specific solvent and flow conditions. To better understand this phenomenon, we systematically measure the effective forces exerted on the colloids. We find that the migration originates from a competition between viscoelastic forces from the polymer solution and hydrodynamically induced inertial forces. Our simulations reveal a significantly stronger fluctuation of the lateral colloid position than expected from thermal motion alone, which originates from the complex interplay between the colloid and polymer chains.

A stable partitioned FSI algorithm for rigid bodies and incompressible flow. Part I: Model problem analysis

NASA Astrophysics Data System (ADS)

Banks, J. W.; Henshaw, W. D.; Schwendeman, D. W.; Tang, Qi

2017-08-01

A stable partitioned algorithm is developed for fluid-structure interaction (FSI) problems involving viscous incompressible flow and rigid bodies. This added-mass partitioned (AMP) algorithm remains stable, without sub-iterations, for light and even zero mass rigid bodies when added-mass and viscous added-damping effects are large. The scheme is based on a generalized Robin interface condition for the fluid pressure that includes terms involving the linear acceleration and angular acceleration of the rigid body. Added-mass effects are handled in the Robin condition by inclusion of a boundary integral term that depends on the pressure. Added-damping effects due to the viscous shear forces on the body are treated by inclusion of added-damping tensors that are derived through a linearization of the integrals defining the force and torque. Added-damping effects may be important at low Reynolds number, or, for example, in the case of a rotating cylinder or rotating sphere when the rotational moments of inertia are small. In this first part of a two-part series, the properties of the AMP scheme are motivated and evaluated through the development and analysis of some model problems. The analysis shows when and why the traditional partitioned scheme becomes unstable due to either added-mass or added-damping effects. The analysis also identifies the proper form of the added-damping which depends on the discrete time-step and the grid-spacing normal to the rigid body. The results of the analysis are confirmed with numerical simulations that also demonstrate a second-order accurate implementation of the AMP scheme.

Linear ultrasonic motor for absolute gravimeter.

PubMed

Jian, Yue; Yao, Zhiyuan; Silberschmidt, Vadim V

2017-05-01

Thanks to their compactness and suitability for vacuum applications, linear ultrasonic motors are considered as substitutes for classical electromagnetic motors as driving elements in absolute gravimeters. Still, their application is prevented by relatively low power output. To overcome this limitation and provide better stability, a V-type linear ultrasonic motor with a new clamping method is proposed for a gravimeter. In this paper, a mechanical model of stators with flexible clamping components is suggested, according to a design criterion for clamps of linear ultrasonic motors. After that, an effect of tangential and normal rigidity of the clamping components on mechanical output is studied. It is followed by discussion of a new clamping method with sufficient tangential rigidity and a capability to facilitate pre-load. Additionally, a prototype of the motor with the proposed clamping method was fabricated and the performance tests in vertical direction were implemented. Experimental results show that the suggested motor has structural stability and high dynamic performance, such as no-load speed of 1.4m/s and maximal thrust of 43N, meeting the requirements for absolute gravimeters. Copyright © 2017 Elsevier B.V. All rights reserved.

Effect of replacing polyol by organosolv and kraft lignin on the property and structure of rigid polyurethane foam

PubMed Central

2013-01-01

Background Lignin is one of the three major components in plant cell walls, and it can be isolated (dissolved) from the cell wall in pretreatment or chemical pulping. However, there is a lack of high-value applications for lignin, and the commonest proposal for lignin is power and steam generation through combustion. Organosolv ethanol process is one of the effective pretreatment methods for woody biomass for cellulosic ethanol production, and kraft process is a dominant chemical pulping method in paper industry. In the present research, the lignins from organosolv pretreatment and kraft pulping were evaluated to replace polyol for producing rigid polyurethane foams (RPFs). Results Petroleum-based polyol was replaced with hardwood ethanol organosolv lignin (HEL) or hardwood kraft lignin (HKL) from 25% to 70% (molar percentage) in preparing rigid polyurethane foam. The prepared foams contained 12-36% (w/w) HEL or 9-28% (w/w) HKL. The density, compressive strength, and cellular structure of the prepared foams were investigated and compared. Chain extenders were used to improve the properties of the RPFs. Conclusions It was found that lignin was chemically crosslinked not just physically trapped in the rigid polyurethane foams. The lignin-containing foams had comparable structure and strength up to 25-30% (w/w) HEL or 19-23% (w/w) HKL addition. The results indicated that HEL performed much better in RPFs and could replace more polyol at the same strength than HKL because the former had a better miscibility with the polyol than the latter. Chain extender such as butanediol could improve the strength of lignin-containing RPFs. PMID:23356502

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

Chang, Yongbin; White, R. D.

In the calculation of the linearized Boltzmann collision operator for an inverse-square force law interaction (Coulomb interaction) F(r)=κ/r{sup 2}, we found the widely used scattering angle cutoff θ≥θ{sub min} is a wrong practise since the divergence still exists after the cutoff has been made. When the correct velocity change cutoff |v′−v|≥δ{sub min} is employed, the scattering angle can be integrated. A unified linearized Boltzmann collision operator for both inverse-square force law and rigid-sphere interactions is obtained. Like many other unified quantities such as transition moments, Fokker-Planck expansion coefficients and energy exchange rates obtained recently [Y. B. Chang and L. A.more » Viehland, AIP Adv. 1, 032128 (2011)], the difference between the two kinds of interactions is characterized by a parameter, γ, which is 1 for rigid-sphere interactions and −3 for inverse-square force law interactions. When the cutoff is removed by setting δ{sub min}=0, Hilbert's well known kernel for rigid-sphere interactions is recovered for γ = 1.« less

Intraplate deformation due to continental collisions: A numerical study of deformation in a thin viscous sheet

NASA Technical Reports Server (NTRS)

Cohen, S. C.; Morgan, R. C.

1985-01-01

A model of crustal deformation from continental collision that involves the penetration of a rigid punch into a deformable sheet is investigated. A linear viscous flow law is used to compute the magnitude and rate of change of crustal thickness, the velocity of mass points, strain rates and their principal axes, modes of deformation, areal changes, and stress. In general, a free lateral boundary reduces the magnitude of changes in crustal thickening by allowing material to more readily escape the advancing punch. The shearing that occurs diagonally in front of the punch terminates in compression or extension depending on whether the lateral boundary is fixed or free. When the ratio of the diameter of the punch to that of the sheet exceeds one-third, the deformation is insenstive to the choice of lateral boundary conditions. When the punch is rigid with sharply defined edges, deformation is concentrated near the punch corners. With non-rigid punches, shearing results in deformation being concentrated near the center of the punch. Variations with respect to linearity and nonlinearity of flow are discussed.

Simulation Studies of LCST-like Phase Transitions in Elastin-like Polypeptides (ELPs) and Conjugates of ELP with Rigid Macromolecules

NASA Astrophysics Data System (ADS)

Condon, Joshua; Martin, Tyler; Jayaraman, Arthi

We use atomistic (AA) and coarse-grained (CG) molecular dynamics simulations to elucidate the thermodynamic driving forces governing lower critical solution temperature (LCST)-like phase transition exhibited by elastin-like peptides (ELPs) and conjugates of ELP with other macromolecules. In the AA simulations, we study ELP oligomers in explicit water, and mark the transition as the temperature at which they undergo a change in ``hydration'' state. While AA simulations are restricted to small systems of short ELPs and do not capture the chain aggregation observed in experiments of ELPs, they guide the phenomenological CG model development by highlighting the solvent induced polymer-polymer effective interactions with changing temperature. In the CG simulations, we capture the LCST polymer aggregation by increasing polymer-polymer effective attractive interactions in an implicit solvent. We examine the impact of conjugating a block of LCST polymer to another rigid unresponsive macromolecular block on the LCST-like transition. We find that when multiple LCST polymers are conjugated to a rigid polymer block, increased crowding of the LCST polymers shifts the onset of chain aggregation to smaller effective polymer-polymer attraction compared to the free LCST polymers. These simulation results provide guidance on the design of conjugated bio-mimetic thermoresponsive materials, and shape the fundamental understanding of the impact of polymer crowding on phase behavior in thermoresponsive LCST polymer systems.

Strong liquid-crystalline polymeric compositions

DOEpatents

Dowell, F.

1993-12-07

Strong liquid-crystalline polymeric (LCP) compositions of matter are described. LCP backbones are combined with liquid crystalline (LC) side chains in a manner which maximizes molecular ordering through interdigitation of the side chains, thereby yielding materials which are predicted to have superior mechanical properties over existing LCPs. The theoretical design of LCPs having such characteristics includes consideration of the spacing distance between side chains along the backbone, the need for rigid sections in the backbone and in the side chains, the degree of polymerization, the length of the side chains, the regularity of the spacing of the side chains along the backbone, the interdigitation of side chains in sub-molecular strips, the packing of the side chains on one or two sides of the backbone to which they are attached, the symmetry of the side chains, the points of attachment of the side chains to the backbone, the flexibility and size of the chemical group connecting each side chain to the backbone, the effect of semiflexible sections in the backbone and the side chains, and the choice of types of dipolar and/or hydrogen bonding forces in the backbones and the side chains for easy alignment. 27 figures.

A recursive approach to the equations of motion for the maneuvering and control of flexible multi-body systems

NASA Technical Reports Server (NTRS)

Kwak, Moon K.; Meirovitch, Leonard

1991-01-01

Interest lies in a mathematical formulation capable of accommodating the problem of maneuvering a space structure consisting of a chain of articulated flexible substructures. Simultaneously, any perturbations from the 'rigid body' maneuvering and any elastic vibration must be suppressed. The equations of motion for flexible bodies undergoing rigid body motions and elastic vibrations can be obtained conveniently by means of Lagrange's equations in terms of quasi-coordinates. The advantage of this approach is that it yields equations in terms of body axes, which are the same axes that are used to express the control forces and torques. The equations of motion are nonlinear hybrid differential quations. The partial differential equations can be discretized (in space) by means of the finite element method or the classical Rayleigh-Ritz method. The result is a set of nonlinear ordinary differential equations of high order. The nonlinearity can be traced to the rigid body motions and the high order to the elastic vibration. Elastic motions tend to be small when compared with rigid body motions.

Flexible histone tails in a new mesoscopic oligonucleosome model.

PubMed

Arya, Gaurav; Zhang, Qing; Schlick, Tamar

2006-07-01

We describe a new mesoscopic model of oligonucleosomes that incorporates flexible histone tails. The nucleosome cores are modeled using the discrete surface-charge optimization model, which treats the nucleosome as an electrostatic surface represented by hundreds of point charges; the linker DNAs are treated using a discrete elastic chain model; and the histone tails are modeled using a bead/chain hydrodynamic approach as chains of connected beads where each bead represents five protein residues. Appropriate charges and force fields are assigned to each histone chain so as to reproduce the electrostatic potential, structure, and dynamics of the corresponding atomistic histone tails at different salt conditions. The dynamics of resulting oligonucleosomes at different sizes and varying salt concentrations are simulated by Brownian dynamics with complete hydrodynamic interactions. The analyses demonstrate that the new mesoscopic model reproduces experimental results better than its predecessors, which modeled histone tails as rigid entities. In particular, our model with flexible histone tails: correctly accounts for salt-dependent conformational changes in the histone tails; yields the experimentally obtained values of histone-tail mediated core/core attraction energies; and considers the partial shielding of electrostatic repulsion between DNA linkers as a result of the spatial distribution of histone tails. These effects are crucial for regulating chromatin structure but are absent or improperly treated in models with rigid histone tails. The development of this model of oligonucleosomes thus opens new avenues for studying the role of histone tails and their variants in mediating gene expression through modulation of chromatin structure.

Nouvelles bornes et estimations pour les milieux poreux à matrice rigide parfaitement plastique

NASA Astrophysics Data System (ADS)

Bilger, Nicolas; Auslender, François; Bornert, Michel; Masson, Renaud

We derive new rigorous bounds and self-consistent estimates for the effective yield surface of porous media with a rigid perfectly plastic matrix and a microstructure similar to Hashin's composite spheres assemblage. These results arise from a homogenisation technique that combines a pattern-based modelling for linear composite materials and a variational formulation for nonlinear media. To cite this article: N. Bilger et al., C. R. Mecanique 330 (2002) 127-132.

Chemical Organization of the Cell Wall Polysaccharide Core of Malassezia restricta

PubMed Central

Stalhberger, Thomas; Simenel, Catherine; Clavaud, Cécile; Eijsink, Vincent G. H.; Jourdain, Roland; Delepierre, Muriel; Latgé, Jean-Paul; Breton, Lionel; Fontaine, Thierry

2014-01-01

Malassezia species are ubiquitous residents of human skin and are associated with several diseases such as seborrheic dermatitis, tinea versicolor, folliculitis, atopic dermatitis, and scalp conditions such as dandruff. Host-Malassezia interactions and mechanisms to evade local immune responses remain largely unknown. Malassezia restricta is one of the most predominant yeasts of the healthy human skin, its cell wall has been investigated in this paper. Polysaccharides in the M. restricta cell wall are almost exclusively alkali-insoluble, showing that they play an essential role in the organization and rigidity of the M. restricta cell wall. Fractionation of cell wall polymers and carbohydrate analyses showed that the polysaccharide core of the cell wall of M. restricta contained an average of 5% chitin, 20% chitosan, 5% β-(1,3)-glucan, and 70% β-(1,6)-glucan. In contrast to other yeasts, chitin and chitosan are relatively abundant, and β-(1,3)-glucans constitute a minor cell wall component. The most abundant polymer is β-(1,6)-glucans, which are large molecules composed of a linear β-(1,6)-glucan chains with β-(1,3)-glucosyl side chain with an average of 1 branch point every 3.8 glucose unit. Both β-glucans are cross-linked, forming a huge alkali-insoluble complex with chitin and chitosan polymers. Data presented here show that M. restricta has a polysaccharide organization very different of all fungal species analyzed to date. PMID:24627479

Chemical organization of the cell wall polysaccharide core of Malassezia restricta.

PubMed

Stalhberger, Thomas; Simenel, Catherine; Clavaud, Cécile; Eijsink, Vincent G H; Jourdain, Roland; Delepierre, Muriel; Latgé, Jean-Paul; Breton, Lionel; Fontaine, Thierry

2014-05-02

Malassezia species are ubiquitous residents of human skin and are associated with several diseases such as seborrheic dermatitis, tinea versicolor, folliculitis, atopic dermatitis, and scalp conditions such as dandruff. Host-Malassezia interactions and mechanisms to evade local immune responses remain largely unknown. Malassezia restricta is one of the most predominant yeasts of the healthy human skin, its cell wall has been investigated in this paper. Polysaccharides in the M. restricta cell wall are almost exclusively alkali-insoluble, showing that they play an essential role in the organization and rigidity of the M. restricta cell wall. Fractionation of cell wall polymers and carbohydrate analyses showed that the polysaccharide core of the cell wall of M. restricta contained an average of 5% chitin, 20% chitosan, 5% β-(1,3)-glucan, and 70% β-(1,6)-glucan. In contrast to other yeasts, chitin and chitosan are relatively abundant, and β-(1,3)-glucans constitute a minor cell wall component. The most abundant polymer is β-(1,6)-glucans, which are large molecules composed of a linear β-(1,6)-glucan chains with β-(1,3)-glucosyl side chain with an average of 1 branch point every 3.8 glucose unit. Both β-glucans are cross-linked, forming a huge alkali-insoluble complex with chitin and chitosan polymers. Data presented here show that M. restricta has a polysaccharide organization very different of all fungal species analyzed to date.

Frequency domain system identification of helicopter rotor dynamics incorporating models with time periodic coefficients

NASA Astrophysics Data System (ADS)

Hwang, Sunghwan

1997-08-01

One of the most prominent features of helicopter rotor dynamics in forward flight is the periodic coefficients in the equations of motion introduced by the rotor rotation. The frequency response characteristics of such a linear time periodic system exhibits sideband behavior, which is not the case for linear time invariant systems. Therefore, a frequency domain identification methodology for linear systems with time periodic coefficients was developed, because the linear time invariant theory cannot account for sideband behavior. The modulated complex Fourier series was introduced to eliminate the smearing effect of Fourier series expansions of exponentially modulated periodic signals. A system identification theory was then developed using modulated complex Fourier series expansion. Correlation and spectral density functions were derived using the modulated complex Fourier series expansion for linear time periodic systems. Expressions of the identified harmonic transfer function were then formulated using the spectral density functions both with and without additive noise processes at input and/or output. A procedure was developed to identify parameters of a model to match the frequency response characteristics between measured and estimated harmonic transfer functions by minimizing an objective function defined in terms of the trace of the squared frequency response error matrix. Feasibility was demonstrated by the identification of the harmonic transfer function and parameters for helicopter rigid blade flapping dynamics in forward flight. This technique is envisioned to satisfy the needs of system identification in the rotating frame, especially in the context of individual blade control. The technique was applied to the coupled flap-lag-inflow dynamics of a rigid blade excited by an active pitch link. The linear time periodic technique results were compared with the linear time invariant technique results. Also, the effect of noise processes and initial parameter guess on the identification procedure were investigated. To study the effect of elastic modes, a rigid blade with a trailing edge flap excited by a smart actuator was selected and system parameters were successfully identified, but with some expense of computational storage and time. Conclusively, the linear time periodic technique substantially improved the identified parameter accuracy compared to the linear time invariant technique. Also, the linear time periodic technique was robust to noises and initial guess of parameters. However, an elastic mode of higher frequency relative to the system pumping frequency tends to increase the computer storage requirement and computing time.

Simulation of spacecraft attitude dynamics using TREETOPS and model-specific computer Codes

NASA Technical Reports Server (NTRS)

Cochran, John E.; No, T. S.; Fitz-Coy, Norman G.

1989-01-01

The simulation of spacecraft attitude dynamics and control using the generic, multi-body code called TREETOPS and other codes written especially to simulate particular systems is discussed. Differences in the methods used to derive equations of motion--Kane's method for TREETOPS and the Lagrangian and Newton-Euler methods, respectively, for the other two codes--are considered. Simulation results from the TREETOPS code are compared with those from the other two codes for two example systems. One system is a chain of rigid bodies; the other consists of two rigid bodies attached to a flexible base body. Since the computer codes were developed independently, consistent results serve as a verification of the correctness of all the programs. Differences in the results are discussed. Results for the two-rigid-body, one-flexible-body system are useful also as information on multi-body, flexible, pointing payload dynamics.

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.

Diffusion of chains in a periodic potential

NASA Astrophysics Data System (ADS)

Terranova, G. R.; Mártin, H. O.; Aldao, C. M.

2017-09-01

We studied the diffusion of 1D rigid chains in a square wave potential of period T. We considered chains of type A (composed of N particles A) and chains of type A-B (composed of N/2 particles A and N/2 particles B). The square wave potential represents domains, a lamellar structure observed for block copolymers, in which the repulsive δ energy between each A particle (B particle) of the chain and B particles (A particles) of the medium where the chains diffuse. From Monte Carlo simulations and analytical results it is found that the normalized diffusivity D, for N\\ll T , presents a universal behavior as a function of X  =  Nδ for chains of type A and X  =  (Nδ  -  lnT 2) for chains of type A-B, with and exponential decay for large values of X. For fixed values of δ and T, D is a periodic function of N with period T and 2T for chains of type A and type A-B, respectively.

Confinement dynamics of a semiflexible chain inside nano-spheres

NASA Astrophysics Data System (ADS)

Fathizadeh, A.; Heidari, Maziar; Eslami-Mossallam, B.; Ejtehadi, M. R.

2013-07-01

We study the conformations of a semiflexible chain, confined in nano-scaled spherical cavities, under two distinct processes of confinement. Radial contraction and packaging are employed as two confining procedures. The former method is performed by gradually decreasing the diameter of a spherical shell which envelopes a confined chain. The latter procedure is carried out by injecting the chain inside a spherical shell through a hole on the shell surface. The chain is modeled with a rigid body molecular dynamics simulation and its parameters are adjusted to DNA base-pair elasticity. Directional order parameter is employed to analyze and compare the confined chain and the conformations of the chain for two different sizes of the spheres are studied in both procedures. It is shown that for the confined chains in the sphere sizes of our study, they appear in spiral or tennis-ball structures, and the tennis-ball structure is more likely to be observed in more compact confinements. Our results also show that the dynamical procedure of confinement and the rate of the confinement are influential parameters of the structure of the chain inside spherical cavities.

Elucidation of atomic scale mechanisms for polytetrafluoroethylene tribology using molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Barry, Peter R.

Polytetrafluoroethylene (PTFE) is a polymer that has been widely exploited commercially as a result of its low friction, 'non-stick' properties. The polymer has found usage as 'non-stick,' chemically resistant coatings for bearings, valves, rollers and pipe linings with applications in industries ranging from food and chemical processing to construction, automotive and aerospace. The major drawback of PTFE in low friction applications involves its excessive wear rate. For decades, scientists and engineers have sought to improve the polymer's wear resistance while maintaining its low sliding friction by reinforcing the polymer matrix with a host of filler materials ranging from fibril to particulate. In this study, a different approach is taken in which the atomic scale phenomena between two crystalline PTFE surfaces in sliding contact are examined. The goal is to obtain atomic-level insights into PTFE's low friction and high wear rate to aid in the designing of effective polymer based tribological composites for extreme condition applications. To accomplish this, several tribological conditions were varied. These included sliding direction of the two polymer surfaces with respect to their chain alignment, sliding velocity, degree of crystalline phase rigidity, interfacial contact pressure, sample temperature and the presence of fluorocarbon fluids between the two crystalline PTFE surfaces. From these studies, it was found that crystalline PTFE-PTFE sliding demonstrates friction anisotropy. Low friction and molecular wear was observed when sliding in the direction of the chain alignment with high friction and wear behavior dominating when sliding in a direction perpendicular to the chain alignment. For the range of cross-link density (average linear density of 6.2 to 11.1 A) and sliding rate (5 m/s to 20 m/s) explored, a significant change in friction behavior or wear mechanisms was not observed. Under conditions of increased normal load or low temperature however, the frictional force increased linearly. Additionally, the inclusion of fluorocarbon molecular fluids at the sliding interface between the two crystalline PTFE surfaces resulted in a significant decrease in both the friction and wear of the surfaces.

Context-Aware Design for Process Flexibility and Adaptation

ERIC Educational Resources Information Center

Yao, Wen

2012-01-01

Today's organizations face continuous and unprecedented changes in their business environment. Traditional process design tools tend to be inflexible and can only support rigidly defined processes (e.g., order processing in the supply chain). This considerably restricts their real-world applications value, especially in the dynamic and…

An Algebraic Method for Exploring Quantum Monodromy and Quantum Phase Transitions in Non-Rigid Molecules

NASA Astrophysics Data System (ADS)

Larese, D.; Iachello, F.

2011-06-01

A simple algebraic Hamiltonian has been used to explore the vibrational and rotational spectra of the skeletal bending modes of HCNO, BrCNO, NCNCS, and other ``floppy`` (quasi-linear or quasi-bent) molecules. These molecules have large-amplitude, low-energy bending modes and champagne-bottle potential surfaces, making them good candidates for observing quantum phase transitions (QPT). We describe the geometric phase transitions from bent to linear in these and other non-rigid molecules, quantitatively analysing the spectroscopy signatures of ground state QPT, excited state QPT, and quantum monodromy.The algebraic framework is ideal for this work because of its small calculational effort yet robust results. Although these methods have historically found success with tri- and four-atomic molecules, we now address five-atomic and simple branched molecules such as CH_3NCO and GeH_3NCO. Extraction of potential functions is completed for several molecules, resulting in predictions of barriers to linearity and equilibrium bond angles.

Numerical modelling of instantaneous plate tectonics

NASA Technical Reports Server (NTRS)

Minster, J. B.; Haines, E.; Jordan, T. H.; Molnar, P.

1974-01-01

Assuming lithospheric plates to be rigid, 68 spreading rates, 62 fracture zones trends, and 106 earthquake slip vectors are systematically inverted to obtain a self-consistent model of instantaneous relative motions for eleven major plates. The inverse problem is linearized and solved iteratively by a maximum-likelihood procedure. Because the uncertainties in the data are small, Gaussian statistics are shown to be adequate. The use of a linear theory permits (1) the calculation of the uncertainties in the various angular velocity vectors caused by uncertainties in the data, and (2) quantitative examination of the distribution of information within the data set. The existence of a self-consistent model satisfying all the data is strong justification of the rigid plate assumption. Slow movement between North and South America is shown to be resolvable.

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

Integration and Interoperability of Special Operations Forces and Conventional Forces in Irregular Warfare

DTIC Science & Technology

2009-06-12

Phasing Model ......................................................................................................9 Figure 2. The Continuum of...the communist periphery. In a high-intensity conflict, doctrine at the time called for conventional forces to fight the traditional, linear fight...operations and proximity of cross component forces in a non- linear battlespace – Rigid business rules, translator applications, or manual workarounds to

Geometric modeling of hepatic arteries in 3D ultrasound with unsupervised MRA fusion during liver interventions.

PubMed

Gérard, Maxime; Michaud, François; Bigot, Alexandre; Tang, An; Soulez, Gilles; Kadoury, Samuel

2017-06-01

Modulating the chemotherapy injection rate with regard to blood flow velocities in the tumor-feeding arteries during intra-arterial therapies may help improve liver tumor targeting while decreasing systemic exposure. These velocities can be obtained noninvasively using Doppler ultrasound (US). However, small vessels situated in the liver are difficult to identify and follow in US. We propose a multimodal fusion approach that non-rigidly registers a 3D geometric mesh model of the hepatic arteries obtained from preoperative MR angiography (MRA) acquisitions with intra-operative 3D US imaging. The proposed fusion tool integrates 3 imaging modalities: an arterial MRA, a portal phase MRA and an intra-operative 3D US. Preoperatively, the arterial phase MRA is used to generate a 3D model of the hepatic arteries, which is then non-rigidly co-registered with the portal phase MRA. Once the intra-operative 3D US is acquired, we register it with the portal MRA using a vessel-based rigid initialization followed by a non-rigid registration using an image-based metric based on linear correlation of linear combination. Using the combined non-rigid transformation matrices, the 3D mesh model is fused with the 3D US. 3D US and multi-phase MRA images acquired from 10 porcine models were used to test the performance of the proposed fusion tool. Unimodal registration of the MRA phases yielded a target registration error (TRE) of [Formula: see text] mm. Initial rigid alignment of the portal MRA and 3D US yielded a mean TRE of [Formula: see text] mm, which was significantly reduced to [Formula: see text] mm ([Formula: see text]) after affine image-based registration. The following deformable registration step allowed for further decrease of the mean TRE to [Formula: see text] mm. The proposed tool could facilitate visualization and localization of these vessels when using 3D US intra-operatively for either intravascular or percutaneous interventions to avoid vessel perforation.

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

Recursive multibody dynamics and discrete-time optimal control

NASA Technical Reports Server (NTRS)

Deleuterio, G. M. T.; Damaren, C. J.

1989-01-01

A recursive algorithm is developed for the solution of the simulation dynamics problem for a chain of rigid bodies. Arbitrary joint constraints are permitted, that is, joints may allow translational and/or rotational degrees of freedom. The recursive procedure is shown to be identical to that encountered in a discrete-time optimal control problem. For each relevant quantity in the multibody dynamics problem, there exists an analog in the context of optimal control. The performance index that is minimized in the control problem is identified as Gibbs' function for the chain of bodies.

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.

NLOphoric rigid pyrazino-phenanthroline donor-π-acceptor compounds: Investigation of structural and solvent effects on non-linear optical properties using computational methods

NASA Astrophysics Data System (ADS)

Kothavale, Shantaram; Katariya, Santosh; Sekar, Nagaiyan

2018-01-01

Rigid pyrazino-phenanthroline based donor-π-acceptor-π-auxiliary acceptor type compounds have been studied for their linear and non-linear optical properties. The non-linear optical (NLO) behavior of these dyes was studied by calculating the values of static α , β and γ using solvatochromic as well as computational methods. The results obtained by solvatochromic method are correlated theoretically with Density Functional Theory (DFT) using B3LYP/6-31G (d), CAM B3LYP/6-31 G(d), B3LYP/6-31++ g(d,P) and CAM B3LYP/6-31++ g(d,P) methods. The results reveal that, among all four computational methods CAM-B3LYP/6-31++ g(d,P) performs well for the calculation of linear polarizability (α) and first order hyperpolarizability (β), while CAM-B3LYP/6-31 g(d,P) for the calculation of second order hyperpolarizability (ϒ). Overall TPA depends on the molecular structure variation with increase in complexity and molecular weight, which implies that both the number of branches and the size of π-framework are important factors for the molecular TPA in this chromophoric system. Generalized Mulliken-Hush (GMH) analysis is performed to study the effective charge transfer from donor to acceptor.

Crack Initiation and Growth in Rigid Polymeric Closed-Cell Foam Cryogenic Applications

NASA Technical Reports Server (NTRS)

Sayyah, Tarek; Steeve, Brian; Wells, Doug

2006-01-01

Cryogenic vessels, such as the Space Shuttle External Tank, are often insulated with closed-cell foam because of its low thermal conductivity. The coefficient of thermal expansion mismatch between the foam and metallic substrate places the foam under a biaxial tension gradient through the foam thickness. The total foam thickness affects the slope of the stress gradient and is considered a significant contributor to the initiation of subsurface cracks. Rigid polymeric foams are brittle in nature and any subsurface cracks tend to propagate a finite distance toward the surface. This presentation investigates the relationship between foam thickness and crack initiation and subsequent crack growth, using linear elastic fracture mechanics, in a rigid polymeric closed-cell foam through analysis and comparison with experimental results.

Modeling and simulation of dynamics of a planar-motion rigid body with friction and surface contact

NASA Astrophysics Data System (ADS)

Wang, Xiaojun; Lv, Jing

2017-07-01

The modeling and numerical method for the dynamics of a planar-motion rigid body with frictional contact between plane surfaces were presented based on the theory of contact mechanics and the algorithm of linear complementarity problem (LCP). The Coulomb’s dry friction model is adopted as the friction law, and the normal contact forces are expressed as functions of the local deformations and their speeds in contact bodies. The dynamic equations of the rigid body are obtained by the Lagrange equation. The transition problem of stick-slip motions between contact surfaces is formulated and solved as LCP through establishing the complementary conditions of the friction law. Finally, a numerical example is presented as an example to show the application.

Housing flexibility effects on rotor stability

NASA Technical Reports Server (NTRS)

Davis, L. B.; Wolfe, E. A.; Beatty, R. F.

1985-01-01

Preliminary rotordynamic evaluations are performed with a housing stiffness assumption that is typically determined only after the hardware is built. In addressing rotor stability, a rigid housing assumption was shown to predict an instability at a lower spin speed than a comparable flexible housing analysis. This rigid housing assumption therefore provides a conservative estimate of the stability threshold speed. A flexible housing appears to act as an energy absorber and dissipated some of the destabilizing force. The fact that a flexible housing is usually asymmetric and considerably heavier than the rotor was related to this apparent increase in rotor stability. Rigid housing analysis is proposed as a valuable screening criteria and may save time and money in construction of elaborate housing finite element models for linear stability analyses.

Development and validation of a general purpose linearization program for rigid aircraft models

NASA Technical Reports Server (NTRS)

Duke, E. L.; Antoniewicz, R. F.

1985-01-01

A FORTRAN program that provides the user with a powerful and flexible tool for the linearization of aircraft models is discussed. The program LINEAR numerically determines a linear systems model using nonlinear equations of motion and a user-supplied, nonlinear aerodynamic model. The system model determined by LINEAR consists of matrices for both the state and observation equations. The program has been designed to allow easy selection and definition of the state, control, and observation variables to be used in a particular model. Also, included in the report is a comparison of linear and nonlinear models for a high performance aircraft.

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.

Electrostatic contribution to the persistence length of a semiflexible dipolar chain.

PubMed

Podgornik, Rudi

2004-09-01

We investigate the electrostatic contribution to the persistence length of a semiflexible polymer chain whose segments interact via a screened Debye-Hückel dipolar interaction potential. We derive the expressions for the renormalized persistence length on the level of a 1/D-expansion method already successfully used in other contexts of polyelectrolye physics. We investigate different limiting forms of the renormalized persistence length of the dipolar chain and show that, in, general, it depends less strongly on the screening length than in the context of a monopolar chain. We show that for a dipolar chain the electrostatic persistence length in the same regime of the parameter phase space as the original Odijk-Skolnick-Fixman (OSF) form for a monopolar chain depends logarithmically on the screening length rather than quadratically. This can be understood solely on the basis of a swifter decay of the dipolar interactions with separation compared to the monopolar electrostatic interactions. We comment also on the general contribution of higher multipoles to the electrostatic renormalization of the bending rigidity.

Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

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

Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D., E-mail: sergei.ivanov@uni-rostock.de

2015-06-28

Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied,more » usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.« less

Biomechanically based simulation of brain deformations for intraoperative image correction: coupling of elastic and fluid models

NASA Astrophysics Data System (ADS)

Hagemann, Alexander; Rohr, Karl; Stiehl, H. Siegfried

2000-06-01

In order to improve the accuracy of image-guided neurosurgery, different biomechanical models have been developed to correct preoperative images w.r.t. intraoperative changes like brain shift or tumor resection. All existing biomechanical models simulate different anatomical structures by using either appropriate boundary conditions or by spatially varying material parameter values, while assuming the same physical model for all anatomical structures. In general, this leads to physically implausible results, especially in the case of adjacent elastic and fluid structures. Therefore, we propose a new approach which allows to couple different physical models. In our case, we simulate rigid, elastic, and fluid regions by using the appropriate physical description for each material, namely either the Navier equation or the Stokes equation. To solve the resulting differential equations, we derive a linear matrix system for each region by applying the finite element method (FEM). Thereafter, the linear matrix systems are linked together, ending up with one overall linear matrix system. Our approach has been tested using synthetic as well as tomographic images. It turns out from experiments, that the integrated treatment of rigid, elastic, and fluid regions significantly improves the prediction results in comparison to a pure linear elastic model.

Free-fall dynamics of a pair of rigidly linked disks

NASA Astrophysics Data System (ADS)

Kim, Taehyun; Chang, Jaehyeock; Kim, Daegyoum

2018-03-01

We investigate experimentally the free-fall motion of a pair of identical disks rigidly connected to each other. The three-dimensional coordinates of the pair of falling disks were constructed to quantitatively describe its trajectory, and the flow structure formed by the disk pair was identified by using dye visualization. The rigidly linked disk pair exhibits a novel falling pattern that creates a helical path with a conical configuration in which the lower disk rotates in a wider radius than the upper disk with respect to a vertical axis. The helical motion occurs consistently for the range of disk separation examined in this study. The dye visualization reveals that a strong, noticeable helical vortex core is generated from the outer tip of the lower disk during the helical motion. With an increasing length ratio, which is the ratio of the disk separation to the diameter of the disks, the nutation angle and the rate of change in the precession angle that characterize the combined helical and conical kinematics decrease linearly, whereas the pitch of the helical path increases linearly. Although all disk pairs undergo this helical motion, the horizontal-drift patterns of the disk pair depend on the length ratio.

Direct Imaging of Deformation and Disorder in Extended-Chain Polymer Fibers

DTIC Science & Technology

1991-03-01

conformation. A comparable physical picture of a rigid-rod molecule is that of a stiff strand of "uncooked linguine ". The linguine " analogy is...standing what happens when these " linguine -like" molecules 2 pack together in the solid state. Also, we wished to under- stand how supposedly completely

Advanced Polymer Network Structures

DTIC Science & Technology

2016-02-01

double networks in a single step was identified from coarse-grained molecular dynamics simulations of polymer solvents bearing rigid side chains dissolved...in a polymer network. Coarse-grained molecular dynamics simulations also explored the mechanical behavior of traditional double networks and...DRI), polymer networks, polymer gels, molecular dynamics simulations , double networks 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF

High-performance functional ecopolymers based on flora and fauna.

PubMed

Kaneko, Tatsuo

2007-01-01

Liquid crystalline (LC) polymers of rigid monomers based on flora and fauna were prepared by in-bulk polymerization. Para-coumaric (p-coumaric) acid [4-hydroxycinnamic acid (4HCA)] and its derivatives were selected as phytomonomers and bile acids were selected as biomonomers. The 4HCA homopolymer showed a thermotropic LC phase only in a state of low molecular weight. The copolymers of 4HCA with bile acids such as lithocholic acid (LCA) and cholic acid (CA) showed excellent cell compatibilities but low molecular weights. However, P(4HCA-co-CA)s allowed LC spinning to create molecularly oriented biofibers, presumably due to the chain entanglement that occurs during in-bulk chain propagation into hyperbranching architecture. P[4HCA-co-3,4-dihydroxycinnamic acid (DHCA)]s showed high molecular weight, high mechanical strength, high Young's modulus, and high softening temperature, which may be achieved through the entanglement by in-bulk formation of hyperbranching, rigid structures. P(4HCA-co-DHCA)s showed a smooth hydrolysis, in-soil degradation, and photo-tunable hydrolysis. Thus, P(4HCA-co-DHCA)s might be applied as an environmentally degradable plastic with extremely high performance.

Combined Use of Residual Dipolar Couplings and Solution X-ray Scattering To Rapidly Probe Rigid-Body Conformational Transitions in a Non-phosphorylatable Active-Site Mutant of the 128 kDa Enzyme I Dimer

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

Takayama, Yuki; Schwieters, Charles D.; Grishaev, Alexander

2012-10-23

The first component of the bacterial phosphotransferase system, enzyme I (EI), is a multidomain 128 kDa dimer that undergoes large rigid-body conformational transitions during the course of its catalytic cycle. Here we investigate the solution structure of a non-phosphorylatable active-site mutant in which the active-site histidine is substituted by glutamine. We show that perturbations in the relative orientations and positions of the domains and subdomains can be rapidly and reliably determined by conjoined rigid-body/torsion angle/Cartesian simulated annealing calculations driven by orientational restraints from residual dipolar couplings and shape and translation information afforded by small- and wide-angle X-ray scattering. Although histidinemore » and glutamine are isosteric, the conformational space available to a Gln side chain is larger than that for the imidazole ring of His. An additional hydrogen bond between the side chain of Gln189 located on the EIN{sup {alpha}/{beta}} subdomain and an aspartate (Asp129) on the EIN{sup {alpha}} subdomain results in a small ({approx}9{sup o}) reorientation of the EIN{sup {alpha}} and EIN{sup {alpha}/{beta}} subdomains that is in turn propagated to a larger reorientation ({approx}26{sup o}) of the EIN domain relative to the EIC dimerization domain, illustrating the positional sensitivity of the EIN domain and its constituent subdomains to small structural perturbations.« less

A stable partitioned FSI algorithm for rigid bodies and incompressible flow. Part II: General formulation

NASA Astrophysics Data System (ADS)

Banks, J. W.; Henshaw, W. D.; Schwendeman, D. W.; Tang, Qi

2017-08-01

A stable partitioned algorithm is developed for fluid-structure interaction (FSI) problems involving viscous incompressible flow and rigid bodies. This added-mass partitioned (AMP) algorithm remains stable, without sub-iterations, for light and even zero mass rigid bodies when added-mass and viscous added-damping effects are large. The scheme is based on a generalized Robin interface condition for the fluid pressure that includes terms involving the linear acceleration and angular acceleration of the rigid body. Added mass effects are handled in the Robin condition by inclusion of a boundary integral term that depends on the pressure. Added-damping effects due to the viscous shear forces on the body are treated by inclusion of added-damping tensors that are derived through a linearization of the integrals defining the force and torque. Added-damping effects may be important at low Reynolds number, or, for example, in the case of a rotating cylinder or rotating sphere when the rotational moments of inertia are small. In this second part of a two-part series, the general formulation of the AMP scheme is presented including the form of the AMP interface conditions and added-damping tensors for general geometries. A fully second-order accurate implementation of the AMP scheme is developed in two dimensions based on a fractional-step method for the incompressible Navier-Stokes equations using finite difference methods and overlapping grids to handle the moving geometry. The numerical scheme is verified on a number of difficult benchmark problems.

Perception of Elasticity in the Kinetic Illusory Object with Phase Differences in Inducer Motion

PubMed Central

Masuda, Tomohiro; Sato, Kazuki; Murakoshi, Takuma; Utsumi, Ken; Kimura, Atsushi; Shirai, Nobu; Kanazawa, So; Yamaguchi, Masami K.; Wada, Yuji

2013-01-01

Background It is known that subjective contours are perceived even when a figure involves motion. However, whether this includes the perception of rigidity or deformation of an illusory surface remains unknown. In particular, since most visual stimuli used in previous studies were generated in order to induce illusory rigid objects, the potential perception of material properties such as rigidity or elasticity in these illusory surfaces has not been examined. Here, we elucidate whether the magnitude of phase difference in oscillation influences the visual impressions of an object's elasticity (Experiment 1) and identify whether such elasticity perceptions are accompanied by the shape of the subjective contours, which can be assumed to be strongly correlated with the perception of rigidity (Experiment 2). Methodology/Principal Findings In Experiment 1, the phase differences in the oscillating motion of inducers were controlled to investigate whether they influenced the visual impression of an illusory object's elasticity. The results demonstrated that the impression of the elasticity of an illusory surface with subjective contours was systematically flipped with the degree of phase difference. In Experiment 2, we examined whether the subjective contours of a perceived object appeared linear or curved using multi-dimensional scaling analysis. The results indicated that the contours of a moving illusory object were perceived as more curved than linear in all phase-difference conditions. Conclusions/Significance These findings suggest that the phase difference in an object's motion is a significant factor in the material perception of motion-related elasticity. PMID:24205281

Evaluation of cast creep occurring during simulated clubfoot correction

PubMed Central

Cohen, Tamara L; Altiok, Haluk; Wang, Mei; McGrady, Linda M; Krzak, Joseph; Graf, Adam; Tarima, Sergey; Smith, Peter A; Harris, Gerald, F

2016-01-01

The Ponseti method is a widely accepted and highly successful conservative treatment of pediatric clubfoot involving weekly manipulations and cast applications. Qualitative assessments have indicated the potential success of the technique with cast materials other than standard plaster of Paris. However, guidelines for clubfoot correction based on the mechanical response of these materials have yet to be investigated. The current study sought to characterize and compare the ability of three standard cast materials to maintain the Ponseti corrected foot position by evaluating cast creep response. A dynamic cast testing device, built to model clubfoot correction, was wrapped in plaster-of-Paris, semi-rigid fiberglass, and rigid fiberglass. Three-dimensional motion responses to two joint stiffnesses were recorded. Rotational creep displacement and linearity of the limb-cast composite were analyzed. Minimal change in position over time was found for all materials. Among cast materials, the rotational creep displacement was significantly different (p < 0.0001). The most creep displacement occurred in the plaster-of-Paris (2.0 degrees), then the semi-rigid fiberglass (1.0 degrees), and then the rigid fiberglass (0.4 degrees). Torque magnitude did not affect creep displacement response. Analysis of normalized rotation showed quasi—linear viscoelastic behavior. This study provided a mechanical evaluation of cast material performance as used for clubfoot correction. Creep displacement dependence on cast material and insensitivity to torque were discovered. This information may provide a quantitative and mechanical basis for future innovations for clubfoot care. PMID:23636764

A Lie-Theoretic Perspective on O(n) Mass Matrix Inversion for Serial Manipulators and Polypeptide Chains.

PubMed

Lee, Kiju; Wang, Yunfeng; Chirikjian, Gregory S

2007-11-01

Over the past several decades a number of O(n) methods for forward and inverse dynamics computations have been developed in the multi-body dynamics and robotics literature. A method was developed in 1974 by Fixman for O(n) computation of the mass-matrix determinant for a serial polymer chain consisting of point masses. In other recent papers, we extended this method in order to compute the inverse of the mass matrix for serial chains consisting of point masses. In the present paper, we extend these ideas further and address the case of serial chains composed of rigid-bodies. This requires the use of relatively deep mathematics associated with the rotation group, SO(3), and the special Euclidean group, SE(3), and specifically, it requires that one differentiates functions of Lie-group-valued argument.

Attitude dynamics simulation subroutines for systems of hinge-connected rigid bodies

NASA Technical Reports Server (NTRS)

Fleischer, G. E.; Likins, P. W.

1974-01-01

Several computer subroutines are designed to provide the solution to minimum-dimension sets of discrete-coordinate equations of motion for systems consisting of an arbitrary number of hinge-connected rigid bodies assembled in a tree topology. In particular, these routines may be applied to: (1) the case of completely unrestricted hinge rotations, (2) the totally linearized case (all system rotations are small), and (3) the mixed, or partially linearized, case. The use of the programs in each case is demonstrated using a five-body spacecraft and attitude control system configuration. The ability of the subroutines to accommodate prescribed motions of system bodies is also demonstrated. Complete listings and user instructions are included for these routines (written in FORTRAN V) which are intended as multi- and general-purpose tools in the simulation of spacecraft and other complex electromechanical systems.

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.

A geometrically controlled rigidity transition in a model for confluent 3D tissues

NASA Astrophysics Data System (ADS)

Merkel, Matthias; Manning, M. Lisa

2018-02-01

The origin of rigidity in disordered materials is an outstanding open problem in statistical physics. Previously, a class of 2D cellular models has been shown to undergo a rigidity transition controlled by a mechanical parameter that specifies cell shapes. Here, we generalize this model to 3D and find a rigidity transition that is similarly controlled by the preferred surface area S 0: the model is solid-like below a dimensionless surface area of {s}0\\equiv {S}0/{\\bar{V}}2/3≈ 5.413 with \\bar{V} being the average cell volume, and fluid-like above this value. We demonstrate that, unlike jamming in soft spheres, residual stresses are necessary to create rigidity. These stresses occur precisely when cells are unable to obtain their desired geometry, and we conjecture that there is a well-defined minimal surface area possible for disordered cellular structures. We show that the behavior of this minimal surface induces a linear scaling of the shear modulus with the control parameter at the transition point, which is different from the scaling observed in particulate matter. The existence of such a minimal surface may be relevant for biological tissues and foams, and helps explain why cell shapes are a good structural order parameter for rigidity transitions in biological tissues.

Green waste cooking oil-based rigid polyurethane foam

NASA Astrophysics Data System (ADS)

Enderus, N. F.; Tahir, S. M.

2017-11-01

Polyurethane is a versatile polymer traditionally prepared using petroleum-based raw material. Petroleum, however, is a non-renewable material and polyurethane produced was found to be non-biodegradable. In quest for a more environmentally friendly alternative, wastecooking oil, a highly abundant domestic waste with easily derivatized structure, is a viable candidate to replace petroleum. In this study,an investigation to determine physical and chemical properties of rigid polyurethane (PU) foam from waste cooking oil (WCO) was carried out. WCO was first adsorbed by using coconut husk activated carbon adsorbent prior to be used for polyol synthesis. The purified WCO was then used to synthesize polyol via transesterification reaction to yield alcohol groups in the WCO chains structure. Finally, the WCO-based polyol was used to prepare rigid PU foam. The optimum formulation for PU formation was found to be 90 polyol: 60 glycerol: 54 water: 40 diethanolamine: 23 diisocyanate. The rigid PU foam has density of 208.4 kg/m3 with maximum compressive strength and capability to receive load at 0.03 MPa and 0.09 kN, respectively. WCO-based PU can potentially be used to replace petroleum-based PU as house construction materials such as insulation panels.

Manual on the Flight of Flexible Aircraft in Turbulence (Manuel sur le Vol des Avions Non-rigides en Milieu Turbulent)

DTIC Science & Technology

1991-05-01

Static Non-Linearity 106 0 y = f(dx/dt) = -f(-dx/dt) = = > Static Non-Linearity • y = f(x,sign(dx/dt)) = = > Hysteresis-Type Non-Linearity = -f(-x,sign... Havilland Division Garratt Blvd., Downsview Ontario M3K I Y5 Canada CONTENTS ABSTRACT NOTATION 1. INTRODUCTION 2. THE SDG GUST MODEL 3. ESTABLISHING CRITICAL...VENT ETRE ADRESSEES DIRECTEMENT N AU SERVICE NATIONAL TECHNIQUE, Dh INFORMATION (NTIS) DONT LADRESSE SUIT AGENCES DE VENTE National Technical

Analysis and simulation of a magnetic bearing suspension system for a laboratory model annular momentum control device

NASA Technical Reports Server (NTRS)

Groom, N. J.; Woolley, C. T.; Joshi, S. M.

1981-01-01

A linear analysis and the results of a nonlinear simulation of a magnetic bearing suspension system which uses permanent magnet flux biasing are presented. The magnetic bearing suspension is part of a 4068 N-m-s (3000 lb-ft-sec) laboratory model annular momentum control device (AMCD). The simulation includes rigid body rim dynamics, linear and nonlinear axial actuators, linear radial actuators, axial and radial rim warp, and power supply and power driver current limits.

Polymerization and Structure of Bio-Based Plastics: A Computer Simulation

NASA Astrophysics Data System (ADS)

Khot, Shrikant N.; Wool, Richard P.

2001-03-01

We recently examined several hundred chemical pathways to convert chemically functionalized plant oil triglycerides, monoglycerides and reactive diluents into high performance plastics with a broad range of properties (US Patent No. 6,121,398). The resulting polymers had linear, branched, light- and highly-crosslinked chain architectures and could be used as pressure sensitive adhesives, elastomers and high performance rigid thermoset composite resins. To optimize the molecular design and minimize the number of chemical trials in this system with excess degrees of freedom, we developed a computer simulation of the free radical polymerization process. The triglyceride structure, degree of chemical substitution, mole fractions, fatty acid distribution function, and reaction kinetic parameters were used as initial inputs on a 3d lattice simulation. The evolution of the network fractal structure was computed and used to measure crosslink density, dangling ends, degree of reaction and defects in the lattice. The molecular connectivity was used to determine strength via a vector percolation model of fracture. The simulation permitted the optimal design of new bio-based materials with respect to monomer selection, cure reaction conditions and desired properties. Supported by the National Science Foundation

Chain Confinement in Electrospun Nanocomposites: using Thermal Analysis to Investigate Polymer-Filler Interactions

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

Q Ma; B Mao; P Cebe

2011-12-31

We investigate the interaction of the polymer matrix and filler in electrospun nanofibers using advanced thermal analysis methods. In particular, we study the ability of silicon dioxide nanoparticles to affect the phase structure of poly(ethylene terephthalate), PET. SiO{sub 2} nanoparticles (either unmodified or modified with silane) ranging from 0 to 2.0 wt% in PET were electrospun from hexafluoro-2-propanol solutions. The morphologies of both the electrospun (ES) nanofibers and the SiO{sub 2} powders were observed by scanning and transmission electron microscopy, while the amorphous or crystalline nature of the fibers was determined by real-time wide-angle X-ray scattering. The fractions of themore » crystal, mobile amorphous, and rigid amorphous phases of the non-woven, nanofibrous composite mats were quantified by using heat capacity measurements. The amount of the immobilized polymer layer, the rigid amorphous fraction, was obtained from the specific reversing heat capacity for both as-spun amorphous fibers and isothermally crystallized fibers. Existence of the rigid amorphous phase in the absence of crystallinity was verified in nanocomposite fibers, and two origins for confinement of the rigid amorphous fraction are proposed. Thermal analysis of electrospun fibers, including quasi-isothermal methods, provides new insights to quantitatively characterize the polymer matrix phase structure and thermal transitions, such as devitrification of the rigid amorphous fraction.« less

The design and analysis of mooring system

NASA Astrophysics Data System (ADS)

Li, Yixuan

2017-05-01

In this paper, the force status and a design method of single chain mooring system for shallow sea observation network are studied. With treating the link of a chain, steel drum and steel pipe as a rigid body, the recurrence model is established by using Newton's first law and the law of Moment equilibrium theorem. Via the simplified calculation of dichotomy searching, we determine the design parameters of mooring system, such as anchor model, anchor chain length, heavy ball quality under different water flow and wind conditions. We apply MATLAB to simulate the internal steady state of the system in the fixed scheme, water depth of buoy and swimming area to meet the decision-making needs, providing an idea for the actual scheme design of mooring system.

Nonlinear vibrational excitations in molecular crystals molecular mechanics calculations

NASA Astrophysics Data System (ADS)

Pumilia, P.; Abbate, S.; Baldini, G.; Ferro, D. R.; Tubino, R.

1992-03-01

The coupling constant for vibrational solitons χ has been examined in a molecular mechanics model for acetanilide (ACN) molecular crystal. According to A.C. Scott, solitons can form and propagate in solid acetanilide over a threshold energy value. This can be regarded as a structural model for the spines of hydrogen bond chains stabilizing the α helical structure of proteins. A one dimensional hydrogen bond chain of ACN has been built, for which we have found that, even though experimental parameters are correctly predicted, the excessive rigidity of the isolated chain prevents the formation of a localized distortion around the excitation. Yet, C=O coupling value with softer lattice modes could be rather high, allowing self-trapping to take place.

Deformable anatomical templates for brachytherapy treatment planning in radiotherapy of cervical cancer

NASA Astrophysics Data System (ADS)

Christensen, Gary E.; Williamson, Jeffrey F.; Chao, K. S. C.; Miller, Michael I.; So, F. B.; Vannier, Michael W.

1997-10-01

This paper describes a new method to register serial, volumetric x-ray computed tomography (CT) data sets for tracking soft-tissue deformation caused by insertion of intracavity brachytherapy applicators to treat cervical cancer. 3D CT scans collected from the same patient with and without a brachytherapy applicator are registered to aid in computation of the radiation dose to tumor and normal tissue. The 3D CT image volume of pelvic anatomy with the applicator. Initial registration is accomplished by rigid alignment of the pelvic bones and non-rigid alignment of gray scale CT data and hand segmentations of the vagina, cervix, bladder, and rectum. A viscous fluid transformation model is used for non-rigid registration to allow for local, non-linear registration of the vagina, cervix, bladder, and rectum without disturbing the rigid registration of the bony pelvis and adjacent structures. Results are presented in which two 3D CT data sets of the same patient - imaged with and without a brachytherapy applicator - are registered.

Motion of a Rigid Body in a Special Lorentz Gas: Loss of Memory Effect

NASA Astrophysics Data System (ADS)

Koike, Kai

2018-06-01

Linear motion of a rigid body in a special kind of Lorentz gas is mathematically analyzed. The rigid body moves against gas drag according to Newton's equation. The gas model is a special Lorentz gas consisting of gas molecules and background obstacles, which was introduced in Tsuji and Aoki (J Stat Phys 146:620-645, 2012). The specular boundary condition is imposed on the resulting kinetic equation. This study complements the numerical study by Tsuji and Aoki cited above—although the setting in this paper is slightly different from theirs, qualitatively the same asymptotic behavior is proved: The velocity V(t) of the rigid body decays exponentially if the obstacles undergo thermal motion; if the obstacles are motionless, then the velocity V(t) decays algebraically with a rate t^{- 5} independent of the spatial dimension. This demonstrates the idea that interaction of the molecules with the background obstacles destroys the memory effect due to recollision.

Polylactide based nanocomposites: Processing, structure and performance relationship

NASA Astrophysics Data System (ADS)

Karami, Shahir

The application of biodegradable polymers has been offered to the packing industry wishing to overcome the environmental consequence of employing the petroleum-based polymers. Furthermore, the unstable oil market urged the industry to look for the substitution of the renewable resources. Polylactide is known as the most popular biodegradable polymer developed on a large scale. Nevertheless, the growing contribution of polylactide to packing industry is somewhat restricted owing to its inherent brittleness and weak barrier properties. Therefore, the main objective of this thesis was defined to build a fundamental relationship between processing parameters and solid-state microstructure to improve the performance of polylactide. Polylactide nanocomposites were prepared through a multi-step melt compounding process. Dispersion of organically modified layered nanoparticles was detected by the WAXS and TEM characterizations, demonstrating the formation of intercalated nanocomposites. Relaxation spectrum exhibited the restricted dynamics of fraction of amorphous phase confined in polymer-particle interphase through dynamic rheological measurements. The fraction of rigid amorphous chains was estimated using TMDSC and DMA. This increased with nanoparticle content, levelling off upon the aggregation of nanoparticles. The annealing-induced molecular ordering was detected by FR-IR, increasing the rigid amorphous fraction. Cold crystallization was investigated during non-isothermal process using TMDSC. Crystallization kinetic was studied through the evaluation of Avrami parameters in isothermal process at the temperature range of Tg+30°C to Tg+70°C. The crystallization rate depressed with the nanoparticle content due to the enhanced fraction of rigid amorphous chains, as well as, the topological constraints derived from the formation of network structure. Nevertheless, the nanoparticles acted as heterogeneous nucleating sites upon devitrification of the rigid amorphous chains at the temperatures above Tg+60°C. The larger nucleation density resulted in the formation of larger rigid amorphous fraction along the semi-crystalline matrix. The variation of complex viscosity at molten state reflected the degradation of polylactide. The NMR characterization was conducted to investigate the effect of dispersed nanoparticle on the degradation of matrix. It was found that the degradation was accelerated with the nanoparticle content. However, the stereoregularity of polylactide chains remained unchanged in the presence of nanoparticles. Mechanical response was measured using Instron mechanical tester. The fractured surface was analyzed by SEM and SAXS. It was found that, toughness improved with the nanoparticle content due to enhanced occupation density upon multiple crazing. Structural evolutions were investigated during a hot-drawing process, at different initial strain rates and the temperatures of Tg+10°C and Tg+30°C, using WAXS and SAXS offline measurements. A mesomorphic phase was developed along the drawing direction, at Tg+10°C, composed of a bundle of parallel extended molecules with a looser lateral chain packing compared to that of the crystalline domain. The mesophase was disordered at the glass transition temperature of the bulk-like chains acting as the precursor of crystalline ordering. A lower fraction of the intermediate ordering was detected with nanoparticle content than that of the neat polymer at constant processing conditions. The slippage of frozen-in mesophase triggered strain hardening behavior during the stretching process at room temperature. This led to the significant improvement of film toughness and stress at break. Spherulitic crystalline domains were formed upon development of point-like nuclei during the drawing process at T g+30°C. No mesophase was detected at Tg+30°C, due to the enhanced contribution of chain relaxation. Line-like nuclei were observed at the highest applied strain rate, resulting in the formation of a fibrillar crystalline structure. Oxygen flux density was measured at constant temperature and relative humidity. Permeability coefficient was distinguished to the diffusivity and solubility, through the analysis of the non-steady state flux density with time by an approximate solution of the Fick's second law. The diffusivity decreased in the presence of the impermeable matters, crystalline domains and nanoparticle layers. Furthermore, the restricted dynamics of rigid amorphous fraction decreased the fraction of dynamic free volumes. Solubility increased with the nanoparticle content due to the accelerated degradation. The aggregation of nanoparticles also intensified the accessible static free volume. The chain architecture of toughening modifier was disclosed using NMR and FT-IR. It was believed to be Ethylene-Butyl Acrylate copolymer with the average sequence length of 10:1. A two-phase morphology was detected by SEM for polylactide/toughening modifier immiscible blend. DMA measurements exhibited a third glass transition, corresponding to development of polylactide-ethylene-butyl acrylate terpolymer at the interface through a transesterification reaction. The enhancement of zero shear viscosity of blends attributed to the Marangoni stresses derived from the uneven distribution of in-situ formed terpolymer at the interface. An intermeshed morphology was observed upon the incorporation of the nanoparticles. The nanoparticles were accommodated within the polylactide phase determined by the calculation of wetting parameter. The morphology connectivity led to the outstanding improvement of toughness.

Changes in conformational dynamics of basic side chains upon protein–DNA association

PubMed Central

Esadze, Alexandre; Chen, Chuanying; Zandarashvili, Levani; Roy, Sourav; Pettitt, B. Montgometry; Iwahara, Junji

2016-01-01

Basic side chains play major roles in recognition of nucleic acids by proteins. However, dynamic properties of these positively charged side chains are not well understood. In this work, we studied changes in conformational dynamics of basic side chains upon protein–DNA association for the zinc-finger protein Egr-1. By nuclear magnetic resonance (NMR) spectroscopy, we characterized the dynamics of all side-chain cationic groups in the free protein and in the complex with target DNA. Our NMR order parameters indicate that the arginine guanidino groups interacting with DNA bases are strongly immobilized, forming rigid interfaces. Despite the strong short-range electrostatic interactions, the majority of the basic side chains interacting with the DNA phosphates exhibited high mobility, forming dynamic interfaces. In particular, the lysine side-chain amino groups exhibited only small changes in the order parameters upon DNA-binding. We found a similar trend in the molecular dynamics (MD) simulations for the free Egr-1 and the Egr-1–DNA complex. Using the MD trajectories, we also analyzed side-chain conformational entropy. The interfacial arginine side chains exhibited substantial entropic loss upon binding to DNA, whereas the interfacial lysine side chains showed relatively small changes in conformational entropy. These data illustrate different dynamic characteristics of the interfacial arginine and lysine side chains. PMID:27288446

Polymer mobility in cell walls of cucumber hypocotyls

NASA Technical Reports Server (NTRS)

Fenwick, K. M.; Apperley, D. C.; Cosgrove, D. J.; Jarvis, M. C.

1999-01-01

Cell walls were prepared from the growing region of cucumber (Cucumis sativus) hypocotyls and examined by solid-state 13C NMR spectroscopy, in both enzymically active and inactivated states. The rigidity of individual polymer segments within the hydrated cell walls was assessed from the proton magnetic relaxation parameter, T2, and from the kinetics of cross-polarisation from 1H to 13C. The microfibrils, including most of the xyloglucan in the cell wall, as well as cellulose, behaved as very rigid solids. A minor xyloglucan fraction, which may correspond to cross-links between microfibrils, shared a lower level of rigidity with some of the pectic galacturonan. Other pectins, including most of the galactan side-chain residues of rhamnogalacturonan I, were much more mobile and behaved in a manner intermediate between the solid and liquid states. The only difference observed between the enzymically active and inactive cell walls, was the loss of a highly mobile, methyl-esterified galacturonan fraction, as the result of pectinesterase activity.

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.

Summary of Research/Publications

NASA Technical Reports Server (NTRS)

1997-01-01

Summary of research/publications include:(1) Comment on broadening of water microwave lines by collisions with helium atoms; (2) Calculations of ion-molecule deuterium fractionation reactions involving HD; (3) Ab initio predictions on the rotational spectra of carbon-chain carbene molecules; (4) Theoretical IR spectra of ionized naphthalene; (5) Improved collisional excitation rates for interstellar water; (6) Calculations on the competition between association and reaction for C3H+ + H2; (7) Theoretical infrared spectra of some model polycyclic aromatic hydrocarbons: effect of ionization; (8) Calculations concerning interstellar isomeric abundance ratios for C3H and C3H2; (9) New calculations on the ion-molecule processes C2H2+ + H2 C2H3+ + H and C2H2+ + H2 C2H4+; (10) Anisotropic rigid rotor potential energy function for H2O-H2; (11) A correlated ab initio study of linear carbon-chain radicals CnH (n=2-7); (12) Ab initio characterization of MgCCH, MgCCH+, and MgC2 and pathways to their formation in the interstellar medium; (13) Why HOC+ is detectable in interstellar clouds: The rate of the reaction between HOC+ and H2; (14) A correlated ab initio study of the X 2A 1 and A 2E states of MgCH3; (15) On the stability of interstellar carbon clusters: The rate of the reaction between C3 and O; and (16) The rate of the reaction between CN and C2H2 at interstellar temperatures.

Molecular Strategies for Morphology Control in Semiconducting Polymers for Optoelectronics.

PubMed

Rahmanudin, Aiman; Sivula, Kevin

2017-06-28

Solution-processable semiconducting polymers have been explored over the last decades for their potential applications in inexpensively fabricated transistors, diodes and photovoltaic cells. However, a remaining challenge in the field is to control the solid-state self-assembly of polymer chains in thin films devices, as the aspects of (semi)crystallinity, grain boundaries, and chain entanglement can drastically affect intra-and inter-molecular charge transport/transfer and thus device performance. In this short review we examine how the aspects of molecular weight and chain rigidity affect solid-state self-assembly and highlight molecular engineering strategies to tune thin film morphology. Side chain engineering, flexibly linking conjugation segments, and block co-polymer strategies are specifically discussed with respect to their effect on field effect charge carrier mobility in transistors and power conversion efficiency in solar cells. Example systems are taken from recent literature including work from our laboratories to illustrate the potential of molecular engineering semiconducting polymers.

Simultaneous covalent and noncovalent hybrid polymerizations

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

Yu, Z.; Tantakitti, F.; Yu, T.

Covalent and supramolecular polymers are two distinct forms of soft matter, composed of long chains of covalently and noncovalently linked structural units, respectively. We report a hybrid system formed by simultaneous covalent and supramolecular polymerizations of monomers. The process yields cylindrical fibers of uniform diameter that contain covalent and supramolecular compartments, a morphology not observed when the two polymers are formed independently. The covalent polymer has a rigid aromatic imine backbone with helicoidal conformation, and its alkylated peptide side chains are structurally identical to the monomer molecules of supramolecular polymers. In the hybrid system, covalent chains grow to higher averagemore » molar mass relative to chains formed via the same polymerization in the absence of a supramolecular compartment. The supramolecular compartments can be reversibly removed and re-formed to reconstitute the hybrid structure, suggesting soft materials with novel delivery or repair functions.« less

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

Alexeev, A. V.; Maltseva, D. V.; Ivanov, V. A., E-mail: ivanov@polly.phys.msu.ru

We study force-extension curves of a single semiflexible chain consisting of several rigid rods connected by flexible spacers. The atomic force microscopy and laser optical or magnetic tweezers apparatus stretching these rod-coil macromolecules are discussed. In addition, the stretching by external isotropic force is analyzed. The main attention is focused on computer simulation and analytical results. We demonstrate that the force-extension curves for rod-coil chains composed of two or three rods of equal length differ not only quantitatively but also qualitatively in different probe methods. These curves have an anomalous shape for a chain of two rods. End-to-end distributions ofmore » rod-coil chains are calculated by Monte Carlo method and compared with analytical equations. The influence of the spacer’s length on the force-extension curves in different probe methods is analyzed. The results can be useful for interpreting experiments on the stretching of rod-coil block-copolymers.« less

A Lie-Theoretic Perspective on O(n) Mass Matrix Inversion for Serial Manipulators and Polypeptide Chains

PubMed Central

Lee, Kiju; Wang, Yunfeng; Chirikjian, Gregory S.

2010-01-01

Over the past several decades a number of O(n) methods for forward and inverse dynamics computations have been developed in the multi-body dynamics and robotics literature. A method was developed in 1974 by Fixman for O(n) computation of the mass-matrix determinant for a serial polymer chain consisting of point masses. In other recent papers, we extended this method in order to compute the inverse of the mass matrix for serial chains consisting of point masses. In the present paper, we extend these ideas further and address the case of serial chains composed of rigid-bodies. This requires the use of relatively deep mathematics associated with the rotation group, SO(3), and the special Euclidean group, SE(3), and specifically, it requires that one differentiates functions of Lie-group-valued argument. PMID:20165563

Dynamics of Cancer Cell near Collagen Fiber Chain

NASA Astrophysics Data System (ADS)

Kim, Jihan; Sun, Bo

Cell migration is an integrated process that is important in life. Migration is essential for embryonic development as well as homeostatic processes such as wound healing and immune responses. When cell migrates through connective extracellular matrix (ECM), it applies cellular traction force to ECM and senses the rigidity of their local environment. We used human breast cancer cell (MDA-MB-231) which is highly invasive and applies strong traction force to ECM. As cancer cell applies traction force to type I collage-based ECM, it deforms collagen fibers near the surface. Patterns of deforming collagen fibers are significantly different with pairs of cancer cells compared to a single cancer cell. While a pair of cancer cells within 60 um creates aligned collagen fiber chains between them permanently, a single cancer cell does not form any fiber chains. In this experiment we measured a cellular response and an interaction between a pair of cells through the chain. Finally, we analyzed correlation of directions between cancer cell migration and the collagen chain alignment.

Thermodynamic and dynamic behaviors of self-organizing polymeric systems

NASA Astrophysics Data System (ADS)

Zhao, Yiqiang

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

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.

A stable partitioned FSI algorithm for rigid bodies and incompressible flow. Part I: Model problem analysis

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

Banks, J. W.; Henshaw, W. D.; Schwendeman, D. W.

A stable partitioned algorithm is developed for fluid-structure interaction (FSI) problems involving viscous incompressible flow and rigid bodies. This added-mass partitioned (AMP) algorithm remains stable, without sub-iterations, for light and even zero mass rigid bodies when added-mass and viscous added-damping effects are large. The scheme is based on a generalized Robin interface condition for the fluid pressure that includes terms involving the linear acceleration and angular acceleration of the rigid body. Added mass effects are handled in the Robin condition by inclusion of a boundary integral term that depends on the pressure. Added-damping effects due to the viscous shear forcesmore » on the body are treated by inclusion of added-damping tensors that are derived through a linearization of the integrals defining the force and torque. Added-damping effects may be important at low Reynolds number, or, for example, in the case of a rotating cylinder or rotating sphere when the rotational moments of inertia are small. In this second part of a two-part series, the general formulation of the AMP scheme is presented including the form of the AMP interface conditions and added-damping tensors for general geometries. A fully second-order accurate implementation of the AMP scheme is developed in two dimensions based on a fractional-step method for the incompressible Navier-Stokes equations using finite difference methods and overlapping grids to handle the moving geometry. Here, the numerical scheme is verified on a number of difficult benchmark problems.« less

A stable partitioned FSI algorithm for rigid bodies and incompressible flow. Part I: Model problem analysis

DOE PAGES

Banks, J. W.; Henshaw, W. D.; Schwendeman, D. W.; ...

2017-01-20

A stable partitioned algorithm is developed for fluid-structure interaction (FSI) problems involving viscous incompressible flow and rigid bodies. This added-mass partitioned (AMP) algorithm remains stable, without sub-iterations, for light and even zero mass rigid bodies when added-mass and viscous added-damping effects are large. The scheme is based on a generalized Robin interface condition for the fluid pressure that includes terms involving the linear acceleration and angular acceleration of the rigid body. Added mass effects are handled in the Robin condition by inclusion of a boundary integral term that depends on the pressure. Added-damping effects due to the viscous shear forcesmore » on the body are treated by inclusion of added-damping tensors that are derived through a linearization of the integrals defining the force and torque. Added-damping effects may be important at low Reynolds number, or, for example, in the case of a rotating cylinder or rotating sphere when the rotational moments of inertia are small. In this second part of a two-part series, the general formulation of the AMP scheme is presented including the form of the AMP interface conditions and added-damping tensors for general geometries. A fully second-order accurate implementation of the AMP scheme is developed in two dimensions based on a fractional-step method for the incompressible Navier-Stokes equations using finite difference methods and overlapping grids to handle the moving geometry. Here, the numerical scheme is verified on a number of difficult benchmark problems.« less

Rigid versus semi-rigid orthotic use following TMC arthroplasty: a randomized controlled trial.

PubMed

Prosser, Rosemary; Hancock, Mark J; Nicholson, Leslie; Merry, Cathy; Thorley, Felicity; Wheen, Douglass

2014-01-01

The trapeziometacarpal (TMC) joint of the human thumb is the second most common joint in the hand affected by osteoarthritis. TMC arthroplasty is a common procedure used to alleviate symptoms. No randomized controlled trials have been published on the efficacy of different post-operative orthotic regimes. Fifty six participants who underwent TMC arthroplasty were allocated to either rigid orthotic or semi-rigid orthotic groups. Both groups started an identical exercise program at two weeks following surgery. Outcome measures were assessed by an assessor blinded to group allocation. The primary outcome was the Patient Rated Wrist and Hand Evaluation (PRWHE) and secondary outcomes included the Michigan Hand Questionnaire (MHQ), thumb palmar abduction, first metacarpophalangeal extension and three point pinch grip. Measures were taken pre-operatively, at six weeks, three months and one year post-operatively. Between-group differences were analyzed with linear regression. Both groups performed equally well. There was no significant between-group difference for PRWHE scores (0.47, CI -11.5 to 12.4), including subscales for pain and function, or for any of the secondary outcomes at one year follow-up. We found no difference in outcomes between using a rigid or semi-rigid orthosis after TMC arthroplasty. Patient comfort, cost and availability may determine choice between orthoses in clinical practice. 1b RCT. Copyright © 2014 Hanley & Belfus. Published by Elsevier Inc. All rights reserved.

Tolman lengths and rigidity constants of multicomponent fluids: Fundamental theory and numerical examples

NASA Astrophysics Data System (ADS)

Aasen, Ailo; Blokhuis, Edgar M.; Wilhelmsen, Øivind

2018-05-01

The curvature dependence of the surface tension can be described by the Tolman length (first-order correction) and the rigidity constants (second-order corrections) through the Helfrich expansion. We present and explain the general theory for this dependence for multicomponent fluids and calculate the Tolman length and rigidity constants for a hexane-heptane mixture by use of square gradient theory. We show that the Tolman length of multicomponent fluids is independent of the choice of dividing surface and present simple formulae that capture the change in the rigidity constants for different choices of dividing surface. For multicomponent fluids, the Tolman length, the rigidity constants, and the accuracy of the Helfrich expansion depend on the choice of path in composition and pressure space along which droplets and bubbles are considered. For the hexane-heptane mixture, we find that the most accurate choice of path is the direction of constant liquid-phase composition. For this path, the Tolman length and rigidity constants are nearly linear in the mole fraction of the liquid phase, and the Helfrich expansion represents the surface tension of hexane-heptane droplets and bubbles within 0.1% down to radii of 3 nm. The presented framework is applicable to a wide range of fluid mixtures and can be used to accurately represent the surface tension of nanoscopic bubbles and droplets.

On geoid heights derived from GEOS 3 altimeter data along the Hawaiian-Emperor seamount chain

NASA Technical Reports Server (NTRS)

Watts, A. B.

1979-01-01

The geoid heights derived from preliminary GEOS 3 satellite radar altimeter data over the Hawaiian-Emperor seamount chain are examined. Two objectives are pursued: (1) to evaluate the contribution of the topography of the seamount chain and its compensation to the marine geoid; and (2) to determine whether geoid heights derived from GEOS 3 altimeter data can be used to provide information on isostasy at geological features such as the Hawaiian-Emperor seamount chain which formed as relatively young loads on the oceanic lithosphere. Short-wavelength geoid highs of 5-12 m over the crest of the seamount chain and geoid lows over flanking regions are observed. The geological undulations can be explained by a simple model in which the seamount-chain load is supported by a strong rigid lithospheric plate. The elastic thickness estimates agree with values based on surface ship gravity and bathymetry observations, and provide further support to the hypothesis that the elastic thickness acquired at a surface load depends on the temperature gradient of the lithosphere at the time of loading.

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.

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.

Dynamics of Multibody Systems Near Lagrangian Points

NASA Astrophysics Data System (ADS)

Wong, Brian

This thesis examines the dynamics of a physically connected multi-spacecraft system in the vicinity of the Lagrangian points of a Circular Restricted Three-Body System. The spacecraft system is arranged in a wheel-spoke configuration with smaller and less massive satellites connected to a central hub using truss/beams or tether connectors. The kinematics of the system is first defined, and the kinetic, gravitational potential energy and elastic potential energy of the system are derived. The Assumed Modes Method is used to discretize the continuous variables of the system, and a general set of ordinary differential equations describing the dynamics of the connectors and the central hub are obtained using the Lagrangian method. The flexible body dynamics of the tethered and truss connected systems are examined using numerical simulations. The results show that these systems experienced only small elastic deflections when they are naturally librating or rotating at moderate angular velocities, and these deflections have relatively small effect on the attitude dynamics of the systems. Based on these results, it is determined that the connectors can be modeled as rigid when only the attitude dynamics of the system is of interest. The equations of motion of rigid satellites stationed at the Lagrangian points are linearized, and the stability conditions of the satellite are obtained from the linear equations. The required conditions are shown to be similar to those of geocentric satellites. Study of the linear equations also revealed the resonant conditions of rigid Lagrangian point satellites, when a librational natural frequency of the satellite matches the frequency of its station-keeping orbit leading to large attitude motions. For tethered satellites, the linear analysis shows that the tethers are in stable equilibrium when they lie along a line joining the two primary celestial bodies of the Three-Body System. Numerical simulations are used to study the long term dynamics of two sample rigid bodies when they are in different periodic orbits around a collinear point, and the tether librations of a two-tether system in the same orbits. The results show that the rigid satellites and the tethered system experience greater attitude motions when they are in larger periodic orbits. The dynamics of variable length systems are also studied in order to determine the control cost associated with moving the end bodies in a gapless spiral to cover the area spanned by the system. The control cost is relatively low during tether deployment, and negligible effort is required to maintain the angular velocity of the tethered system after deployment. A set of recommendations for the applications of Lagrangian-point physically-connected systems are presented as well as some future research directions are suggested.

Molecular theory of lipid-protein interaction and the Lalpha-HII transition.

PubMed Central

May, S; Ben-Shaul, A

1999-01-01

We present a molecular-level theory for lipid-protein interaction and apply it to the study of lipid-mediated interactions between proteins and the protein-induced transition from the planar bilayer (Lalpha) to the inverse-hexagonal (HII) phase. The proteins are treated as rigid, membrane-spanning, hydrophobic inclusions of different size and shape, e.g., "cylinder-like," "barrel-like," or "vase-like." We assume strong hydrophobic coupling between the protein and its neighbor lipids. This means that, if necessary, the flexible lipid chains surrounding the protein will stretch, compress, and/or tilt to bridge the hydrophobic thickness mismatch between the protein and the unperturbed bilayer. The system free energy is expressed as an integral over local molecular contributions, the latter accounting for interheadgroup repulsion, hydrocarbon-water surface energy, and chain stretching-tilting effects. We show that the molecular interaction constants are intimately related to familiar elastic (continuum) characteristics of the membrane, such as the bending rigidity and spontaneous curvature, as well as to the less familiar tilt modulus. The equilibrium configuration of the membrane is determined by minimizing the free energy functional, subject to boundary conditions dictated by the size, shape, and spatial distribution of inclusions. A similar procedure is used to calculate the free energy and structure of peptide-free and peptide-rich hexagonal phases. Two degrees of freedom are involved in the variational minimization procedure: the local length and local tilt angle of the lipid chains. The inclusion of chain tilt is particularly important for studying noncylindrical (for instance, barrel-like) inclusions and analyzing the structure of the HII lipid phase; e.g., we find that chain tilt relaxation implies strong faceting of the lipid monolayers in the hexagonal phase. Consistent with experiment, we find that only short peptides (large negative mismatch) can induce the Lalpha --> HII transition. At the transition, a peptide-poor Lalpha phase coexists with a peptide-rich HII phase. PMID:9929479

Propagating synchrony in feed-forward networks

PubMed Central

Jahnke, Sven; Memmesheimer, Raoul-Martin; Timme, Marc

2013-01-01

Coordinated patterns of precisely timed action potentials (spikes) emerge in a variety of neural circuits but their dynamical origin is still not well understood. One hypothesis states that synchronous activity propagating through feed-forward chains of groups of neurons (synfire chains) may dynamically generate such spike patterns. Additionally, synfire chains offer the possibility to enable reliable signal transmission. So far, mostly densely connected chains, often with all-to-all connectivity between groups, have been theoretically and computationally studied. Yet, such prominent feed-forward structures have not been observed experimentally. Here we analytically and numerically investigate under which conditions diluted feed-forward chains may exhibit synchrony propagation. In addition to conventional linear input summation, we study the impact of non-linear, non-additive summation accounting for the effect of fast dendritic spikes. The non-linearities promote synchronous inputs to generate precisely timed spikes. We identify how non-additive coupling relaxes the conditions on connectivity such that it enables synchrony propagation at connectivities substantially lower than required for linearly coupled chains. Although the analytical treatment is based on a simple leaky integrate-and-fire neuron model, we show how to generalize our methods to biologically more detailed neuron models and verify our results by numerical simulations with, e.g., Hodgkin Huxley type neurons. PMID:24298251

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

Rheological behaviors of an exopolysaccharide from fermentation medium of a Cordyceps sinensis fungus (Cs-HK1).

PubMed

Sun, Fengyuan; Huang, Qilin; Wu, Jianyong

2014-12-19

The rheological behaviors of an exopolysaccharide (EPS) from a Cordyceps sinensis fungus fermentation were investigated. The intrinsic viscosity of 1986 ± 55 mL/g indicated an extended and rigid chain for EPS. Shear-thinning behavior was observed and became apparent with increasing concentration. According to cross model, two critical transition concentrations (c(*) and c(**)) from dilute solution to semidilute and then to concentrated domain were 0.45 and 6.14 mg/mL. Flow activation energy was calculated by Arrhenius equation and decreased with increasing concentration, indicating a lower sensitivity to temperature. From dynamic frequency sweep, EPS system was classified to three regions including dilution solution (1.25mg/mL), entanglement network (3.75 and 5.00 mg/mL) and weak gel (≥ 7.50 mg/mL). Notably, the increase in η(*) at high frequencies was attributed to a large flow resistance depended on the rigid chain of EPS. Based on Winter-Chambon criterion, EPS formed gel at 2.6 mg/mL (cgel) and showed typical weak gel from temperature ramp and repetitive strain sweep. Copyright © 2014 Elsevier Ltd. All rights reserved.

Crosslinked polymer nanoparticles containing single conjugated polymer chains

NASA Astrophysics Data System (ADS)

Ponzio, Rodrigo A.; Marcato, Yésica L.; Gómez, María L.; Waiman, Carolina V.; Chesta, Carlos A.; Palacios, Rodrigo E.

2017-06-01

Conjugated polymer nanoparticles are widely used in fluorescent labeling and sensing, as they have mean radii between 5 and 100 nm, narrow size dispersion, high brightness, and are photochemically stable, allowing single particle detection with high spatial and temporal resolution. Highly crosslinked polymers formed by linking individual chains through covalent bonds yield high-strength rigid materials capable of withstanding dissolution by organic solvents. Hence, the combination of crosslinked polymers and conjugated polymers in a nanoparticulated material presents the possibility of interesting applications that require the combined properties of constituent polymers and nanosized dimension. In the present work, F8BT@pEGDMA nanoparticles composed of poly(ethylene glycol dimethacrylate) (pEGDMA; a crosslinked polymer) and containing the commercial conjugated polymer poly(9,9-dioctylfluorene-alt-benzothiadiazole) (F8BT) were synthesized and characterized. Microemulsion polymerization was applied to produce F8BT@pEDGMA particles with nanosized dimensions in a ∼25% yield. Photophysical and size distribution properties of F8BT@pEDGMA nanoparticles were evaluated by various methods, in particular single particle fluorescence microscopy techniques. The results demonstrate that the crosslinking/polymerization process imparts structural rigidity to the F8BT@pEDGMA particles by providing resistance against dissolution/disintegration in organic solvents. The synthesized fluorescent crosslinked nanoparticles contain (for the most part) single F8BT chains and can be detected at the single particle level, using fluorescence microscopy, which bodes well for their potential application as molecularly imprinted polymer fluorescent nanosensors with high spatial and temporal resolution.

Diabetes mellitus affects the biomechanical function of the callus and the expression of TGF-beta1 and BMP2 in an early stage of fracture healing.

PubMed

Xu, M T; Sun, S; Zhang, L; Xu, F; Du, S L; Zhang, X D; Wang, D W

2016-01-01

Transforming growth factor beta 1 (TGF-β1) and bone morphogenetic protein-2 (BMP-2) are important regulators of bone repair and regeneration. In this study, we examined whether TGF-β1 and BMP-2 expressions were delayed during bone healing in type 1 diabetes mellitus. Tibial fractures were created in 95 diabetic and 95 control adult male Wistar rats of 10 weeks of age. At 1, 2, 3, 4, and 5 weeks after fracture induction, five rats were sacrificed from each group. The expressions of TGF-β1 and BMP2 in the fractured tibias were measured by immunohistochemistry and quantitative reverse-transcription polymerase chain reaction, weekly for the first 5 weeks post-fracture. Mechanical parameters (bending rigidity, torsional rigidity, destruction torque) of the healing bones were also assessed at 3, 4, and 5 weeks post-fracture, after the rats were sacrificed. The bending rigidity, torsional rigidity and destruction torque of the two groups increased continuously during the healing process. The diabetes group had lower mean values for bending rigidity, torsional rigidity and destruction torque compared with the control group (P<0.05). TGF-β1 and BMP-2 expression were significantly lower (P<0.05) in the control group than in the diabetes group at postoperative weeks 1, 2, and 3. Peak levels of TGF-β1 and BMP-2 expression were delayed by 1 week in the diabetes group compared with the control group. Our results demonstrate that there was a delayed recovery in the biomechanical function of the fractured bones in diabetic rats. This delay may be associated with a delayed expression of the growth factors TGF-β1 and BMP-2.

The exact thermal rotational spectrum of a two-dimensional rigid rotor obtained using Gaussian wave packet dynamics

NASA Technical Reports Server (NTRS)

Reimers, J. R.; Heller, E. J.

1985-01-01

The exact thermal rotational spectrum of a two-dimensional rigid rotor is obtained using Gaussian wave packet dynamics. The spectrum is obtained by propagating, without approximation, infinite sets of Gaussian wave packets. These sets are constructed so that collectively they have the correct periodicity, and indeed, are coherent states appropriate to this problem. Also, simple, almost classical, approximations to full wave packet dynamics are shown to give results which are either exact or very nearly exact. Advantages of the use of Gaussian wave packet dynamics over conventional linear response theory are discussed.

Changes in conformational dynamics of basic side chains upon protein-DNA association.

PubMed

Esadze, Alexandre; Chen, Chuanying; Zandarashvili, Levani; Roy, Sourav; Pettitt, B Montgometry; Iwahara, Junji

2016-08-19

Basic side chains play major roles in recognition of nucleic acids by proteins. However, dynamic properties of these positively charged side chains are not well understood. In this work, we studied changes in conformational dynamics of basic side chains upon protein-DNA association for the zinc-finger protein Egr-1. By nuclear magnetic resonance (NMR) spectroscopy, we characterized the dynamics of all side-chain cationic groups in the free protein and in the complex with target DNA. Our NMR order parameters indicate that the arginine guanidino groups interacting with DNA bases are strongly immobilized, forming rigid interfaces. Despite the strong short-range electrostatic interactions, the majority of the basic side chains interacting with the DNA phosphates exhibited high mobility, forming dynamic interfaces. In particular, the lysine side-chain amino groups exhibited only small changes in the order parameters upon DNA-binding. We found a similar trend in the molecular dynamics (MD) simulations for the free Egr-1 and the Egr-1-DNA complex. Using the MD trajectories, we also analyzed side-chain conformational entropy. The interfacial arginine side chains exhibited substantial entropic loss upon binding to DNA, whereas the interfacial lysine side chains showed relatively small changes in conformational entropy. These data illustrate different dynamic characteristics of the interfacial arginine and lysine side chains. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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.

The Synergize effect of Chain extender to Phosporic acid catalyst to the ultimate property of Soy-Polyurethane

NASA Astrophysics Data System (ADS)

Elvistia Firdaus, Flora

2016-04-01

The polyurethanes (PUs) foam were made from vegetable oil; a soybean based polyol. The foams were categorized into flexible and semi rigid. This research is manufacturally designed polyurethane foams by a process requiring the reaction of mixture of 2, 4- and 2, 6-Toluene di Isocyanate isomers, soy polyol in the presence of other ingredients. The objective of this work was to functionalized soy-polyol using phosporic acid catalyst and chain extender, study their collaborative reaction in producing ultimate property of PU foam. Correlates the foam morphology images in accordance to mechanical properties of foams.

Modified-hypernetted-chain determination of the phase diagram of rigid C60 molecules

NASA Astrophysics Data System (ADS)

Caccamo, C.

1995-02-01

The modified-hypernetted-chain theory is applied to the determination of the phase diagram of the Lennard-Jones (LJ) fluid, and of a model of C60 previously investigated [Phys. Rev. Lett. 71, 1200 (1993)] through molecular-dynamics (MD) simulation and a different theoretical approach. In the LJ case the agreement with available MD data is quantitative and superior to other theories. For C60, the phase diagram obtained is in quite good agreement with previous MD results: in particular, the theory confirms the existence of a liquid phase between 1600 and 1920 K, the estimated triple point and critical temperature, respectively.

The role of axis embedding on rigid rotor decomposition analysis of variational rovibrational wave functions.

PubMed

Szidarovszky, Tamás; Fábri, Csaba; Császár, Attila G

2012-05-07

Approximate rotational characterization of variational rovibrational wave functions via the rigid rotor decomposition (RRD) protocol is developed for Hamiltonians based on arbitrary sets of internal coordinates and axis embeddings. An efficient and general procedure is given that allows employing the Eckart embedding with arbitrary polyatomic Hamiltonians through a fully numerical approach. RRD tables formed by projecting rotational-vibrational wave functions into products of rigid-rotor basis functions and previously determined vibrational eigenstates yield rigid-rotor labels for rovibrational eigenstates by selecting the largest overlap. Embedding-dependent RRD analyses are performed, up to high energies and rotational excitations, for the H(2) (16)O isotopologue of the water molecule. Irrespective of the embedding chosen, the RRD procedure proves effective in providing unambiguous rotational assignments at low energies and J values. Rotational labeling of rovibrational states of H(2) (16)O proves to be increasingly difficult beyond about 10,000 cm(-1), close to the barrier to linearity of the water molecule. For medium energies and excitations the Eckart embedding yields the largest RRD coefficients, thus providing the largest number of unambiguous rotational labels.

Tension-referenced measures of gastrocnemius slack length and stiffness in Parkinson's disease.

PubMed

Tan, Benedict; Double, Kay L; Burne, John; Diong, Joanna

2016-12-01

It is not known how passive muscle length and stiffness contribute to rigidity in Parkinson's disease. The objective of this study was to compare passive gastrocnemius muscle-tendon slack length and stiffness at known tension in Parkinson's disease subjects with ankle rigidity and in able-bodied people. Passive ankle torque-angle curves were obtained from 15 Parkinson's disease subjects with rigidity and 15 control subjects. Torque-angle data were used to derive passive gastrocnemius length-tension data and calculate slack length and stiffness of the gastrocnemius muscle. Between-group comparisons were made with linear models. Gastrocnemius muscle-tendon slack lengths (adjusted between-group difference, 0.01 m; 95% CI, -0.02 to 0.04 m; P = 0.37) and stiffness (adjusted between-group difference, 15.7 m -1 ; 95% CI, -8.5 to 39.9 m -1 ; P = 0.19) were not significantly different between groups. Parkinson's disease subjects with ankle rigidity did not have significantly shorter or stiffer gastrocnemius muscles compared with control subjects. © 2016 International Parkinson and Movement Disorder Society. © 2016 International Parkinson and Movement Disorder Society.

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.

Finite Element Studies of Solitary Waves in Granular Chains

NASA Astrophysics Data System (ADS)

Musson, Ryan W.

Solitary wave propagation in a monodisperse metallic granular chain was simulated using the finite element method. The model was built to address a discrepancy between numerical and experimental results from Lazaridi and Nesterenko (J. Appl. Mech. Tech. Phys., 26 [3] 405-408 1985). In their work, solitary waves were generated in a chain of particles through impact of a piston, and results were quantified by comparing the chains' reactions to a rigid wall. Their numerical calculations resulted in a solitary wave with a force amplitude of 83 N, while it was measured experimentally to be 71 N. In the present work, the configuration of the granular chain and piston was duplicated from Lazaridi and Nesterenko (J. Appl. Mech. Tech. Phys., 26 [3] 405-408 1985). Qualitatively similar solitary waves were produced, and von Mises stress values indicated that localized plastic deformation is possible, even at low piston impact velocities. These results show that localized plastic deformation was a likely source of dissipation in experiments performed by Lazaridi and Nesterenko. Solitary wave response was investigated in the same 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 the metallic granular chain, even 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. The response of an aluminum oxide granular chain was subsequently compared to that of a steel chain because ceramics are inherently elastic. It was shown that solitary waves travel faster and the initial peak is slightly lower when compared to a steel chain. The response of granular chains to impulse loading was investigated as a function of material properties. COMSOL Multiphysics was used to study the effect of density and elastic modulus on a granular chain with fixed Poisson's ratio. Solitary wave velocity and amplitude increased with elastic modulus. Increasing density caused a decrease in wave velocity and an increase in amplitude. In addition, higher density granular chains exhibited a decrease in the number of solitary waves in their respective solitary wave trains. LS-DYNA was then used to explore the response of a variety of ceramic and metallic granular chains. Density, elastic modulus, and Poisson's ratio were all set to representative values for the respective material. It was shown that solitary wave development and decay occur at different rates for different materials. In addition, the kinetic energy decay of the impactor was slower for glass compared with tungsten. Finally, it was shown that a single solitary wave with no train could be produced by impacting a high density, high modulus chain such as tungsten with a glass piston, which has relatively low density and elastic modulus. Increasing impact velocity for this case resulted in a single high-amplitude solitary wave with no train.

RELATIONSHIP BETWEEN RIGIDITY OF EXTERNAL FIXATOR AND NUMBER OF PINS: COMPUTER ANALYSIS USING FINITE ELEMENTS

PubMed Central

Sternick, Marcelo Back; Dallacosta, Darlan; Bento, Daniela Águida; do Reis, Marcelo Lemos

2015-01-01

Objective: To analyze the rigidity of a platform-type external fixator assembly, according to different numbers of pins on each clamp. Methods: Computer simulation on a large-sized Cromus dynamic external fixator (Baumer SA) was performed using a finite element method, in accordance with the standard ASTM F1541. The models were generated with approximately 450,000 quadratic tetrahedral elements. Assemblies with two, three and four Schanz pins of 5.5 mm in diameter in each clamp were compared. Every model was subjected to a maximum force of 200 N, divided into 10 sub-steps. For the components, the behavior of the material was assumed to be linear, elastic, isotropic and homogeneous. For each model, the rigidity of the assembly and the Von Mises stress distribution were evaluated. Results: The rigidity of the system was 307.6 N/mm for two pins, 369.0 N/mm for three and 437.9 N/mm for four. Conclusion: The results showed that four Schanz pins in each clamp promoted rigidity that was 19% greater than in the configuration with three pins and 42% greater than with two pins. Higher tension occurred in configurations with fewer pins. In the models analyzed, the maximum tension occurred on the surface of the pin, close to the fixation area. PMID:27047879

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.

Chains are more flexible under tension

PubMed Central

Carrillo, Jan-Michael Y.; Rubinstein, Michael

2010-01-01

The mechanical response of networks, gels, and brush layers is a manifestation of the elastic properties of the individual macromolecules. Furthermore, the elastic response of macromolecules to an applied force is the foundation of the single-molecule force spectroscopy techniques. The two main classes of models describing chain elasticity include the worm-like and freely-jointed chain models. The selection between these two classes of models is based on the assumptions about chain flexibility. In many experimental situations the choice is not clear and a model describing the crossover between these two limiting classes is therefore in high demand. We are proposing a unified chain deformation model which describes the force-deformation curve in terms of the chain bending constant K and bond length b. This model demonstrates that the worm-like and freely-jointed chain models correspond to two different regimes of polymer deformation and the crossover between these two regimes depends on the chain bending rigidity and the magnitude of the applied force. Polymer chains with bending constant K>1 behave as a worm-like chain under tension in the interval of the applied forces f ≤ KkBT/b and as a freely-jointed chain for f ≥ KkBT/b (kB is the Boltzmann constant and T is the absolute temperature). The proposed crossover expression for chain deformation is in excellent agreement with the results of the molecular dynamics simulations of chain deformation and single-molecule deformation experiments of biological and synthetic macromolecules. PMID:21415940

Asymptotic behavior of modulated Taylor-Couette flows with a crystalline inner cylinder

NASA Technical Reports Server (NTRS)

Braun, R. J.; Mcfadden, G. B.; Murray, B. T.; Coriell, S. R.; Glicksman, M. E.; Selleck, M. E.

1993-01-01

The linear stability of a modulated Taylor-Couette system when the inner cylindrical boundary consists of a crystalline solid-liquid interface is considered. Both experimentally and in numerical calculations it is found that the two-phase system is significantly less stable than the analogous rigid-walled system for materials with moderately large Prandtl numbers. A numerical treatment based on Floquet theory is described, which gives results that are in good agreement with preliminary experimental findings. In addition, this instability is further examined by carrying out a formal asymptotic expansion of the solution in the limit of large Prandtl number. In this limit the Floquet analysis is considerably simplified, and the linear stability of the modulated system can be determined to leading order through a conventional stability analysis, without recourse to Floquet theory. The resulting simplified problem is then studied for both the narrow gap geometry and for the case of a finite gap. It is surprising that the determination of the linear stability of the two-phase system is considerably simpler than that of the rigid-walled system, despite the complications introduced by the presence of the crystal-melt interface.

Remarks on Polyelectrolyte Conformation

NASA Astrophysics Data System (ADS)

de Gennes, P. G.; Pincus, P.; Velasco, R. M.; Brochard, F.

Nous discutons des conformations de polymères linéaires chargés en faisant les hypothèses suivantes : a) la chaĬne sans charge est flexible, b) la force éctrostatique domine les interactions monomère-monomère c) il n'y a pas de sels. 1) Pour le cas dilué (chaĬne non enchevetrees) en corrigeant le calcul self-consistant fait récemment par Richmond [1a], on trouve une taille des polyions égale a = R ND, qui est une fonction linéaire de l'indice de polymérisation N. Ce rèsultat est en accord avec les prècèdents travaux de Hermans et Overbeek [1b], Kuhn, Kunzle et Katchalsky [1c]. 2) Il existe un domaine pour des concentrations très petites c (c** < c < c*) oò les interactions èlectrostatiques entre les polyions sont supèrieures aux ènergies thermiques, il semble donc possible que les polyions puissent former un rèseau pèriodique à trois dimensions. Nèanmoins, il semble difficile de mettre en èvidence un rèseau si diluè. 3) Jusqu'ici toutes les expériences avec les polyélectrolytes sans sels ont été pratiquement faites à des concentrations c > c*, pour lesquelles les différentes cha.nes sont enchevêtrées. Pour discuter ce régime on s.intéresse uniquement au cas où la charge par unité de longueur est près du (ou audessus du) seuil de condensation, donc il existe une seule longueur ξ(c) caractérisant les corrélations; à trois dimensions 03BE a le même comportement que le rayon de Debye pour les contre-ions. On a considéré quelques conformations possibles : a) un réseau hexagonal de batonnets; b) un réseau cubique de batonnets; c) une phase isotrope de cha.nes partiellement flexibles. Les différentes structures formées de batonnets semblent avoir la même énergie électrostatique. Ce fait suggère que la phase isotrope peut être la plus favorable. On analyse cette dernière phase en utilisant les mêmes méthodes qui se sont révélées efficaces pour les solutions des polymères neutres. Dans le modèle isotrope chaque cha.ne a le comportement d.une succession des petites pelotes (blobs) de taille 03BE. Les effets électrostatiques sont importants à l.intérieur d'un blobs et analogues au cas (1). Mais ces interactions sont écrantées entre les blobs ; chaque cha.ne a un comportement idéal à grande échelle et son rayon est R(c) ~ c-¼ N½. Si on suppose que les effets dynamiques des enchevêtrements sont faibles on trouve une valeur pour la viscosité ηsp/c ~ Nc-½ We discuss the conformations of linear polyions assuming that a) the corresponding uncharged chain is flexible ; b) electrostatic forces dominate the monomer-monomer interactions; c) no salt is added. 1) For the dilute case (non overlapping chains) correcting a recent self-consistent calculation by Richmond [1a], we find an overall polyion size R = Nd which is a linear function of the polymerization index N in agreement with the early work of Hermans and Overbeek, [1b], Kuhn, Kunzle, and Katchalsky [1c]. 2) There is a range of very low concentration c (c** < c < c*) where the chains do not overlap (c < c*) but where the electrostatic interactions between polyions are much larger than thermal energies (c > c**) : here we expect that the polyions build up a 3-dimensional periodic lattice ; however, the detection of such an extremely dilute lattice appears difficult. 3) Practically all experiments on salt-free polyelectrolytes have been performed at concentrations c > c* where different chains overlap each other. To discuss this regime we restrict our attention to cases where the charge per unit length is near (or above) the condensation threshold : then a single length ξ(c) characterizes the correlation; in 3 dimensions ξ scales like the Debye radius associated with the counter ions. We consider several possible conformations : a) hexagonal lattice of rigid rods ; b) cubic lattice of rigid rods; c) isotropic phase of partially flexible chains. The various rigid rod structures appear to have very similar electrostatic energies. This suggests that the isotropic phase might possibly be the most favorable. We analyse this latter phase using the same scaling methods which have recently been helpful for neutral polymer solutions (2). In the isotropic model each chain behaves like a succession of segments of size. Inside one segment electrostatic effects are important and similar to case (1) above. Between segments the interactions are screened out, and tach chain is ideal on a large scale, with radius R(c) ~ c-¼ N½. If we (tentatively) assume that the dynamical effects of entanglements are weak, we are than led to a viscosity ηsp/c ~ Nc-½.

Numerical study of rigid and flexible wing shapes in hover

NASA Astrophysics Data System (ADS)

Shahzad, Aamer; Tian, Fang-Bao; Young, John; Lai, Joseph C. S.

2017-04-01

This study is focused on evaluating the aerodynamic performance of rigid and isotropic flexible wing shapes defined by the radius of the first moment of wing area ({\\bar{r}}1) at Reynolds number of 6000. An immersed boundary method was used to solve the 3D, viscous, incompressible Navier-Stokes equations, and coupled with an in-house non-linear finite element solver for fluid structure interaction simulations. Numerical simulations of flexible {\\bar{r}}1=0.43,0.53{and}0.63 wing shapes performed with a single degree of freedom flapping shows that thrust and peak lift coefficients increase with {\\bar{r}}1. Higher thrust in the {\\bar{r}}1=0.63 wing is attributed to the large induced pitch angle, and higher peak lift (compared to the rigid counterpart) results from an increase in the stroke amplitude and spanwise deformation of the wing that anchors the leading edge vortex.

Condensin confers the longitudinal rigidity of chromosomes.

PubMed

Houlard, Martin; Godwin, Jonathan; Metson, Jean; Lee, Jibak; Hirano, Tatsuya; Nasmyth, Kim

2015-06-01

In addition to inter-chromatid cohesion, mitotic and meiotic chromatids must have three physical properties: compaction into 'threads' roughly co-linear with their DNA sequence, intra-chromatid cohesion determining their rigidity, and a mechanism to promote sister chromatid disentanglement. A fundamental issue in chromosome biology is whether a single molecular process accounts for all three features. There is universal agreement that a pair of Smc-kleisin complexes called condensin I and II facilitate sister chromatid disentanglement, but whether they also confer thread formation or longitudinal rigidity is either controversial or has never been directly addressed respectively. We show here that condensin II (beta-kleisin) has an essential role in all three processes during meiosis I in mouse oocytes and that its function overlaps with that of condensin I (gamma-kleisin), which is otherwise redundant. Pre-assembled meiotic bivalents unravel when condensin is inactivated by TEV cleavage, proving that it actually holds chromatin fibres together.

Maneuvering and control of flexible space robots

NASA Technical Reports Server (NTRS)

Meirovitch, Leonard; Lim, Seungchul

1994-01-01

This paper is concerned with a flexible space robot capable of maneuvering payloads. The robot is assumed to consist of two hinge-connected flexible arms and a rigid end-effector holding a payload; the robot is mounted on a rigid platform floating in space. The equations of motion are nonlinear and of high order. Based on the assumption that the maneuvering motions are one order of magnitude larger than the elastic vibrations, a perturbation approach permits design of controls for the two types of motion separately. The rigid-body maneuvering is carried out open loop, but the elastic motions are controlled closed loop, by means of discrete-time linear quadratic regulator theory with prescribed degree of stability. A numerical example demonstrates the approach. In the example, the controls derived by the perturbation approach are applied to the original nonlinear system and errors are found to be relatively small.

Rigidly rotating zero-angular-momentum observer surfaces in the Kerr spacetime

NASA Astrophysics Data System (ADS)

Frolov, Andrei V.; Frolov, Valeri P.

2014-12-01

A stationary observer in the Kerr spacetime has zero angular momentum if their angular velocity ω has a particular value, which depends on the position of the observer. Worldlines of such zero-angular-momentum observers (ZAMOs) with the same value of the angular velocity ω form a three-dimensional surface, which has the property that the Killing vectors generating time translation and rotation are tangent to it. We call such a surface a rigidly rotating ZAMO surface. This definition allows for a natural generalization to the surfaces inside the black hole, where ZAMO trajectories formally become spacelike. A general property of such a surface is that there exist linear combinations of the Killing vectors with constant coefficients which make them orthogonal on it. In this paper we discuss properties of the rigidly rotating ZAMO surfaces both outside and inside the black hole and the relevance of these objects to a couple of interesting physical problems.

Control strategy on the double-diffusive convection in a nanofluid layer with internal heat generation

NASA Astrophysics Data System (ADS)

Mokhtar, N. F. M.; Khalid, I. K.; Siri, Z.; Ibrahim, Z. B.; Gani, S. S. A.

2017-10-01

The influences of feedback control and internal heat source on the onset of Rayleigh-Bénard convection in a horizontal nanofluid layer is studied analytically due to Soret and Dufour parameters. The confining boundaries of the nanofluid layer (bottom boundary-top boundary) are assumed to be free-free, rigid-free, and rigid-rigid, with a source of heat from below. Linear stability theory is applied, and the eigenvalue solution is obtained numerically using the Galerkin technique. Focusing on the stationary convection, it is shown that there is a positive thermal resistance in the presence of feedback control on the onset of double-diffusive convection, while there is a positive thermal efficiency in the existence of internal heat generation. The possibilities of suppress or augment of the Rayleigh-Bénard convection in a nanofluid layer are also discussed in detail.

Non-rigid alignment in electron tomography in materials science.

PubMed

Printemps, Tony; Bernier, Nicolas; Bleuet, Pierre; Mula, Guido; Hervé, Lionel

2016-09-01

Electron tomography is a key technique that enables the visualization of an object in three dimensions with a resolution of about a nanometre. High-quality 3D reconstruction is possible thanks to the latest compressed sensing algorithms and/or better alignment and preprocessing of the 2D projections. Rigid alignment of 2D projections is routine in electron tomography. However, it cannot correct misalignments induced by (i) deformations of the sample due to radiation damage or (ii) drifting of the sample during the acquisition of an image in scanning transmission electron microscope mode. In both cases, those misalignments can give rise to artefacts in the reconstruction. We propose a simple-to-implement non-rigid alignment technique to correct those artefacts. This technique is particularly suited for needle-shaped samples in materials science. It is initiated by a rigid alignment of the projections and it is then followed by several rigid alignments of different parts of the projections. Piecewise linear deformations are applied to each projection to force them to simultaneously satisfy the rigid alignments of the different parts. The efficiency of this technique is demonstrated on three samples, an intermetallic sample with deformation misalignments due to a high electron dose typical to spectroscopic electron tomography, a porous silicon sample with an extremely thin end particularly sensitive to electron beam and another porous silicon sample that was drifting during image acquisitions. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

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.

Position and force control of coordinated multiple arms

NASA Technical Reports Server (NTRS)

Hayati, Samad A.

1988-01-01

A technique is presented for controlling multiple manipulators which are holding a single object and therefore form a closed kinematic chain. The object, which may or may not be in contact with a rigid environment, is assumed to be held rigidly by n robot end-effectors. The derivation is based on setting up constraint equations which reduce the 6 x n degrees of freedom of n manipulators each having six joints. Additional constraint equations are considered when one or more degrees of freedom of the object are reduced due to external constraints. Utilizing the operational space dynamic equations, a decoupling controller is designed to control both the position and the interaction forces of the object with the environment. Simulation results for the control of a pair of two-link manipulators are presented.

Macromolecular properties of cepacian in water and in dimethylsulfoxide.

PubMed

Herasimenka, Yury; Cescutti, Paola; Sampaio Noguera, Carlos E; Ruggiero, Josè R; Urbani, Ranieri; Impallomeni, Giuseppe; Zanetti, Flavio; Campidelli, Stéphane; Prato, Maurizio; Rizzo, Roberto

2008-01-14

Cepacian is the exopolysaccharide produced by the majority of the so far investigated clinical strains of the Burkholderia cepacia complex. This is a group of nine closely related bacterial species that might cause serious lung infections in cystic fibrosis patients, in some cases leading to death. In this paper the aggregation ability and the conformational properties of cepacian chain were investigated to understand its role in biofilm formation. Viscosity and atomic force microscopy studies in water and in mixed (dimethylsulfoxide/water) solvent indicated the formation of double stranded molecular structures in aqueous solutions. Inter-residue short distances along cepacian chain were investigated by NOE NMR, which showed that two side chains of cepacian were not conformationally free due to strong interactions with the polymer backbone. These interactions were attributed to hydrogen bonding and contributed to structure rigidity.

Motions, efforts and actuations in constrained dynamic systems: a multi-link open-chain example

NASA Astrophysics Data System (ADS)

Duke Perreira, N.

1999-08-01

The effort-motion method, which describes the dynamics of open- and closed-chain topologies of rigid bodies interconnected with revolute and prismatic pairs, is interpreted geometrically. Systems are identified for which the simultaneous control of forces and velocities is desirable, and a representative open-chain system is selected for use in the ensuing analysis. Gauge invariant transformations are used to recast the commonly used kinetic and kinematic equations into a dimensional gauge invariant form. Constraint elimination techniques based on singular value decompositions then recast the invariant equations into orthogonal and reciprocal sets of motion and effort equations written in state variable form. The ideal actuation is found that simultaneously achieves the obtainable portions of the desired constraining efforts and motions. The performance is then evaluated of using the actuation closest to the ideal actuation.

A linear stepping endovascular intervention robot with variable stiffness and force sensing.

PubMed

He, Chengbin; Wang, Shuxin; Zuo, Siyang

2018-05-01

Robotic-assisted endovascular intervention surgery has attracted significant attention and interest in recent years. However, limited designs have focused on the variable stiffness mechanism of the catheter shaft. Flexible catheter needs to be partially switched to a rigid state that can hold its shape against external force to achieve a stable and effective insertion procedure. Furthermore, driving catheter in a similar way with manual procedures has the potential to make full use of the extensive experience from conventional catheter navigation. Besides driving method, force sensing is another significant factor for endovascular intervention. This paper presents a variable stiffness catheterization system that can provide stable and accurate endovascular intervention procedure with a linear stepping mechanism that has a similar operation mode to the conventional catheter navigation. A specially designed shape-memory polymer tube with water cooling structure is used to achieve variable stiffness of the catheter. Hence, four FBG sensors are attached to the catheter tip in order to monitor the tip contact force situation with temperature compensation. Experimental results show that the actuation unit is able to deliver linear and rotational motions. We have shown the feasibility of FBG force sensing to reduce the effect of temperature and detect the tip contact force. The designed catheter can change its stiffness partially, and the stiffness of the catheter can be remarkably increased in rigid state. Hence, in the rigid state, the catheter can hold its shape against a [Formula: see text] load. The prototype has also been validated with a vascular phantom, demonstrating the potential clinical value of the system. The proposed system provides important insights into the design of compact robotic-assisted catheter incorporating effective variable stiffness mechanism and real-time force sensing for intraoperative endovascular intervention.

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

Zhang, X; Sisniega, A; Zbijewski, W

Purpose: Visualization and quantification of coronary artery calcification and atherosclerotic plaque benefits from coronary artery motion (CAM) artifact elimination. This work applies a rigid linear motion model to a Volume of Interest (VoI) for estimating motion estimation and compensation of image degradation in Coronary Computed Tomography Angiography (CCTA). Methods: In both simulation and testbench experiments, translational CAM was generated by displacement of the imaging object (i.e. simulated coronary artery and explanted human heart) by ∼8 mm, approximating the motion of a main coronary branch. Rotation was assumed to be negligible. A motion degraded region containing a calcification was selected asmore » the VoI. Local residual motion was assumed to be rigid and linear over the acquisition window, simulating motion observed during diastasis. The (negative) magnitude of the image gradient of the reconstructed VoI was chosen as the motion estimation objective and was minimized with Covariance Matrix Adaptation Evolution Strategy (CMAES). Results: Reconstruction incorporated the estimated CAM yielded signification recovery of fine calcification structures as well as reduced motion artifacts within the selected local region. The compensated reconstruction was further evaluated using two image similarity metrics, the structural similarity index (SSIM) and Root Mean Square Error (RMSE). At the calcification site, the compensated data achieved a 3% increase in SSIM and a 91.2% decrease in RMSE in comparison with the uncompensated reconstruction. Conclusion: Results demonstrate the feasibility of our image-based motion estimation method exploiting a local rigid linear model for CAM compensation. The method shows promising preliminary results for the application of such estimation in CCTA. Further work will involve motion estimation of complex motion corrupted patient data acquired from clinical CT scanner.« less

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.

Ultrasonic Linear Motor with Two Independent Vibrations

NASA Astrophysics Data System (ADS)

Muneishi, Takeshi; Tomikawa, Yoshiro

2004-09-01

We propose a new structure of an ultrasonic linear motor in order to solve the problems of high-power ultrasonic linear motors that drive the XY-stage for electron beam equipment and to expand the application fields of the motor. We pay special attention to the following three points: (1) the vibration in two directions of the ultrasonic linear motor should not influence mutually each other, (2) the vibration in two directions should be divided into the stage traveling direction and the pressing direction of the ultrasonic linear motor, and (3) the rigidity of the stage traveling direction of the ultrasonic linear motor should be increased. As a result, the supporting method of ultrasonic linear motors is simplified. The efficiency of the motor is improved and temperature rise is reduced. The stage position drift is also improved.

A linear quadratic tracker for Control Moment Gyro based attitude control of the Space Station

NASA Technical Reports Server (NTRS)

Kaidy, J. T.

1986-01-01

The paper discusses a design for an attitude control system for the Space Station which produces fast response, with minimal overshoot and cross-coupling with the use of Control Moment Gyros (CMG). The rigid body equations of motion are linearized and discretized and a Linear Quadratic Regulator (LQR) design and analysis study is performed. The resulting design is then modified such that integral and differential terms are added to the state equations to enhance response characteristics. Methods for reduction of computation time through channelization are discussed as well as the reduction of initial torque requirements.

Probabilistic structural analysis by extremum methods

NASA Technical Reports Server (NTRS)

Nafday, Avinash M.

1990-01-01

The objective is to demonstrate discrete extremum methods of structural analysis as a tool for structural system reliability evaluation. Specifically, linear and multiobjective linear programming models for analysis of rigid plastic frames under proportional and multiparametric loadings, respectively, are considered. Kinematic and static approaches for analysis form a primal-dual pair in each of these models and have a polyhedral format. Duality relations link extreme points and hyperplanes of these polyhedra and lead naturally to dual methods for system reliability evaluation.

Impact of kerogen heterogeneity on sorption of organic pollutants. 2. Sorption equilibria

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

Yang, C.; Yu, Z.Q.; Xiao, B.H.

2009-08-15

Phenanthrene and naphthalene sorption isotherms were measured for three different series of kerogen materials using completely mixed batch reactors. Sorption isotherms were nonlinear for each sorbate-sorbent system, and the Freundlich isotherm equation fit the sorption data well. The Freundlich isotherm linearity parameter n ranged from 0.192 to 0.729 for phenanthrene and from 0.389 to 0.731 for naphthalene. The n values correlated linearly with rigidity and aromaticity of the kerogen matrix, but the single-point, organic carbon-normalized distribution coefficients varied dramatically among the tested sorbents. A dual-mode sorption equation consisting of a linear partitioning domain and a Langmuir adsorption domain adequately quantifiedmore » the overall sorption equilibrium for each sorbent-sorbate system. Both models fit the data well, with r{sup 2} values of 0.965 to 0.996 for the Freundlich model and 0.963 to 0.997 for the dual-mode model for the phenanthrene sorption isotherms. The dual-mode model fitting results showed that as the rigidity and aromaticity of the kerogen matrix increased, the contribution of the linear partitioning domain to the overall sorption equilibrium decreased, whereas the contribution of the Langmuir adsorption domain increased. The present study suggested that kerogen materials found in soils and sediments should not be treated as a single, unified, carbonaceous sorbent phase.« less

Interaction of a magnetic island chain in a tokamak plasma with a resonant magnetic perturbation of rapidly oscillating phase

NASA Astrophysics Data System (ADS)

Fitzpatrick, Richard

2017-12-01

An investigation is made into the interaction of a magnetic island chain, embedded in a tokamak plasma, with an externally generated magnetic perturbation of the same helicity whose helical phase is rapidly oscillating. The analysis is similar in form to the classic analysis used by Kapitza [Sov. Phys. JETP 21, 588 (1951)] to examine the angular motion of a rigid pendulum whose pivot point undergoes rapid vertical oscillations. The phase oscillations are found to modify the existing terms, and also to give rise to new terms, in the equations governing the secular evolution of the island chain's radial width and helical phase. An examination of the properties of the new secular evolution equation reveals that it is possible to phase-lock an island chain to an external magnetic perturbation with an oscillating helical phase in a stabilizing phase relation provided that the amplitude, ɛ, of the phase oscillations (in radians) is such that |J0(ɛ )|≪1 , and the mean angular frequency of the perturbation closely matches the natural angular frequency of the island chain.

Experimentally biased model structure of the Hsc70/auxilin complex: Substrate transfer and interdomain structural change

PubMed Central

Gruschus, James M.; Greene, Lois E.; Eisenberg, Evan; Ferretti, James A.

2004-01-01

A model structure of the Hsc70/auxilin complex has been constructed to gain insight into interprotein substrate transfer and ATP hydrolysis induced conformational changes in the multidomain Hsc70 structure. The Hsc70/auxilin system, which is a member of the Hsp70/Hsp40 chaperone system family, uncoats clathrin-coated vesicles in an ATP hydrolysis-driven process. Incorporating previous results from NMR and mutant binding studies, the auxilin J-domain was docked into the Hsc70 ATPase domain lower cleft using rigid backbone/flexible side chain molecular dynamics, and the Hsc70 substrate binding domain was docked by a similar procedure. For comparison, J-domain and substrate binding domain docking sites were obtained by the rigid-body docking programs DOT and ZDOCK, filtered and ranked by the program ClusPro, and relaxed using the same rigid backbone/flexible side chain dynamics. The substrate binding domain sites were assessed in terms of conserved surface complementarity and feasibility in the context of substrate transfer, both for auxilin and another Hsp40 protein, Hsc20. This assessment favors placement of the substrate binding domain near D152 on the ATPase domain surface adjacent to the J-domain invariant HPD segment, with the Hsc70 interdomain linker in the lower cleft. Examining Hsc70 interdomain energetics, we propose that long-range electrostatic interactions, perhaps due to a difference in the pKa values of bound ATP and ADP, could play a major role in the structural change induced by ATP hydrolysis. Interdomain electrostatic interactions also appear to play a role in stimulation of ATPase activity due to J-domain binding and substrate binding by Hsc70. PMID:15273304

Registration of terrestrial mobile laser data on 2D or 3D geographic database by use of a non-rigid ICP approach.

NASA Astrophysics Data System (ADS)

Monnier, F.; Vallet, B.; Paparoditis, N.; Papelard, J.-P.; David, N.

2013-10-01

This article presents a generic and efficient method to register terrestrial mobile data with imperfect location on a geographic database with better overall accuracy but less details. The registration method proposed in this paper is based on a semi-rigid point to plane ICP ("Iterative Closest Point"). The main applications of such registration is to improve existing geographic databases, particularly in terms of accuracy, level of detail and diversity of represented objects. Other applications include fine geometric modelling and fine façade texturing, object extraction such as trees, poles, road signs marks, facilities, vehicles, etc. The geopositionning system of mobile mapping systems is affected by GPS masks that are only partially corrected by an Inertial Navigation System (INS) which can cause an important drift. As this drift varies non-linearly, but slowly in time, it will be modelled by a translation defined as a piecewise linear function of time which variation over time will be minimized (rigidity term). For each iteration of the ICP, the drift is estimated in order to minimise the distance between laser points and planar model primitives (data attachment term). The method has been tested on real data (a scan of the city of Paris of 3.6 million laser points registered on a 3D model of approximately 71,400 triangles).

Certification of a hybrid parameter model of the fully flexible Shuttle Remote Manipulator System

NASA Technical Reports Server (NTRS)

Barhorst, Alan A.

1995-01-01

The development of high fidelity models of mechanical systems with flexible components is in flux. Many working models of these devices assume the elastic motion is small and can be superimposed on the overall rigid body motion. A drawback associated with this type of modeling technique is that it is required to regenerate the linear modal model of the device if the elastic motion is sufficiently far from the base rigid motion. An advantage to this type of modeling is that it uses NASTRAN modal data which is the NASA standard means of modal information exchange. A disadvantage to the linear modeling is that it fails to accurately represent large motion of the system, unless constant modal updates are performed. In this study, which is a continuation of a project started last year, the drawback of the currently used modal snapshot modeling technique is addressed in a rigorous fashion by novel and easily applied means.

Application of variable teeth pitch face mill as chatter suppression method for non-rigid technological system

NASA Astrophysics Data System (ADS)

Svinin, V. M.; Savilov, A. V.

2018-03-01

The article describes the results of experimental studies on the effects of variation type for variable teeth pitches on low-rigidity workpiece chatter suppression efficiency in a feed direction and in a direction of the normal to the machined surface. Mill operation performance was identified by comparing the amplitudes of dominant chatter harmonics using constant and variable teeth pitches. The following variable pitch formation variants were studied: alternative, linear rising, and linear rising falling. The angle difference of adjacent teeth pitches ranged from 0 to 10°, from 5 to 8° and from 5 to 10° with interval of 1°. The experiments showed that for all variants, machining dynamics performance resulted from the difference of adjacent pitches corresponding to a half the chatter wavelength along the cutting surface. The alternative nature of a variable teeth pitch is most efficient as it almost completely suppresses the chatters. Theoretical explanations of the results are presented

Unified control/structure design and modeling research

NASA Technical Reports Server (NTRS)

Mingori, D. L.; Gibson, J. S.; Blelloch, P. A.; Adamian, A.

1986-01-01

To demonstrate the applicability of the control theory for distributed systems to large flexible space structures, research was focused on a model of a space antenna which consists of a rigid hub, flexible ribs, and a mesh reflecting surface. The space antenna model used is discussed along with the finite element approximation of the distributed model. The basic control problem is to design an optimal or near-optimal compensator to suppress the linear vibrations and rigid-body displacements of the structure. The application of an infinite dimensional Linear Quadratic Gaussian (LQG) control theory to flexible structure is discussed. Two basic approaches for robustness enhancement were investigated: loop transfer recovery and sensitivity optimization. A third approach synthesized from elements of these two basic approaches is currently under development. The control driven finite element approximation of flexible structures is discussed. Three sets of finite element basic vectors for computing functional control gains are compared. The possibility of constructing a finite element scheme to approximate the infinite dimensional Hamiltonian system directly, instead of indirectly is discussed.

Instability dynamics and breather formation in a horizontally shaken pendulum chain.

PubMed

Xu, Y; Alexander, T J; Sidhu, H; Kevrekidis, P G

2014-10-01

Inspired by the experimental results of Cuevas et al. [Phys. Rev. Lett. 102, 224101 (2009)], we consider theoretically the behavior of a chain of planar rigid pendulums suspended in a uniform gravitational field and subjected to a horizontal periodic driving force applied to the pendulum pivots. We characterize the motion of a single pendulum, finding bistability near the fundamental resonance and near the period-3 subharmonic resonance. We examine the development of modulational instability in a driven pendulum chain and find both a critical chain length and a critical frequency for the appearance of the instability. We study the breather solutions and show their connection to the single-pendulum dynamics and extend our analysis to consider multifrequency breathers connected to the period-3 periodic solution, showing also the possibility of stability in these breather states. Finally we examine the problem of breather generation and demonstrate a robust scheme for generation of on-site and off-site breathers.

Fundamentals of poly(lactic acid) microstructure, crystallization behavior, and properties

NASA Astrophysics Data System (ADS)

Kang, Shuhui

Poly(lactic acid) is an environmentally-benign biodegradable and sustainable thermoplastic material, which has found broad applications as food packaging films and as non-woven fibers. The crystallization and deformation mechanisms of the polymer are largely determined by the distribution of conformation and configuration. Knowledge of these mechanisms is needed to understand the mechanical and thermal properties on which processing conditions mainly depend. In conjunction with laser light scattering, Raman spectroscopy and normal coordinate analysis are used in this thesis to elucidate these properties. Vibrational spectroscopic theory, Flory's rotational isomeric state (RIS) theory, Gaussian chain statistics and statistical mechanics are used to relate experimental data to molecular chain structure. A refined RIS model is proposed, chain rigidity recalculated and chain statistics discussed. A Raman spectroscopic characterization method for crystalline and amorphous phase orientation has been developed. A shrinkage model is also proposed to interpret the dimensional stability for fibers and uni- or biaxially stretched films. A study of stereocomplexation formed by poly(l-lactic acid) and poly(d-lactic acid) is also presented.

Redistribution of flexibility in stabilizing antibody fragment mutants follows Le Châtelier's principle.

PubMed

Li, Tong; Tracka, Malgorzata B; Uddin, Shahid; Casas-Finet, Jose; Jacobs, Donald J; Livesay, Dennis R

2014-01-01

Le Châtelier's principle is the cornerstone of our understanding of chemical equilibria. When a system at equilibrium undergoes a change in concentration or thermodynamic state (i.e., temperature, pressure, etc.), La Châtelier's principle states that an equilibrium shift will occur to offset the perturbation and a new equilibrium is established. We demonstrate that the effects of stabilizing mutations on the rigidity ⇔ flexibility equilibrium within the native state ensemble manifest themselves through enthalpy-entropy compensation as the protein structure adjusts to restore the global balance between the two. Specifically, we characterize the effects of mutation to single chain fragments of the anti-lymphotoxin-β receptor antibody using a computational Distance Constraint Model. Statistically significant changes in the distribution of both rigidity and flexibility within the molecular structure is typically observed, where the local perturbations often lead to distal shifts in flexibility and rigidity profiles. Nevertheless, the net gain or loss in flexibility of individual mutants can be skewed. Despite all mutants being exclusively stabilizing in this dataset, increased flexibility is slightly more common than increased rigidity. Mechanistically the redistribution of flexibility is largely controlled by changes in the H-bond network. For example, a stabilizing mutation can induce an increase in rigidity locally due to the formation of new H-bonds, and simultaneously break H-bonds elsewhere leading to increased flexibility distant from the mutation site via Le Châtelier. Increased flexibility within the VH β4/β5 loop is a noteworthy illustration of this long-range effect.

Redistribution of Flexibility in Stabilizing Antibody Fragment Mutants Follows Le Châtelier’s Principle

PubMed Central

Li, Tong; Tracka, Malgorzata B.; Uddin, Shahid; Casas-Finet, Jose; Jacobs, Donald J.; Livesay, Dennis R.

2014-01-01

Le Châtelier’s principle is the cornerstone of our understanding of chemical equilibria. When a system at equilibrium undergoes a change in concentration or thermodynamic state (i.e., temperature, pressure, etc.), La Châtelier’s principle states that an equilibrium shift will occur to offset the perturbation and a new equilibrium is established. We demonstrate that the effects of stabilizing mutations on the rigidity ⇔ flexibility equilibrium within the native state ensemble manifest themselves through enthalpy-entropy compensation as the protein structure adjusts to restore the global balance between the two. Specifically, we characterize the effects of mutation to single chain fragments of the anti-lymphotoxin-β receptor antibody using a computational Distance Constraint Model. Statistically significant changes in the distribution of both rigidity and flexibility within the molecular structure is typically observed, where the local perturbations often lead to distal shifts in flexibility and rigidity profiles. Nevertheless, the net gain or loss in flexibility of individual mutants can be skewed. Despite all mutants being exclusively stabilizing in this dataset, increased flexibility is slightly more common than increased rigidity. Mechanistically the redistribution of flexibility is largely controlled by changes in the H-bond network. For example, a stabilizing mutation can induce an increase in rigidity locally due to the formation of new H-bonds, and simultaneously break H-bonds elsewhere leading to increased flexibility distant from the mutation site via Le Châtelier. Increased flexibility within the VH β4/β5 loop is a noteworthy illustration of this long-range effect. PMID:24671209

Rotationally Molded Liquid Crystalline Polymers

NASA Technical Reports Server (NTRS)

Rogers, Martin; Scribben, Eric; Baird, Donald; Hulcher, Bruce

2002-01-01

Rotational molding is a unique process for producing hollow plastic parts. Rotational molding offers low cost tooling and can produce very large parts with complicated shapes. Products made by rotational molding include water tanks with capacities up to 20,000 gallons, truck bed liners, playground equipment, air ducts, Nylon fuel tanks, pipes, toys, stretchers, kayaks, pallets, and many others. Thermotropic liquid crystalline polymers are an important class of engineering resins employed in a wide variety of applications. Thermotropic liquid crystalline polymers resins are composed of semirigid, nearly linear polymeric chains resulting in an ordered mesomorphic phase between the crystalline solid and the isotropic liquid. Ordering of the rigid rod-like polymers in the melt phase yields microfibrous, self-reinforcing polymer structures with outstanding mechanical and thermal properties. Rotational molding of liquid crystalline polymer resins results in high strength and high temperature hollow structures useful in a variety of applications. Various fillers and reinforcements can potentially be added to improve properties of the hollow structures. This paper focuses on the process and properties of rotationally molded liquid crystalline polymers. This paper will also highlight the interactions between academia and small businesses in developing new products and processes.

Polymer flexibility and turbulent drag reduction.

PubMed

Gillissen, J J J

2008-10-01

Polymer-induced drag reduction is the phenomenon by which the friction factor of a turbulent flow is reduced by the addition of small amounts of high-molecular-weight linear polymers, which conformation in solution at rest can vary between randomly coiled and rodlike. It is well known that drag reduction is positively correlated to viscous stresses, which are generated by extended polymers. Rodlike polymers always assume this favorable conformation, while randomly coiling chains need to be unraveled by fluid strain rate in order to become effective. The coiling and stretching of flexible polymers in turbulent flow produce an additional elastic component in the polymer stress. The effect of the elastic stresses on drag reduction is unclear. To study this issue, we compare direct numerical simulations of turbulent drag reduction in channel flow using constitutive equations describing solutions of rigid and flexible polymers. When compared at constant phi r2, both simulations predict the same amount of drag reduction. Here phi is the polymer volume fraction and r is the polymer aspect ratio, which for flexible polymers is based on average polymer extension at the channel wall. This demonstrates that polymer elasticity plays a marginal role in the mechanism for drag reduction.

Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation

PubMed Central

Swigon, David; Coleman, Bernard D.; Olson, Wilma K.

2006-01-01

Repression of transcription of the Escherichia coli Lac operon by the Lac repressor (LacR) is accompanied by the simultaneous binding of LacR to two operators and the formation of a DNA loop. A recently developed theory of sequence-dependent DNA elasticity enables one to relate the fine structure of the LacR–DNA complex to a wide range of heretofore-unconnected experimental observations. Here, that theory is used to calculate the configuration and free energy of the DNA loop as a function of its length and base-pair sequence, its linking number, and the end conditions imposed by the LacR tetramer. The tetramer can assume two types of conformations. Whereas a rigid V-shaped structure is observed in the crystal, EM images show extended forms in which two dimer subunits are flexibly joined. Upon comparing our computed loop configurations with published experimental observations of permanganate sensitivities, DNase I cutting patterns, and loop stabilities, we conclude that linear DNA segments of short-to-medium chain length (50–180 bp) give rise to loops with the extended form of LacR and that loops formed within negatively supercoiled plasmids induce the V-shaped structure. PMID:16785444

Aggregation and Gelation of Aromatic Polyamides with Parallel and Anti-parallel Alignment of Molecular Dipole Along the Backbone

NASA Astrophysics Data System (ADS)

Zhu, Dan; Shang, Jing; Ye, Xiaodong; Shen, Jian

2016-12-01

The understanding of macromolecular structures and interactions is important but difficult, due to the facts that a macromolecules are of versatile conformations and aggregate states, which vary with environmental conditions and histories. In this work two polyamides with parallel or anti-parallel dipoles along the linear backbone, named as ABAB (parallel) and AABB (anti-parallel) have been studied. By using a combination of methods, the phase behaviors of the polymers during the aggregate and gelation, i.e., the forming or dissociation processes of nuclei and fibril, cluster of fibrils, and cluster-cluster aggregation have been revealed. Such abundant phase behaviors are dominated by the inter-chain interactions, including dispersion, polarity and hydrogen bonding, and correlatd with the solubility parameters of solvents, the temperature, and the polymer concentration. The results of X-ray diffraction and fast-mode dielectric relaxation indicate that AABB possesses more rigid conformation than ABAB, and because of that AABB aggregates are of long fibers while ABAB is of hairy fibril clusters, the gelation concentration in toluene is 1 w/v% for AABB, lower than the 3 w/v% for ABAB.

Understanding the interfacial chain dynamics of fiber-reinforced polymer composite

NASA Astrophysics Data System (ADS)

Goswami, Monojoy; Carrillo, Jan-Michael; Naskar, Amit; Sumpter, Bobby

The polymer-fiber interface plays a major role in determining the structural and dynamical properties of fiber reinforced composite materials. We utilized LAMMPS MD package to understand the interfacial properties at the nanoscale. Coarse-grained flexible polymer chains are introduced to compare the various structures and dynamics of the polymer chains. Our preliminary simulation study shows that the rigidity of the polymer chain affects the interfacial morphology and dynamics of the chain on a flat surface. In this work, we identified the `immobile inter-phase' morphology and relate it to rheological properties. We calculated the viscoelastic properties, e.g., shear modulus and storage modulus, which are compared with experiments. MD simulations are used to show the variation of viscoelastic properties with polymer volume fraction. The nanoscale segmental and chain relaxation are calculated from the MD simulations and compared to the experimental data. These observations will be able to identify the fundamental physics behind the effect of the polymer-fiber interactions and orientation of the fiber to the overall rheological properties of the fiber reinforced polymer matrix. Funding for the project was provided by ORNLs Laboratory Directed Research and Development (LDRD) program.

Deployment Testing of Flexible Composite Hinges in Bi-Material Beams

NASA Technical Reports Server (NTRS)

Sauder, Jonathan F.; Trease, Brian

2016-01-01

Composites have excellent properties for strength, thermal stability, and weight. However, they are traditionally highly rigid, and when used in deployable structures require hinges bonded to the composite material, which increases complexity and opportunities for failure. Recent research in composites has found by adding an elastomeric soft matrix, often silicone instead of an epoxy, the composite becomes flexible. This work explores the deployment repeatability of silicone matrix composite hinges which join rigid composite beams. The hinges were found to have sub-millimeter linear deployment repeatability, and sub-degree angular deployment repeatability. Also, an interesting relaxation effect was discovered, as a hinges deployment error would decrease with time.

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.

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.

Different singularities in the functions of extended kinetic theory at the origin of the yield stress in granular flows

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

Berzi, Diego; Vescovi, Dalila

2015-01-15

We use previous results from discrete element simulations of simple shear flows of rigid, identical spheres in the collisional regime to show that the volume fraction-dependence of the stresses is singular at the shear rigidity. Here, we identify the shear rigidity, which is a decreasing function of the interparticle friction, as the maximum volume fraction beyond which a random collisional assembly of grains cannot be sheared without developing force chains that span the entire domain. In the framework of extended kinetic theory, i.e., kinetic theory that accounts for the decreasing in the collisional dissipation due to the breaking of molecularmore » chaos at volume fractions larger than 0.49, we also show that the volume fraction-dependence of the correlation length (measure of the velocity correlation) is singular at random close packing, independent of the interparticle friction. The difference in the singularities ensures that the ratio of the shear stress to the pressure at shear rigidity is different from zero even in the case of frictionless spheres: we identify that with the yield stress ratio of granular materials, and we show that the theoretical predictions, once the different singularities are inserted into the functions of extended kinetic theory, are in excellent agreement with the results of numerical simulations.« less

Topology of polymer chains under nanoscale confinement.

PubMed

Satarifard, Vahid; Heidari, Maziar; Mashaghi, Samaneh; Tans, Sander J; Ejtehadi, Mohammad Reza; Mashaghi, Alireza

2017-08-24

Spatial confinement limits the conformational space accessible to biomolecules but the implications for bimolecular topology are not yet known. Folded linear biopolymers can be seen as molecular circuits formed by intramolecular contacts. The pairwise arrangement of intra-chain contacts can be categorized as parallel, series or cross, and has been identified as a topological property. Using molecular dynamics simulations, we determine the contact order distributions and topological circuits of short semi-flexible linear and ring polymer chains with a persistence length of l p under a spherical confinement of radius R c . At low values of l p /R c , the entropy of the linear chain leads to the formation of independent contacts along the chain and accordingly, increases the fraction of series topology with respect to other topologies. However, at high l p /R c , the fraction of cross and parallel topologies are enhanced in the chain topological circuits with cross becoming predominant. At an intermediate confining regime, we identify a critical value of l p /R c , at which all topological states have equal probability. Confinement thus equalizes the probability of more complex cross and parallel topologies to the level of the more simple, non-cooperative series topology. Moreover, our topology analysis reveals distinct behaviours for ring- and linear polymers under weak confinement; however, we find no difference between ring- and linear polymers under strong confinement. Under weak confinement, ring polymers adopt parallel and series topologies with equal likelihood, while linear polymers show a higher tendency for series arrangement. The radial distribution analysis of the topology reveals a non-uniform effect of confinement on the topology of polymer chains, thereby imposing more pronounced effects on the core region than on the confinement surface. Additionally, our results reveal that over a wide range of confining radii, loops arranged in parallel and cross topologies have nearly the same contact orders. Such degeneracy implies that the kinetics and transition rates between the topological states cannot be solely explained by contact order. We expect these findings to be of general importance in understanding chaperone assisted protein folding, chromosome architecture, and the evolution of molecular folds.

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.

Newtonian Analysis of a Folded Chain Drop

NASA Astrophysics Data System (ADS)

Mungan, Carl E.

2018-05-01

Consider a chain of length L that hangs in a U shape with end A fixed to a rigid support and free end E released from rest starting from the same initial height (call it y = 0) as A. Figure 1 sketches the chain after end E has fallen a distance y. Points O and A are assumed to be close enough to each other and the chain flexible enough that the radius of curvature r at the bottom point C can be taken to be negligibly small (compared to the length of the chain). The problem is to compare the speed of descent v(y) = dy/dt of the free end E of the chain to the speed vfree(y )=√{2 g y } of a free-falling point mass that has descended the same distance y. If v(y) > vfree (y) for all y > 0, then, in a race to fall any arbitrary distance Y (where 0 < Y < L), the chain end E will always beat a simultaneously released point mass, because the fall time t for E will be shorter than tfree for the point mass, t = ∫0 Y d/y v (y )

From strings to coils: Rotational dynamics of DNA-linked colloidal chains

NASA Astrophysics Data System (ADS)

Kuei, Steve; Garza, Burke; Biswal, Sibani Lisa

2017-10-01

We investigate the dynamical behavior of deformable filaments experimentally using a tunable model system consisting of linked paramagnetic colloidal particles, where the persistence length lp, the contour length lc, and the strength and frequency of the external driving force are controlled. We find that upon forcing by an external magnetic field, a variety of structural and conformational regimes exist. Depending on the competition of forces and torques on the chain, we see classic rigid rotator behavior, as well as dynamically rich wagging, coiling, and folding behavior. Through a combination of experiments, computational models, and theoretical calculations, we are able to observe, classify, and predict these dynamics as a function of the dimensionless Mason and magnetoelastic numbers.

Front propagation in a vortex lattice: dependence on boundary conditions and vortex depth.

PubMed

Beauvier, E; Bodea, S; Pocheau, A

2016-11-04

We experimentally address the propagation of reaction-diffusion fronts in vortex lattices by combining, in a Hele-Shaw cell and at low Reynolds number, forced electroconvective flows and an autocatalytic reaction in solution. We consider both vortex chains and vortex arrays, the former referring to mixed free/rigid boundary conditions for vortices and the latter to free boundary conditions. Varying the depth of the fluid layer, we observe no variation of the mean front velocities for vortex arrays and a noticeable variation for vortex chains. This questions the two-dimensional character of front propagation in low Reynolds number vortex lattices, as well as the mechanisms of this dependence.

Capillarity theory for the fly-casting mechanism

PubMed Central

Trizac, Emmanuel; Levy, Yaakov; Wolynes, Peter G.

2010-01-01

Biomolecular folding and function are often coupled. During molecular recognition events, one of the binding partners may transiently or partially unfold, allowing more rapid access to a binding site. We describe a simple model for this fly-casting mechanism based on the capillarity approximation and polymer chain statistics. The model shows that fly casting is most effective when the protein unfolding barrier is small and the part of the chain which extends toward the target is relatively rigid. These features are often seen in known examples of fly casting in protein–DNA binding. Simulations of protein–DNA binding based on well-funneled native-topology models with electrostatic forces confirm the trends of the analytical theory. PMID:20133683

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.

The relation between disparity and velocity signals of rigidly moving objects constrains depth order perception.

PubMed

Di Luca, Massimiliano; Domini, Fulvio; Caudek, Corrado

2007-05-01

In two experiments, observers were asked to judge the relative depth of a probe and one or two flanker dots. In Experiment 1, we found that such judgments were influenced by the properties of adjacent image regions, that is, by the amount of angular rotation of a surrounding cloud of dots. In Experiment 2, we found that the properties of the adjacent image regions affected the precision of the observers' judgments. With only the probe and the flanker dots presented in isolation, the precision of observers' judgments was much lower than when probe and the flanker dots were surrounded by a rigidly-connected cloud of dots. Conversely, a non-rigid rotation of the surrounding dots was detrimental to the precision of visual performance. These data can be accounted for by the Intrinsic Constraint model [Domini, F., Caudek, C., & Tassinari, H. (2006). Stereo and motion information are not independently processed by the visual system. Vision Research, 46, 1707-1723], which incorporates the mutual constraints relating disparity and motion signals. The present investigation does not show that the rigidity constraint affects the visual interpretation of motion information alone. Rather, our results show that perceptual performance is affected by the linear relation between disparity and velocity signals, when both depth-cues are present and the distal object is, in fact, rigid.

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.

Synthesis of Long-Chain-Branched (LCB) Polysulfones for Multifunctional Transport Membranes

DTIC Science & Technology

2010-09-01

R.; Dutta, N. K. Interfacial Interactions in Aprotic Ionic Liquid Based Protonic Membrane and Its Correlation with High Temperature Conductivity...rigidity. The series of novel polymers was characterized for chemical structure, thermal transitions, and molecular weight. Ionic conductivity was tested...Although much progress exists based on perfluorosulfonated platforms ( Nafion , σ ≈ 10-1 – 10-2 S/cm) new and more complicated parameters arise as

Apparent negative mass in QCM sensors due to punctual rigid loading

NASA Astrophysics Data System (ADS)

Castro, P.; Resa, P.; Elvira, L.

2012-12-01

Quartz Crystal Microbalances (QCM) are highly sensitive piezoelectric sensors able to detect very small loads attached to them. These devices are widely employed in many applications including process control and industrial and environmental monitoring. Mass loading is usually related to frequency shift by the well-known Sauerbrey's equation, valid for thin rigid homogeneous films. However, a significant deviation from this equation can occur when the mass is not uniformly distributed over the surface. Whereas the effects of a thin film on a QCM have been thoroughly studied, there are relatively few results on punctual loads, even though particles are usually deposited randomly and non-uniformly on the resonator surface. In this work, we have studied the effect of punctual rigid loading on the resonant frequency shift of a QCM sensor, both experimentally and using finite element method (FEM). The FEM numerical analysis was done using COMSOL software, 3D modeling a linear elastic piezoelectric solid and introducing the properties of an AT-cut quartz crystal. It is shown that a punctual rigid mass deposition on the surface of a QCM sensor can lead to positive shifts of resonance frequency, contrary to Sauerbrey's equation.

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.

Influence of Chain Rigidity and Dielectric Constant on the Glass Transition Temperature in Polymerized Ionic Liquids

DOE PAGES

Bocharova, V.; Wojnarowska, Z.; Cao, Peng-Fei; ...

2017-11-28

Polymerized ionic liquids (PolyILs) are promising candidates for a wide range of technological applications due to their single ion conductivity and good mechanical properties. Tuning the glass transition temperature (T g) in these materials constitutes a major strategy to improve room temperature conductivity while controlling their mechanical properties. In this paper, we show experimental and simulation results demonstrating that in these materials T g does not follow a universal scaling behavior with the volume of the structural units V m (including monomer and counterion). Instead, T g is significantly influenced by the chain flexibility and polymer dielectric constant. We proposemore » a simplified empirical model that includes the electrostatic interactions and chain flexibility to describe T g in PolyILs. Finally, our model enables design of new functional PolyILs with the desired T g.« less

Degradation of poly(2-hydroxyethyl methacrylate) by gamma irradiation

NASA Astrophysics Data System (ADS)

Hill, David J. T.; O'Donnell, James H.; Pomery, Peter J.; Saadat, Giti

1996-11-01

Electron Spin Resinance (ESR) spectroscopy has been utilised to examine the effect of high energy radiation on poly(2-hydroxyethyl methacrylate) PHEMA. Radiation chemical yields ( G-values) for radicals were 1.7 and 1.2 for γ-irradiation at 77 K and ambient temperature, respectively. The ESR spectra at 77 and 300 K were simulated. The ESR spectrum at 77 K is a combination of six types of radicals ·CH 3, ·CH 2CH 2OH, COOCHCH 2OH, ·COO-, -CH- and ·CHO. However, after room temperature irradiation, the spectrum is a combination of methacrylate main chain scission radical and -CH-. The high stability of this radical at room temperature indicates the system is very rigid as a result of hydrogen bonding from the inherent side chain structure and radiation induced crosslinking due to labile hydrogen atoms in the side chain.

Influence of Chain Rigidity and Dielectric Constant on the Glass Transition Temperature in Polymerized Ionic Liquids

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

Bocharova, V.; Wojnarowska, Z.; Cao, Peng-Fei

Polymerized ionic liquids (PolyILs) are promising candidates for a wide range of technological applications due to their single ion conductivity and good mechanical properties. Tuning the glass transition temperature (T g) in these materials constitutes a major strategy to improve room temperature conductivity while controlling their mechanical properties. In this paper, we show experimental and simulation results demonstrating that in these materials T g does not follow a universal scaling behavior with the volume of the structural units V m (including monomer and counterion). Instead, T g is significantly influenced by the chain flexibility and polymer dielectric constant. We proposemore » a simplified empirical model that includes the electrostatic interactions and chain flexibility to describe T g in PolyILs. Finally, our model enables design of new functional PolyILs with the desired T g.« less

Organically Modified Nanoclay-Reinforced Rigid Polyurethane Films

NASA Astrophysics Data System (ADS)

Park, Yong Tae; Qian, Yuqiang; Lindsay, Chris; Stein, Andreas; Macosko, Christopher

2012-02-01

The nanodispersion of vermiculite in polyurethanes was investigated to produce organoclay-reinforced rigid gas barrier films. Reducing gas transport can improve the insulation performance of closed cell polyurethane foam. In a previous study, the dispersion of vermiculite in polyurethanes without organic modification was not sufficient due to the non-uniform dispersion morphology. When vermiculite was modified by cation exchange with long-chain quaternary ammonium cations, the dispersion in methylene diphenyl diisocyanate (MDI) was significantly improved. Dispersion was improved by combining high intensity dispersive mixing with efficient distributive mixing. Polymerization conditions were also optimized in order to provide a high state of nanodispersion in the polyurethane nanocomposite. The dispersions were characterized using rheological, microscopic and scattering/diffraction techniques. The final nanocomposites showed enhancement of mechanical properties and reduction in permeability to carbon dioxide at low clay concentration (around 2 wt percent).

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). ...

Valuing Essays: Essaying Values

ERIC Educational Resources Information Center

Badley, Graham

2010-01-01

The essay regularly comes under attack. It is criticised for being rigidly linear rather than flexible and reflective. I first challenge this view by examining reasons why the essay should be valued as an important genre. Secondly, I propose that in using the essay form students and academics necessarily exemplify their own critical values. Essays…

Effect of gravitational and aerodynamic torques on a rigid Skylab-type satellite

NASA Technical Reports Server (NTRS)

Sperling, H. J.

1974-01-01

A theoretical investigation of the influence of the aerodynamic torque on a Skylab-type satellite is presented. Only the case of free flow of uniform velocity and completely diffuse reflection is considered. It is found by linear stability analysis that the satellite has no stable equilibrium.

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.

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.

Modeling meniscus rise in capillary tubes using fluid in rigid-body motion approach

NASA Astrophysics Data System (ADS)

Hamdan, Mohammad O.; Abu-Nabah, Bassam A.

2018-04-01

In this study, a new term representing net flux rate of linear momentum is introduced to Lucas-Washburn equation. Following a fluid in rigid-body motion in modeling the meniscus rise in vertical capillary tubes transforms the nonlinear Lucas-Washburn equation to a linear mass-spring-damper system. The linear nature of mass-spring-damper system with constant coefficients offers a nondimensional analytical solution where meniscus dynamics are dictated by two parameters, namely the system damping ratio and its natural frequency. This connects the numerous fluid-surface interaction physical and geometrical properties to rather two nondimensional parameters, which capture the underlying physics of meniscus dynamics in three distinct cases, namely overdamped, critically damped, and underdamped systems. Based on experimental data available in the literature and the understanding meniscus dynamics, the proposed model brings a new approach of understanding the system initial conditions. Accordingly, a closed form relation is produced for the imbibition velocity, which equals half of the Bosanquet velocity divided by the damping ratio. The proposed general analytical model is ideal for overdamped and critically damped systems. While for underdamped systems, the solution shows fair agreement with experimental measurements once the effective viscosity is determined. Moreover, the presented model shows meniscus oscillations around equilibrium height occur if the damping ratio is less than one.

Linear dynamic coupling in geared rotor systems

NASA Technical Reports Server (NTRS)

David, J. W.; Mitchell, L. D.

1986-01-01

The effects of high frequency oscillations caused by the gear mesh, on components of a geared system that can be modeled as rigid discs are analyzed using linear dynamic coupling terms. The coupled, nonlinear equations of motion for a disc attached to a rotating shaft are presented. The results of a trial problem analysis show that the inclusion of the linear dynamic coupling terms can produce significant changes in the predicted response of geared rotor systems, and that the produced sideband responses are greater than the unbalanced response. The method is useful in designing gear drives for heavy-lift helicopters, industrial speed reducers, naval propulsion systems, and heavy off-road equipment.

ON THE DECOMPOSITION OF STRESS AND STRAIN TENSORS INTO SPHERICAL AND DEVIATORIC PARTS

PubMed Central

Augusti, G.; Martin, J. B.; Prager, W.

1969-01-01

It is well known that Hooke's law for a linearly elastic, isotropic solid may be written in the form of two relations that involve only the spherical or only the deviatoric parts of the tensors of stress and strain. The example of the linearly elastic, transversely isotropic solid is used to show that this decomposition is not, in general, feasible for linearly elastic, anisotropic solids. The discussion is extended to a large class of work-hardening rigid, plastic solids, and it is shown that the considered decomposition can only be achieved for the incompressible solids of this class. PMID:16591754

Effect of fatty acids on self-assembly of soybean lecithin systems.

PubMed

Godoy, C A; Valiente, M; Pons, R; Montalvo, G

2015-07-01

With the increasing interest in natural formulations for drug administration and functional foods, it is desirable a good knowledge of the phase behavior of lecithin/fatty acid formulations. Phase structure and properties of ternary lecithin/fatty acids/water systems are studied at 37°C, making emphasis in regions with relatively low water and fatty acid content. The effect of fatty acid saturation degree on the phase microstructure is studied by comparing a fully saturated (palmitic acid, C16:0), monounsaturated (oleic acid, C18:1), and diunsaturated (linoleic acid, C18:2) fatty acids. Phase determinations are based on a combination of polarized light microscopy and small-angle X-ray scattering measurements. Interestingly, unsaturated (oleic acid and linoleic acid) fatty acid destabilizes the lamellar bilayer. Slight differences are observed between the phase diagrams produced by the unsaturated ones: small lamellar, medium cubic and large hexagonal regions. A narrow isotropic fluid region also appears on the lecithin-fatty acid axis, up to 8wt% water. In contrast, a marked difference in phase microsctructure was observed between unsaturated and saturated systems in which the cubic and isotropic fluid phases are not formed. These differences are, probably, a consequence of the high Krafft point of the C16 saturated chains that imply rather rigid chains. However, unsaturated fatty acids result in more flexible tails. The frequent presence of, at least, one unsaturated chain in phospholipids makes it very likely a better mixing situation than in the case of more rigid chains. This swelling potential favors the formation of reverse hexagonal, cubic, and micellar phases. Both unsaturated fatty acid systems evolve by aging, with a reduction of the extension of reverse hexagonal phase and migration of the cubic phase to lower fatty acid and water contents. The kinetic stability of the systems seems to be controlled by the unsaturation of fatty acids. Copyright © 2015 Elsevier B.V. All rights reserved.

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.

The Fundamental Solution of the Linearized Navier Stokes Equations for Spinning Bodies in Three Spatial Dimensions Time Dependent Case

NASA Astrophysics Data System (ADS)

Thomann, Enrique A.; Guenther, Ronald B.

2006-02-01

Explicit formulae for the fundamental solution of the linearized time dependent Navier Stokes equations in three spatial dimensions are obtained. The linear equations considered in this paper include those used to model rigid bodies that are translating and rotating at a constant velocity. Estimates extending those obtained by Solonnikov in [23] for the fundamental solution of the time dependent Stokes equations, corresponding to zero translational and angular velocity, are established. Existence and uniqueness of solutions of these linearized problems is obtained for a class of functions that includes the classical Lebesgue spaces L p (R 3), 1 < p < ∞. Finally, the asymptotic behavior and semigroup properties of the fundamental solution are established.

Fourier-based linear systems description of free-breathing pulmonary magnetic resonance imaging

NASA Astrophysics Data System (ADS)

Capaldi, D. P. I.; Svenningsen, S.; Cunningham, I. A.; Parraga, G.

2015-03-01

Fourier-decomposition of free-breathing pulmonary magnetic resonance imaging (FDMRI) was recently piloted as a way to provide rapid quantitative pulmonary maps of ventilation and perfusion without the use of exogenous contrast agents. This method exploits fast pulmonary MRI acquisition of free-breathing proton (1H) pulmonary images and non-rigid registration to compensate for changes in position and shape of the thorax associated with breathing. In this way, ventilation imaging using conventional MRI systems can be undertaken but there has been no systematic evaluation of fundamental image quality measurements based on linear systems theory. We investigated the performance of free-breathing pulmonary ventilation imaging using a Fourier-based linear system description of each operation required to generate FDMRI ventilation maps. Twelve subjects with chronic obstructive pulmonary disease (COPD) or bronchiectasis underwent pulmonary function tests and MRI. Non-rigid registration was used to co-register the temporal series of pulmonary images. Pulmonary voxel intensities were aligned along a time axis and discrete Fourier transforms were performed on the periodic signal intensity pattern to generate frequency spectra. We determined the signal-to-noise ratio (SNR) of the FDMRI ventilation maps using a conventional approach (SNRC) and using the Fourier-based description (SNRF). Mean SNR was 4.7 ± 1.3 for subjects with bronchiectasis and 3.4 ± 1.8, for COPD subjects (p>.05). SNRF was significantly different than SNRC (p<.01). SNRF was approximately 50% of SNRC suggesting that the linear system model well-estimates the current approach.

Dynamic cross-correlations between entangled biofilaments as they diffuse

PubMed Central

Tsang, Boyce; Dell, Zachary E.; Jiang, Lingxiang; Schweizer, Kenneth S.; Granick, Steve

2017-01-01

Entanglement in polymer and biological physics involves a state in which linear interthreaded macromolecules in isotropic liquids diffuse in a spatially anisotropic manner beyond a characteristic mesoscopic time and length scale (tube diameter). The physical reason is that linear macromolecules become transiently localized in directions transverse to their backbone but diffuse with relative ease parallel to it. Within the resulting broad spectrum of relaxation times there is an extended period before the longest relaxation time when filaments occupy a time-averaged cylindrical space of near-constant density. Here we show its implication with experiments based on fluorescence tracking of dilutely labeled macromolecules. The entangled pairs of aqueous F-actin biofilaments diffuse with separation-dependent dynamic cross-correlations that exceed those expected from continuum hydrodynamics up to strikingly large spatial distances of ≈15 µm, which is more than 104 times the size of the solvent water molecules in which they are dissolved, and is more than 50 times the dynamic tube diameter, but is almost equal to the filament length. Modeling this entangled system as a collection of rigid rods, we present a statistical mechanical theory that predicts these long-range dynamic correlations as an emergent consequence of an effective long-range interpolymer repulsion due to the de Gennes correlation hole, which is a combined consequence of chain connectivity and uncrossability. The key physical assumption needed to make theory and experiment agree is that solutions of entangled biofilaments localized in tubes that are effectively dynamically incompressible over the relevant intermediate time and length scales. PMID:28283664

Mathematical Modeling of Torsional Surface Wave Propagation in a Non-Homogeneous Transverse Isotropic Elastic Solid Semi-Infinite Medium Under a Layer

NASA Astrophysics Data System (ADS)

Sethi, M.; Sharma, A.; Vasishth, A.

2017-05-01

The present paper deals with the mathematical modeling of the propagation of torsional surface waves in a non-homogeneous transverse isotropic elastic half-space under a rigid layer. Both rigidities and density of the half-space are assumed to vary inversely linearly with depth. Separation of variable method has been used to get the analytical solutions for the dispersion equation of the torsional surface waves. Also, the effects of nonhomogeneities on the phase velocity of torsional surface waves have been shown graphically. Also, dispersion equations have been derived for some particular cases, which are in complete agreement with some classical results.

Persistence-Driven Durotaxis: Generic, Directed Motility in Rigidity Gradients

NASA Astrophysics Data System (ADS)

Novikova, Elizaveta A.; Raab, Matthew; Discher, Dennis E.; Storm, Cornelis

2017-02-01

Cells move differently on substrates with different rigidities: the persistence time of their motion is higher on stiffer substrates. We show that this behavior—in and of itself—results in a net flux of cells directed up a soft-to-stiff gradient. Using simple random walk models with varying persistence and stochastic simulations, we characterize the propensity to move in terms of the durotactic index also measured in experiments. A one-dimensional model captures the essential features and highlights the competition between diffusive spreading and linear, wavelike propagation. Persistence-driven durokinesis is generic and may be of use in the design of instructive environments for cells and other motile, mechanosensitive objects.

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

Mesoscopic Rigid Body Modelling of the Extracellular Matrix Self-Assembly.

PubMed

Wong, Hua; Prévoteau-Jonquet, Jessica; Baud, Stéphanie; Dauchez, Manuel; Belloy, Nicolas

2018-06-11

The extracellular matrix (ECM) plays an important role in supporting tissues and organs. It even has a functional role in morphogenesis and differentiation by acting as a source of active molecules (matrikines). Many diseases are linked to dysfunction of ECM components and fragments or changes in their structures. As such it is a prime target for drugs. Because of technological limitations for observations at mesoscopic scales, the precise structural organisation of the ECM is not well-known, with sparse or fuzzy experimental observables. Based on the Unity3D game and physics engines, along with rigid body dynamics, we propose a virtual sandbox to model large biological molecules as dynamic chains of rigid bodies interacting together to gain insight into ECM components behaviour in the mesoscopic range. We have preliminary results showing how parameters such as fibre flexibility or the nature and number of interactions between molecules can induce different structures in the basement membrane. Using the Unity3D game engine and virtual reality headset coupled with haptic controllers, we immerse the user inside the corresponding simulation. Untrained users are able to navigate a complex virtual sandbox crowded with large biomolecules models in a matter of seconds.

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

Unseren, M.A.

The report reviews a method for modeling and controlling two serial link manipulators which mutually lift and transport a rigid body object in a three dimensional workspace. A new vector variable is introduced which parameterizes the internal contact force controlled degrees of freedom. A technique for dynamically distributing the payload between the manipulators is suggested which yields a family of solutions for the contact forces and torques the manipulators impart to the object. A set of rigid body kinematic constraints which restricts the values of the joint velocities of both manipulators is derived. A rigid body dynamical model for themore » closed chain system is first developed in the joint space. The model is obtained by generalizing the previous methods for deriving the model. The joint velocity and acceleration variables in the model are expressed in terms of independent pseudovariables. The pseudospace model is transformed to obtain reduced order equations of motion and a separate set of equations governing the internal components of the contact forces and torques. A theoretic control architecture is suggested which explicitly decouples the two sets of equations comprising the model. The controller enables the designer to develop independent, non-interacting control laws for the position control and internal force control of the system.« less

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

Unseren, M.A.

The paper reviews a method for modeling and controlling two serial link manipulators which mutually lift and transport a rigid body object in a three dimensional workspace. A new vector variable is introduced which parameterizes the internal contact force controlled degrees of freedom. A technique for dynamically distributing the payload between the manipulators is suggested which yields a family of solutions for the contact forces and torques the manipulators impart to the object. A set of rigid body kinematic constraints which restrict the values of the joint velocities of both manipulators is derived. A rigid body dynamical model for themore » closed chain system is first developed in the joint space. The model is obtained by generalizing the previous methods for deriving the model. The joint velocity and acceleration variables in the model are expressed in terms of independent pseudovariables. The pseudospace model is transformed to obtain reduced order equations of motion and a separate set of equations governing the internal components of the contact forces and torques. A theoretic control architecture is suggested which explicitly decouples the two sets of equations comprising the model. The controller enables the designer to develop independent, non-interacting control laws for the position control and internal force control of the system.« less

Modeling and Experiments with a High-Performance Flexible Swimming Robot

NASA Astrophysics Data System (ADS)

Wiens, Alexander; Hosoi, Anette

2017-11-01

Conventionally, fish-like swimming robots consist of a chain of rigid links connected by a series of rigid actuators. Devices of this nature have demonstrated impressive speeds and maneuverability, but from a practical perspective, their mechanical complexity makes them expensive to build and prone to failure. To address this problem, we present an alternative design approach which employs a single actuator to generate undulatory waves along a passive flexible structure. Through simulations and experiments we find that our robot can match the speed and agility of its rigid counterparts, while being simple, robust, and significantly less expensive. Physically, our robot consists of a small ellipsoidal head connected to a long flexible beam. Actuation is provided by a motor-driven flywheel within the head, which oscillates to produce a periodic torque. This torque propagates along the beam to generate an undulatory wave and propel the robot forwards. We construct a numerical model of the system using Lighthill's large-amplitude elongated-body theory coupled with a nonlinear model of elastic beam deformation. We then use this simulation to optimize the velocity and efficiency of the robot. The optimized design is validated through experiments with a prototype device. NSF DMS-1517842.

Two-dimensional membrane as elastic shell with proof on the folds revealed by three-dimensional atomic mapping

NASA Astrophysics Data System (ADS)

Zhao, Jiong; Deng, Qingming; Ly, Thuc Hue; Han, Gang Hee; Sandeep, Gorantla; Rümmeli, Mark H.

2015-11-01

The great application potential for two-dimensional (2D) membranes (MoS2, WSe2, graphene and so on) aroused much effort to understand their fundamental mechanical properties. The out-of-plane bending rigidity is the key factor that controls the membrane morphology under external fields. Herein we provide an easy method to reconstruct the 3D structures of the folded edges of these 2D membranes on the atomic scale, using high-resolution (S)TEM images. After quantitative comparison with continuum mechanics shell model, it is verified that the bending behaviour of the studied 2D materials can be well explained by the linear elastic shell model. And the bending rigidities can thus be derived by fitting with our experimental results. Recall almost only theoretical approaches can access the bending properties of these 2D membranes before, now a new experimental method to measure the bending rigidity of such flexible and atomic thick 2D membranes is proposed.

Surface instability of an imperfectly bonded thin elastic film under surface van der Waals forces

NASA Astrophysics Data System (ADS)

Wang, Xu; Jing, Rong

2017-02-01

This paper studies surface instability of a thin elastic film imperfectly bonded to a rigid substrate interacting with a rigid contactor through van der Waals forces under plane strain conditions. The film-substrate interface is modeled as a linear spring with vanishing thickness described in terms of the normal and tangential interface parameters. Depending on the ratio of the two imperfect interface parameters, the critical value of the Poisson's ratio for the occurrence of surface wrinkling in the absence of surface energy can be greater than, equal to, or smaller than 0.25, which is the critical Poisson's ratio for a perfect film-substrate interface. The critical surface energy for the inhibition of the surface wrinkling is also obtained. Finally, we propose a very simple and effective method to study the surface instability of a multilayered elastic film with imperfect interfaces interacting with a rigid contactor or with another multilayered elastic film (or a multilayered simply supported plate) with imperfect interfaces.

Coupling molecular dynamics with lattice Boltzmann method based on the immersed boundary method

NASA Astrophysics Data System (ADS)

Tan, Jifu; Sinno, Talid; Diamond, Scott

2017-11-01

The study of viscous fluid flow coupled with rigid or deformable solids has many applications in biological and engineering problems, e.g., blood cell transport, drug delivery, and particulate flow. We developed a partitioned approach to solve this coupled Multiphysics problem. The fluid motion was solved by Palabos (Parallel Lattice Boltzmann Solver), while the solid displacement and deformation was simulated by LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). The coupling was achieved through the immersed boundary method (IBM). The code modeled both rigid and deformable solids exposed to flow. The code was validated with the classic problem of rigid ellipsoid particle orbit in shear flow, blood cell stretching test and effective blood viscosity, and demonstrated essentially linear scaling over 16 cores. An example of the fluid-solid coupling was given for flexible filaments (drug carriers) transport in a flowing blood cell suspensions, highlighting the advantages and capabilities of the developed code. NIH 1U01HL131053-01A1.

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

Chemistry and Technology of the Production of Fiber Nitron (Khimiya i Tekhnologiya Proizvodstva Volokna Nitron),

DTIC Science & Technology

1987-07-17

of some salts, mainly thiocyanate sodium. With wet spinning are used water/aqueous precipitation baths or organic coagulants (glycerin, hexanetriol ...comparatively small. During utilization of glycerine, isopropyl, butyl, hexanetriol baths into composition of bath for increasing elasticity of fiber...the number of C-atoms in the chain of their molecules. Therefore the glycerine bath is more than "rigid", than hexanetriol , whose effect/action is

Structure Formation in Solutions of Rigid Polymers Undergoing a Phase Transition

DTIC Science & Technology

1987-04-01

cyclohexene dioxide (ERL-4206) - 10 g. nonenyl succinic anhydride (NSA) - 26 g. dimethyl amino ethanol ( DMAE ) - 0.4 g. After infiltration, short segments...existence of a significant number of defects within the individual microfibril. The presence of defects in the lateral packing of PBT chains is also suggested...of the D- and L- enantiomers yields a nematic phase. The ordered phases exhi- bit complex textures due to defects (disclinations) which depend on

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.

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

Linear Look-Ahead in Conjunctive Cells: An Entorhinal Mechanism for Vector-Based Navigation

PubMed Central

Kubie, John L.; Fenton, André A.

2012-01-01

The crisp organization of the “firing bumps” of entorhinal grid cells and conjunctive cells leads to the notion that the entorhinal cortex may compute linear navigation routes. Specifically, we propose a process, termed “linear look-ahead,” by which a stationary animal could compute a series of locations in the direction it is facing. We speculate that this computation could be achieved through learned patterns of connection strengths among entorhinal neurons. This paper has three sections. First, we describe the minimal grid cell properties that will be built into our network. Specifically, the network relies on “rigid modules” of neurons, where all members have identical grid scale and orientation, but differ in spatial phase. Additionally, these neurons must be densely interconnected with synapses that are modifiable early in the animal’s life. Second, we investigate whether plasticity during short bouts of locomotion could induce patterns of connections amongst grid cells or conjunctive cells. Finally, we run a simulation to test whether the learned connection patterns can exhibit linear look-ahead. Our results are straightforward. A simulated 30-min walk produces weak strengthening of synapses between grid cells that do not support linear look-ahead. Similar training in a conjunctive cell module produces a small subset of very strong connections between cells. These strong pairs have three properties: the pre- and post-synaptic cells have similar heading direction. The cell pairs have neighboring grid bumps. Finally, the spatial offset of firing bumps of the cell pair is in the direction of the common heading preference. Such a module can produce strong and accurate linear look-ahead starting in any location and extending in any direction. We speculate that this process may: (1) compute linear paths to goals; (2) update grid cell firing during navigation; and (3) stabilize the rigid modules of grid cells and conjunctive cells. PMID:22557948

Enhanced enzyme kinetic stability by increasing rigidity within the active site.

PubMed

Xie, Yuan; An, Jiao; Yang, Guangyu; Wu, Geng; Zhang, Yong; Cui, Li; Feng, Yan

2014-03-14

Enzyme stability is an important issue for protein engineers. Understanding how rigidity in the active site affects protein kinetic stability will provide new insight into enzyme stabilization. In this study, we demonstrated enhanced kinetic stability of Candida antarctica lipase B (CalB) by mutating the structurally flexible residues within the active site. Six residues within 10 Å of the catalytic Ser(105) residue with a high B factor were selected for iterative saturation mutagenesis. After screening 2200 colonies, we obtained the D223G/L278M mutant, which exhibited a 13-fold increase in half-life at 48 °C and a 12 °C higher T50(15), the temperature at which enzyme activity is reduced to 50% after a 15-min heat treatment. Further characterization showed that global unfolding resistance against both thermal and chemical denaturation also improved. Analysis of the crystal structures of wild-type CalB and the D223G/L278M mutant revealed that the latter formed an extra main chain hydrogen bond network with seven structurally coupled residues within the flexible α10 helix that are primarily involved in forming the active site. Further investigation of the relative B factor profile and molecular dynamics simulation confirmed that the enhanced rigidity decreased fluctuation of the active site residues at high temperature. These results indicate that enhancing the rigidity of the flexible segment within the active site may provide an efficient method for improving enzyme kinetic stability.

Role of Sequence and Structural Polymorphism on the Mechanical Properties of Amyloid Fibrils

PubMed Central

Kim, Jae In; Na, Sungsoo; Eom, Kilho

2014-01-01

Amyloid fibrils playing a critical role in disease expression, have recently been found to exhibit the excellent mechanical properties such as elastic modulus in the order of 10 GPa, which is comparable to that of other mechanical proteins such as microtubule, actin filament, and spider silk. These remarkable mechanical properties of amyloid fibrils are correlated with their functional role in disease expression. This suggests the importance in understanding how these excellent mechanical properties are originated through self-assembly process that may depend on the amino acid sequence. However, the sequence-structure-property relationship of amyloid fibrils has not been fully understood yet. In this work, we characterize the mechanical properties of human islet amyloid polypeptide (hIAPP) fibrils with respect to their molecular structures as well as their amino acid sequence by using all-atom explicit water molecular dynamics (MD) simulation. The simulation result suggests that the remarkable bending rigidity of amyloid fibrils can be achieved through a specific self-aggregation pattern such as antiparallel stacking of β strands (peptide chain). Moreover, we have shown that a single point mutation of hIAPP chain constituting a hIAPP fibril significantly affects the thermodynamic stability of hIAPP fibril formed by parallel stacking of peptide chain, and that a single point mutation results in a significant change in the bending rigidity of hIAPP fibrils formed by antiparallel stacking of β strands. This clearly elucidates the role of amino acid sequence on not only the equilibrium conformations of amyloid fibrils but also their mechanical properties. Our study sheds light on sequence-structure-property relationships of amyloid fibrils, which suggests that the mechanical properties of amyloid fibrils are encoded in their sequence-dependent molecular architecture. PMID:24551113

Dynamic Scaling Theory of the Forced Translocation of a Semi-flexible Polymer Through a Nanopore

NASA Astrophysics Data System (ADS)

Lam, Pui-Man; Zhen, Yi

2015-10-01

We present a theoretical description of the dynamics of a semi-flexible polymer being pulled through a nanopore by an external force acting at the pore. Our theory is based on the tensile blob picture of Pincus in which the front of the tensile force propagates through the backbone of the polymer, as suggested by Sakaue and recently applied to study a completely flexible polymer with self-avoidance, by Dubbledam et al. For a semi-flexible polymer with a persistence length P, its statistics is self-avoiding for a very long chain. As the local force increases, the blob size starts to decrease. At the blob size , where a is the size of a monomer, the statistics becomes that of an ideal chain. As the blob size further decreases to below the persistence length P, the statistics is that of a rigid rod. We argue that semi-flexible polymer in translocation should include the three regions: a self-avoiding region, an ideal chain region and a rigid rod region, under uneven tension propagation, instead of a uniform scaling picture as in the case of a completely flexible polymer. In various regimes under the effect of weak, intermediate and strong driving forces we derive equations from which we can calculate the translocation time of the polymer. The translocation exponent is given by , where is an effective exponent for the end-to-end distance of the semi-flexible polymer, having a value between 1/2 and 3/5, depending on the total contour length of the polymer. Our results are of relevance for forced translocation of biological polymers such as DNA through a nanopore.

Structure of Cellulose Microfibrils in Primary Cell Walls from Collenchyma1[C][W][OA

PubMed Central

Thomas, Lynne H.; Forsyth, V. Trevor; Šturcová, Adriana; Kennedy, Craig J.; May, Roland P.; Altaner, Clemens M.; Apperley, David C.; Wess, Timothy J.; Jarvis, Michael C.

2013-01-01

In the primary walls of growing plant cells, the glucose polymer cellulose is assembled into long microfibrils a few nanometers in diameter. The rigidity and orientation of these microfibrils control cell expansion; therefore, cellulose synthesis is a key factor in the growth and morphogenesis of plants. Celery (Apium graveolens) collenchyma is a useful model system for the study of primary wall microfibril structure because its microfibrils are oriented with unusual uniformity, facilitating spectroscopic and diffraction experiments. Using a combination of x-ray and neutron scattering methods with vibrational and nuclear magnetic resonance spectroscopy, we show that celery collenchyma microfibrils were 2.9 to 3.0 nm in mean diameter, with a most probable structure containing 24 chains in cross section, arranged in eight hydrogen-bonded sheets of three chains, with extensive disorder in lateral packing, conformation, and hydrogen bonding. A similar 18-chain structure, and 24-chain structures of different shape, fitted the data less well. Conformational disorder was largely restricted to the surface chains, but disorder in chain packing was not. That is, in position and orientation, the surface chains conformed to the disordered lattice constituting the core of each microfibril. There was evidence that adjacent microfibrils were noncovalently aggregated together over part of their length, suggesting that the need to disrupt these aggregates might be a constraining factor in growth and in the hydrolysis of cellulose for biofuel production. PMID:23175754

Structure of cellulose microfibrils in primary cell walls from collenchyma.

PubMed

Thomas, Lynne H; Forsyth, V Trevor; Sturcová, Adriana; Kennedy, Craig J; May, Roland P; Altaner, Clemens M; Apperley, David C; Wess, Timothy J; Jarvis, Michael C

2013-01-01

In the primary walls of growing plant cells, the glucose polymer cellulose is assembled into long microfibrils a few nanometers in diameter. The rigidity and orientation of these microfibrils control cell expansion; therefore, cellulose synthesis is a key factor in the growth and morphogenesis of plants. Celery (Apium graveolens) collenchyma is a useful model system for the study of primary wall microfibril structure because its microfibrils are oriented with unusual uniformity, facilitating spectroscopic and diffraction experiments. Using a combination of x-ray and neutron scattering methods with vibrational and nuclear magnetic resonance spectroscopy, we show that celery collenchyma microfibrils were 2.9 to 3.0 nm in mean diameter, with a most probable structure containing 24 chains in cross section, arranged in eight hydrogen-bonded sheets of three chains, with extensive disorder in lateral packing, conformation, and hydrogen bonding. A similar 18-chain structure, and 24-chain structures of different shape, fitted the data less well. Conformational disorder was largely restricted to the surface chains, but disorder in chain packing was not. That is, in position and orientation, the surface chains conformed to the disordered lattice constituting the core of each microfibril. There was evidence that adjacent microfibrils were noncovalently aggregated together over part of their length, suggesting that the need to disrupt these aggregates might be a constraining factor in growth and in the hydrolysis of cellulose for biofuel production.

Systematic and efficient side chain optimization for molecular docking using a cheapest-path procedure.

PubMed

Schumann, Marcel; Armen, Roger S

2013-05-30

Molecular docking of small-molecules is an important procedure for computer-aided drug design. Modeling receptor side chain flexibility is often important or even crucial, as it allows the receptor to adopt new conformations as induced by ligand binding. However, the accurate and efficient incorporation of receptor side chain flexibility has proven to be a challenge due to the huge computational complexity required to adequately address this problem. Here we describe a new docking approach with a very fast, graph-based optimization algorithm for assignment of the near-optimal set of residue rotamers. We extensively validate our approach using the 40 DUD target benchmarks commonly used to assess virtual screening performance and demonstrate a large improvement using the developed side chain optimization over rigid receptor docking (average ROC AUC of 0.693 vs. 0.623). Compared to numerous benchmarks, the overall performance is better than nearly all other commonly used procedures. Furthermore, we provide a detailed analysis of the level of receptor flexibility observed in docking results for different classes of residues and elucidate potential avenues for further improvement. Copyright © 2013 Wiley Periodicals, Inc.

Role of internal motions and molecular geometry on the NMR relaxation of hydrocarbons

NASA Astrophysics Data System (ADS)

Singer, P. M.; Asthagiri, D.; Chen, Z.; Valiya Parambathu, A.; Hirasaki, G. J.; Chapman, W. G.

2018-04-01

The role of internal motions and molecular geometry on 1H NMR relaxation rates in liquid-state hydrocarbons is investigated using MD (molecular dynamics) simulations of the autocorrelation functions for intramolecular and intermolecular 1H-1H dipole-dipole interactions. The effects of molecular geometry and internal motions on the functional form of the autocorrelation functions are studied by comparing symmetric molecules such as neopentane and benzene to corresponding straight-chain alkanes n-pentane and n-hexane, respectively. Comparison of rigid versus flexible molecules shows that internal motions cause the intramolecular and intermolecular correlation-times to get significantly shorter, and the corresponding relaxation rates to get significantly smaller, especially for longer-chain n-alkanes. Site-by-site simulations of 1H's across the chains indicate significant variations in correlation times and relaxation rates across the molecule, and comparison with measurements reveals insights into cross-relaxation effects. Furthermore, the simulations reveal new insights into the relative strength of intramolecular versus intermolecular relaxation as a function of internal motions, as a function of molecular geometry, and on a site-by-site basis across the chain.

Aeromechanical stability of helicopters with a bearingless main rotor. Part 1: Equations of motion

NASA Technical Reports Server (NTRS)

Hodges, D. H.

1978-01-01

Equations of motion for a coupled rotor-body system were derived for the purpose of studying air and ground resonance characteristics of helicopters that have bearingless main rotors. For the fuselage, only four rigid body degrees of freedom are considered; longitudinal and lateral translations, pitch, and roll. The rotor is assumed to consist of three or more rigid blades. Each blade is joined to the hub by means of a flexible beam segment (flexbeam or strap). Pitch change is accomplished by twisting the flexbeam with the pitch-control system, the characteristics of which are variable. Thus, the analysis is capable of implicitly treating aeroelastic couplings generated by the flexbeam elastic deflections, the pitch-control system, and the angular offsets of the blade and flexbeam. The linearized equations are written in the nonrotating system retaining only the cyclic rotor modes; thus, they comprise a system of homogeneous ordinary differential equations with constant coefficients. All contributions to the linearized perturbation equations from inertia, gravity, quasi-steady aerodynamics, and the flexbeam equilibrium deflections are retained exactly.

Effect of a crystal-melt interface on Taylor-vortex flow

NASA Technical Reports Server (NTRS)

Mcfadden, G. B.; Coriell, S. R.; Murray, B. T.; Glicksman, M. E.; Selleck, M. E.

1990-01-01

The linear stability of circular Couette flow between concentric infinite cylinders is considered for the case that the stationary outer cylinder is a crystal-melt interface rather than a rigid surface. A radial temperature difference is maintained across the liquid gap, and equations for heat transport in the crystal and melt phases are included to extend the ordinary formulation of this problem. The stability of this two-phase system depends on the Prandtl number. For small Prandtl number the linear stability of the two-phase system is given by the classical results for a rigid-walled system. For increasing values of the Prandtl number, convective heat transport becomes significant and the system becomes increasingly less stable. Previous results in a narrow-gap approximation are extended to the case of a finite gap, and both axisymmetric and nonaxisymmetric disturbance modes are considered. The two-phase system becomes less stable as the finite gap tends to the narrow-gap limit. The two-phase system is more stable to nonaxisymmetric modes with azimuthal wavenumber n = 1; the stability of these n = 1 modes is sensitive to the latent heat of fusion.

Decoupled and linear quadratic regulator control of a large, flexible space antenna with an observer in the control loop

NASA Technical Reports Server (NTRS)

Hamer, H. A.; Johnson, K. G.; Young, J. W.

1985-01-01

An analysis is performed to compare decoupled and linear quadratic regulator (LQR) procedures for the control of a large, flexible space antenna. Control objectives involve: (1) commanding changes in the rigid-body modes, (2) nulling initial disturbances in the rigid-body modes, or (3) nulling initial disturbances in the first three flexible modes. Control is achieved with two three-axis control-moment gyros located on the antenna column. Results are presented to illustrate various effects on control requirements for the two procedures. These effects include errors in the initial estimates of state variables, variations in the type, number, and location of sensors, and deletions of state-variable estimates for certain flexible modes after control activation. The advantages of incorporating a time lag in the control feedback are also illustrated. In addition, the effects of inoperative-control situations are analyzed with regard to control requirements and resultant modal responses. Comparisons are included which show the effects of perfect state feedback with no residual modes (ideal case). Time-history responses are presented to illustrate the various effects on the control procedures.

A Coupled Aeroelastic Model for Launch Vehicle Stability Analysis

NASA Technical Reports Server (NTRS)

Orr, Jeb S.

2010-01-01

A technique for incorporating distributed aerodynamic normal forces and aeroelastic coupling effects into a stability analysis model of a launch vehicle is presented. The formulation augments the linear state-space launch vehicle plant dynamics that are compactly derived as a system of coupled linear differential equations representing small angular and translational perturbations of the rigid body, nozzle, and sloshing propellant coupled with normal vibration of a set of orthogonal modes. The interaction of generalized forces due to aeroelastic coupling and thrust can be expressed as a set of augmenting non-diagonal stiffness and damping matrices in modal coordinates with no penalty on system order. While the eigenvalues of the structural response in the presence of thrust and aeroelastic forcing can be predicted at a given flight condition independent of the remaining degrees of freedom, the coupled model provides confidence in closed-loop stability in the presence of rigid-body, slosh, and actuator dynamics. Simulation results are presented that characterize the coupled dynamic response of the Ares I launch vehicle and the impact of aeroelasticity on control system stability margins.

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.

Evolution of flexural rigidity according to the cross-sectional dimension of a superelastic nickel titanium orthodontic wire.

PubMed

Garrec, Pascal; Tavernier, Bruno; Jordan, Laurence

2005-08-01

The choice of the most suitable orthodontic wire for each stage of treatment requires estimation of the forces generated. In theory, the selection of wire sequences should initially utilize a lower flexural rigidity; thus clinicians use smaller round cross-sectional dimension wires to generate lighter forces during the preliminary alignment stage. This assessment is true for conventional alloys, but not necessarily for superelastic nickel titanium (NiTi). In this case, the flexural rigidity dependence on cross-sectional dimension differs from the linear elasticity prediction because of the martensitic transformation process. It decreases with increasing deflection and this phenomenon is accentuated in the unloading process. This behaviour should lead us to consider differently the biomechanical approach to orthodontic treatment. The present study compared bending in 10 archwires made from NiTi orthodontics alloy of two cross-sectional dimensions. The results were based on microstructural and mechanical investigations. With conventional alloys, the flexural rigidity was constant for each wire and increased largely with the cross-sectional dimension for the same strain. With NiTi alloys, the flexural rigidity is not constant and the influence of size was not as important as it should be. This result can be explained by the non-constant elastic modulus during the martensite transformation process. Thus, in some cases, treatment can begin with full-size (rectangular) wires that nearly fill the bracket slot with a force application deemed to be physiologically desirable for tooth movement and compatible with patient comfort.

Rigidity-patterned polyelectrolyte films to control myoblast cell adhesion and spatial organization

PubMed Central

Monge, Claire; Saha, Naresh; Boudou, Thomas; Pózos-Vásquez, Cuauhtemoc; Dulong, Virginie; Glinel, Karine; Picart, Catherine

2014-01-01

In vivo, cells are sensitive to the stiffness of their micro-environment and especially to the spatial organization of the stiffness. In vitro studies of this phenomenon can help to better understand the mechanisms of the cell response to spatial variations of the matrix stiffness. In this work, we design polelyelectrolyte multilayer films made of poly(L-lysine) and a photo-reactive hyaluronan derivative. These films can be photo-crosslinked through a photomask to create spatial patterns of rigidity. Quartz substrates incorporating a chromium mask are prepared to expose selectively the film to UV light (in a physiological buffer), without any direct contact between the photomask and the soft film. We show that these micropatterns are chemically homogeneous and flat, without any preferential adsorption of adhesive proteins. Three groups of pattern geometries differing by their shape (circles or lines), size (form 2 to 100 μm) or interspacing distance between the motifs are used to study the adhesion and spatial organization of myoblast cells. On large circular micropatterns, the cells form large assemblies that are confined to the stiffest parts. Conversely, when the size of the rigidity patterns is subcellular, the cells respond by forming protrusions. Finally, on linear micropatterns of rigidity, myoblasts align and their nuclei drastically elongate in specific conditions. These results pave the way for the study of the different steps of myoblast fusion in response to matrix rigidity in well-defined geometrical conditions. PMID:25100929

Defects in regular nanosystems and interference spectra at reemission of electromagnetic field attosecond pulses

NASA Astrophysics Data System (ADS)

Matveev, V. I.; Makarov, D. N.

2017-01-01

The effect of defects in nanostructured targets on interference spectra at the reemission of attosecond electromagnetic pulses has been considered. General expressions have been obtained for calculations of spectral distributions for one-, two-, and three-dimensional multiatomic nanosystems consisting of identical complex atoms with defects such as bends, vacancies, and breaks. Changes in interference spectra by a linear chain with several removed atoms (chain with breaks) and by a linear chain with a bend have been calculated as examples allowing a simple analytical representation. Generalization to two- and three-dimensional nanosystems has been developed.

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

Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase

PubMed Central

Preiswerk, Nathalie; Beck, Tobias; Schulz, Jessica D.; Milovník, Peter; Mayer, Clemens; Siegel, Justin B.; Baker, David; Hilvert, Donald

2014-01-01

By combining targeted mutagenesis, computational refinement, and directed evolution, a modestly active, computationally designed Diels-Alderase was converted into the most proficient biocatalyst for [4+2] cycloadditions known. The high stereoselectivity and minimal product inhibition of the evolved enzyme enabled preparative scale synthesis of a single product diastereomer. X-ray crystallography of the enzyme–product complex shows that the molecular changes introduced over the course of optimization, including addition of a lid structure, gradually reshaped the pocket for more effective substrate preorganization and transition state stabilization. The good overall agreement between the experimental structure and the original design model with respect to the orientations of both the bound product and the catalytic side chains contrasts with other computationally designed enzymes. Because design accuracy appears to correlate with scaffold rigidity, improved control over backbone conformation will likely be the key to future efforts to design more efficient enzymes for diverse chemical reactions. PMID:24847076

Cell Membrane Softening in Cancer Cells

NASA Astrophysics Data System (ADS)

Schmidt, Sebastian; Händel, Chris; Käs, Josef

Biomechanical properties are useful characteristics and regulators of the cell's state. Current research connects mechanical properties of the cytoskeleton to many cellular processes but does not investigate the biomechanics of the plasma membrane. We evaluated thermal fluctuations of giant plasma membrane vesicles, directly derived from the plasma membranes of primary breast and cervical cells and observed a lowered rigidity in the plasma membrane of malignant cells compared to non-malignant cells. To investigate the specific role of membrane rigidity changes, we treated two cell lines with the Acetyl-CoA carboxylase inhibitor Soraphen A. It changed the lipidome of cells and drastically increased membrane stiffness by up regulating short chained membrane lipids. These altered cells had a decreased motility in Boyden chamber assays. Our results indicate that the thermal fluctuations of the membrane, which are much smaller than the fluctuations driven by the cytoskeleton, can be modulated by the cell and have an impact on adhesion and motility.

Discrete Time Crystals: Rigidity, Criticality, and Realizations.

PubMed

Yao, N Y; Potter, A C; Potirniche, I-D; Vishwanath, A

2017-01-20

Despite being forbidden in equilibrium, spontaneous breaking of time translation symmetry can occur in periodically driven, Floquet systems with discrete time-translation symmetry. The period of the resulting discrete time crystal is quantized to an integer multiple of the drive period, arising from a combination of collective synchronization and many body localization. Here, we consider a simple model for a one-dimensional discrete time crystal which explicitly reveals the rigidity of the emergent oscillations as the drive is varied. We numerically map out its phase diagram and compute the properties of the dynamical phase transition where the time crystal melts into a trivial Floquet insulator. Moreover, we demonstrate that the model can be realized with current experimental technologies and propose a blueprint based upon a one dimensional chain of trapped ions. Using experimental parameters (featuring long-range interactions), we identify the phase boundaries of the ion-time-crystal and propose a measurable signature of the symmetry breaking phase transition.

Rigidity and pH dependent Morphology of Beta-Lactoglobulin Spherulites

NASA Astrophysics Data System (ADS)

Gayetsky, Lisa; Armstead, Douglas

2008-03-01

Beta-Lactoglobulin is a milk protein that will denature in acidic solution (less than 2.0 pH) and if heated for extended periods (greater than 18 hours) it will form radial structures called Spherulites. Spherulites, along with the amyloid fibrils that compose them, are of practical importance because they form in the human body and cause the amyloidosis diseases. Different amyloidosis are caused by different types of denatured proteins occurring in different parts of the body. Since it is believed that Spherulite formation is a generic protein characteristic, Beta-Lactoglobulin is a legitimate and easy to use protein to study these structures. In this study we are quantifying the shape of Beta-Lactoglobulin Spherulites to determine if the pH of the protein solution has an impact on the morphology due to side chain interactions or other causes. We are also testing the rigidity of these structures to determine the relevance of small shape changes.

Isohexide and Sorbitol-Derived, Enzymatically Synthesized Renewable Polyesters with Enhanced Tg.

PubMed

Gustini, Liliana; Lavilla, Cristina; de Ilarduya, Antxon Martínez; Muñoz-Guerra, Sebastián; Koning, Cor E

2016-10-10

Sugar-based polyesters derived from sorbitol and isohexides were obtained via solvent-free enzymatic catalysis. Pendant hydroxyl groups, coming from the sorbitol units, were present along the polyester backbone, whereas the two isohexides, namely, isomannide and isoidide dimethyl ester monomers, were selected to introduce rigidity into the polyester chains. The feasibility of incorporating isomannide as a diol compared to the isoidide dimethyl ester as acyl-donor via lipase-catalyzed polycondensation was investigated. The presence of bicyclic units resulted in enhanced T g with respect to the parent sorbitol-containing polyester lacking isohexides. The different capability of the two isohexides to boost the thermal properties confirmed the more flexible character provided by the isoidide diester derivative. Solvent-borne coatings were prepared by cross-linking the sugar-based polyester polyols with polyisocyanates. The increased rigidity of the obtained sugar-based polyester polyols led to an enhancement in hardness of the resulting coatings.

Flexure Based Linear and Rotary Bearings

NASA Technical Reports Server (NTRS)

Voellmer, George M. (Inventor)

2016-01-01

A flexure based linear bearing includes top and bottom parallel rigid plates; first and second flexures connecting the top and bottom plates and constraining exactly four degrees of freedom of relative motion of the plates, the four degrees of freedom being X and Y axis translation and rotation about the X and Y axes; and a strut connecting the top and bottom plates and further constraining exactly one degree of freedom of the plates, the one degree of freedom being one of Z axis translation and rotation about the Z axis.

LIMAO: Cross-platform software for simulating laser-induced alignment and orientation dynamics of linear-, symmetric- and asymmetric tops

NASA Astrophysics Data System (ADS)

Szidarovszky, Tamás; Jono, Maho; Yamanouchi, Kaoru

2018-07-01

A user-friendly and cross-platform software called Laser-Induced Molecular Alignment and Orientation simulator (LIMAO) has been developed. The program can be used to simulate within the rigid rotor approximation the rotational dynamics of gas phase molecules induced by linearly polarized intense laser fields at a given temperature. The software is implemented in the Java and Mathematica programming languages. The primary aim of LIMAO is to aid experimental scientists in predicting and analyzing experimental data representing laser-induced spatial alignment and orientation of molecules.

Dynamics of DNA/intercalator complexes

NASA Astrophysics Data System (ADS)

Schurr, J. M.; Wu, Pengguang; Fujimoto, Bryant S.

1990-05-01

Complexes of linear and supercoiled DNAs with different intercalating dyes are studied by time-resolved fluorescence polarization anisotropy using intercalated ethidium as the probe. Existing theory is generalized to take account of excitation transfer between intercalated ethidiums, and Forster theory is shown to be valid in this context. The effects of intercalated ethidium, 9-aminoacridine, and proflavine on the torsional rigidity of linear and supercoiled DNAs are studied up to rather high binding ratios. Evidence is presented that metastable secondary structure persists in dye-relaxed supercoiled DNAs, which contradicts the standard model of supercoiled DNAs.

Nanoporous poly(3-hexylthiophene) thin film structures from self-organization of a tunable molecular bottlebrush scaffold

DOE PAGES

Ahn, Suk-kyun; Carrillo, Jan-Michael Y.; Keum, Jong K.; ...

2017-04-07

The ability to widely tune the design of macromolecular bottlebrushes provides access to self-assembled nanostructures formed by microphase segregation in melt, thin film and solution that depart from structures adopted by simple linear copolymers. A series of random bottlebrush copolymers containing poly(3-hexylthiophene) (P3HT) and poly(D,L-lactide) (PLA) side chains grafted on a poly(norbornene) backbone were synthesized via ring-opening metathesis polymerization (ROMP) using the grafting through approach. P3HT side chains induce a physical aggregation of the bottlebrush copolymers upon solvent removal by vacuum drying, primarily driven by attractive π–π interactions; however, the amount of aggregation can be controlled by adjusting side chainmore » composition or by adding linear P3HT chains to the bottlebrush copolymers. Coarse-grained molecular dynamics simulations reveal that linear P3HT chains preferentially associate with P3HT side chains of bottlebrush copolymers, which tends to reduce the aggregation. The nanoscale morphology of microphase segregated thin films created by casting P3HT–PLA random bottlebrush copolymers is highly dependent on the composition of P3HT and PLA side chains, while domain spacing of nanostructures is mainly determined by the length of the side chains. The selective removal of PLA side chains under alkaline conditions generates nanoporous P3HT structures that can be tuned by manipulating molecular design of the bottlebrush scaffold, which is affected by molecular weight and grafting density of the side chains, and their sequence. Furthermore, the ability to exploit the unusual architecture of bottlebrushes to fabricate tunable nanoporous P3HT thin film structures may be a useful way to design templates for optoelectronic applications or membranes for separations.« less

Nanoporous poly(3-hexylthiophene) thin film structures from self-organization of a tunable molecular bottlebrush scaffold

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

Ahn, Suk-kyun; Carrillo, Jan-Michael Y.; Keum, Jong K.

The ability to widely tune the design of macromolecular bottlebrushes provides access to self-assembled nanostructures formed by microphase segregation in melt, thin film and solution that depart from structures adopted by simple linear copolymers. A series of random bottlebrush copolymers containing poly(3-hexylthiophene) (P3HT) and poly(D,L-lactide) (PLA) side chains grafted on a poly(norbornene) backbone were synthesized via ring-opening metathesis polymerization (ROMP) using the grafting through approach. P3HT side chains induce a physical aggregation of the bottlebrush copolymers upon solvent removal by vacuum drying, primarily driven by attractive π–π interactions; however, the amount of aggregation can be controlled by adjusting side chainmore » composition or by adding linear P3HT chains to the bottlebrush copolymers. Coarse-grained molecular dynamics simulations reveal that linear P3HT chains preferentially associate with P3HT side chains of bottlebrush copolymers, which tends to reduce the aggregation. The nanoscale morphology of microphase segregated thin films created by casting P3HT–PLA random bottlebrush copolymers is highly dependent on the composition of P3HT and PLA side chains, while domain spacing of nanostructures is mainly determined by the length of the side chains. The selective removal of PLA side chains under alkaline conditions generates nanoporous P3HT structures that can be tuned by manipulating molecular design of the bottlebrush scaffold, which is affected by molecular weight and grafting density of the side chains, and their sequence. Furthermore, the ability to exploit the unusual architecture of bottlebrushes to fabricate tunable nanoporous P3HT thin film structures may be a useful way to design templates for optoelectronic applications or membranes for separations.« less

Synthesis, crystal structures, and luminescent properties of Cd(II) coordination polymers assembled from semi-rigid multi-dentate N-containing ligand

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

Yuan, Gang; Shao, Kui-Zhan; Chen, Lei

2012-12-15

Three new polymers, [Cd(L){sub 2}(H{sub 2}O){sub 2}]{sub n} (1), [Cd{sub 3}(L){sub 2}({mu}{sub 3}-OH){sub 2}({mu}{sub 2}-Cl){sub 2}(H{sub 2}O){sub 2}]{sub n} (2), {l_brace}[Cd{sub 2}(L){sub 2}(nic){sub 2}(H{sub 2}O){sub 2}]{center_dot}H{sub 2}O{r_brace}{sub n} (3) (HL=5-(4-((1H-1,2,4-triazol-1-yl)methyl)phenyl)-1H-tetrazole, Hnic=nicotinic acid) have been prepared and structurally characterized. Compounds 1 and 2 display 2D monomolecular layers built by the inter-linking single helical chains and L{sup -} ligands connecting chain-like [Cd({mu}{sub 3}-OH)({mu}{sub 2}-Cl)]{sub n} secondary building units, respectively. Compound 3 is constructed from the mixed ligands and possesses a (3,4)-connected framework with (4{center_dot}8{sup 2})(4{center_dot}8{sup 2}{center_dot}10{sup 3}) topology. Moreover, the fluorescent properties of HL ligand and compounds 1-3 are also been investigated.more » - Graphical abstract: Three new coordination polymers based on the semi-rigid multidentate N-donor ligand have been successfully synthesized by hydrothermal reaction. Complexes 1 and 2 exhibit the 2D layers formed by inter-linking single helices and L{sup -} anions bridging 1D chain-like SBUs, respectively. Complex 3 is buit by L{sup -} and assistant nic{sup -} ligands connecting metal centers and possesses a (3,4)-connected framework with (4 Multiplication-Sign 8{sup 2})(4 Multiplication-Sign 8{sup 2} Multiplication-Sign 10{sup 3}) topology. Moreover, these complexes display fluorescent properties indicating that they may have potential applications as optical materials. Highlights: Black-Right-Pointing-Pointer Three Cd-compounds were prepared from semi-rigid HL ligand with different N-containing groups. Black-Right-Pointing-Pointer They exhibit diverse structures from 2D monomolecular layer to 3D covalent framework. Black-Right-Pointing-Pointer The HL ligands displayed various coordination modes under different reaction conditions. Black-Right-Pointing-Pointer These compounds exhibit good luminescent properties.« less

CT-derived indices of canine osteosarcoma-affected antebrachial strength.

PubMed

Garcia, Tanya C; Steffey, Michele A; Zwingenberger, Allison L; Daniel, Leticia; Stover, Susan M

2017-05-01

To improve the prediction of fractures in dogs with bone tumors of the distal radius by identifying computed tomography (CT) indices that correlate with antebrachial bone strength and fracture location. Prospective experimental study. Dogs with antebrachial osteosarcoma (n = 10), and normal cadaver bones (n=9). Antebrachia were imaged with quantitative CT prior to biomechanical testing to failure. CT indices of structural properties were compared to yield force and maximum force using Pearson correlation tests. Straight beam failure (Fs), axial rigidity, curved beam failure (Fc), and craniocaudal bending moment of inertia (MOICrCd) CT indices most highly correlated (0.77 > R > 0.57) with yield and maximum forces when iOSA-affected and control bones were included in the analysis. Considering only OSA-affected bones, Fs, Fc, and axial rigidity correlated highly (0.85 > R > 0.80) with maximum force. In affected bones, the location of minimum axial rigidity and maximum MOICrCd correlated highly (R > 0.85) with the actual fracture location. CT-derived axial rigidity, Fs, and MOICrCd have strong linear relationships with yield and maximum force. These indices should be further evaluated prospectively in OSA-affected dogs that do, and do not, experience pathologic fracture. © 2017 The American College of Veterinary Surgeons.

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…

Applied Time Domain Stability Margin Assessment for Nonlinear Time-Varying Systems

NASA Technical Reports Server (NTRS)

Kiefer, J. M.; Johnson, M. D.; Wall, J. H.; Dominguez, A.

2016-01-01

The baseline stability margins for NASA's Space Launch System (SLS) launch vehicle were generated via the classical approach of linearizing the system equations of motion and determining the gain and phase margins from the resulting frequency domain model. To improve the fidelity of the classical methods, the linear frequency domain approach can be extended by replacing static, memoryless nonlinearities with describing functions. This technique, however, does not address the time varying nature of the dynamics of a launch vehicle in flight. An alternative technique for the evaluation of the stability of the nonlinear launch vehicle dynamics along its trajectory is to incrementally adjust the gain and/or time delay in the time domain simulation until the system exhibits unstable behavior. This technique has the added benefit of providing a direct comparison between the time domain and frequency domain tools in support of simulation validation. This technique was implemented by using the Stability Aerospace Vehicle Analysis Tool (SAVANT) computer simulation to evaluate the stability of the SLS system with the Adaptive Augmenting Control (AAC) active and inactive along its ascent trajectory. The gains for which the vehicle maintains apparent time-domain stability defines the gain margins, and the time delay similarly defines the phase margin. This method of extracting the control stability margins from the time-domain simulation is relatively straightforward and the resultant margins can be compared to the linearized system results. The sections herein describe the techniques employed to extract the time-domain margins, compare the results between these nonlinear and the linear methods, and provide explanations for observed discrepancies. The SLS ascent trajectory was simulated with SAVANT and the classical linear stability margins were evaluated at one second intervals. The linear analysis was performed with the AAC algorithm disabled to attain baseline stability margins. At each time point, the system was linearized about the current operating point using Simulink's built-in solver. Each linearized system in time was evaluated for its rigid-body gain margin (high frequency gain margin), rigid-body phase margin, and aero gain margin (low frequency gain margin) for each control axis. Using the stability margins derived from the baseline linearization approach, the time domain derived stability margins were determined by executing time domain simulations in which axis-specific incremental gain and phase adjustments were made to the nominal system about the expected neutral stability point at specific flight times. The baseline stability margin time histories were used to shift the system gain to various values around the zero margin point such that a precise amount of expected gain margin was maintained throughout flight. When assessing the gain margins, the gain was applied starting at the time point under consideration, thereafter following the variation in the margin found in the linear analysis. When assessing the rigid-body phase margin, a constant time delay was applied to the system starting at the time point under consideration. If the baseline stability margins were correctly determined via the linear analysis, the time domain simulation results should contain unstable behavior at certain gain and phase values. Examples will be shown from repeated simulations with variable added gain and phase lag. Faithfulness of margins calculated from the linear analysis to the nonlinear system will be demonstrated.

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.

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

Focus: Structure and dynamics of the interfacial layer in polymer nanocomposites with attractive interactions

DOE PAGES

Cheng, Shiwang; Carroll, Bobby; Bocharova, Vera; ...

2017-03-30

In recent years it has become clear that the interfacial layer formed around nanoparticles in polymer nanocomposites (PNCs) is critical for controlling their macroscopic properties. The interfacial layer occupies a significant volume fraction of the polymer matrix in PNCs and creates strong intrinsic heterogeneity in their structure and dynamics. In this paper, we focus on analysis of the structure and dynamics of the interfacial region in model PNCs with well-dispersed, spherical nanoparticles with attractive interactions. First, we discuss several experimental techniques that provide structural and dynamic information on the interfacial region in PNCs. Then, we discuss the role of variousmore » microscopic parameters in controlling structure and dynamics of the interfacial layer. The analysis presented emphasizes the importance of the polymer-nanoparticle interactions for the slowing down dynamics in the interfacial region, while the thickness of the interfacial layer appears to be dependent on chain rigidity, and has been shown to increase with cooling upon approaching the glass transition. Aside from chain rigidity and polymer-nanoparticle interactions, the interfacial layer properties are also affected by the molecular weight of the polymer and the size of the nanoparticles. Finally, in the last part of this focus article, we emphasize the important challenges in the field of polymer nanocomposites and a potential analogy with the behavior observed in thin films.« less

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

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.

Protein side chain conformation predictions with an MMGBSA energy function.

PubMed

Gaillard, Thomas; Panel, Nicolas; Simonson, Thomas

2016-06-01

The prediction of protein side chain conformations from backbone coordinates is an important task in structural biology, with applications in structure prediction and protein design. It is a difficult problem due to its combinatorial nature. We study the performance of an "MMGBSA" energy function, implemented in our protein design program Proteus, which combines molecular mechanics terms, a Generalized Born and Surface Area (GBSA) solvent model, with approximations that make the model pairwise additive. Proteus is not a competitor to specialized side chain prediction programs due to its cost, but it allows protein design applications, where side chain prediction is an important step and MMGBSA an effective energy model. We predict the side chain conformations for 18 proteins. The side chains are first predicted individually, with the rest of the protein in its crystallographic conformation. Next, all side chains are predicted together. The contributions of individual energy terms are evaluated and various parameterizations are compared. We find that the GB and SA terms, with an appropriate choice of the dielectric constant and surface energy coefficients, are beneficial for single side chain predictions. For the prediction of all side chains, however, errors due to the pairwise additive approximation overcome the improvement brought by these terms. We also show the crucial contribution of side chain minimization to alleviate the rigid rotamer approximation. Even without GB and SA terms, we obtain accuracies comparable to SCWRL4, a specialized side chain prediction program. In particular, we obtain a better RMSD than SCWRL4 for core residues (at a higher cost), despite our simpler rotamer library. Proteins 2016; 84:803-819. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

SCARLET I: Mechanization solutions for deployable concentrator optics integrated with rigid array technology

NASA Technical Reports Server (NTRS)

Wachholz, James J.; Murphy, David M.

1996-01-01

The SCARLET I (Solar Concentrator Army with Refractive Linear Element Technology) solar array wing was designed and built to demonstrate, in flight, the feasibility of integrating deployable concentrator optics within the design envelope of typical rigid array technology. Innovative mechanism designs were used throughout the array, and a full series of qualification tests were successfully performed in anticipation of a flight on the Multiple Experiment Transporter to Earth Orbit and Return (METEOR) spacecraft. Even though the Conestoga launch vehicle was unable to place the spacecraft in orbit, the program effort was successful in achieving the milestones of analytical and design development functional validation, and flight qualification, thus leading to a future flight evaluation for the SCARLET technology.

Chaotic sources of noise in machine acoustics

NASA Astrophysics Data System (ADS)

Moon, F. C., Prof.; Broschart, Dipl.-Ing. T.

1994-05-01

In this paper a model is posited for deterministic, random-like noise in machines with sliding rigid parts impacting linear continuous machine structures. Such problems occur in gear transmission systems. A mathematical model is proposed to explain the random-like structure-borne and air-borne noise from such systems when the input is a periodic deterministic excitation of the quasi-rigid impacting parts. An experimental study is presented which supports the model. A thin circular plate is impacted by a chaotically vibrating mass excited by a sinusoidal moving base. The results suggest that the plate vibrations might be predicted by replacing the chaotic vibrating mass with a probabilistic forcing function. Prechaotic vibrations of the impacting mass show classical period doubling phenomena.

SCARLET I: Mechanization solutions for deployable concentrator optics integrated with rigid array technology

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

Wachholz, J.J.; Murphy, D.M.

1996-05-01

The SCARLET I (Solar Concentrator Army with Refractive Linear Element Technology) solar array wing was designed and built to demonstrate, in flight, the feasibility of integrating deployable concentrator optics within the design envelope of typical rigid array technology. Innovative mechanism designs were used throughout the array, and a full series of qualification tests were successfully performed in anticipation of a flight on the Multiple Experiment Transporter to Earth Orbit and Return (METEOR) spacecraft. Even though the Conestoga launch vehicle was unable to place the spacecraft in orbit, the program effort was successful in achieving the milestones of analytical and designmore » development functional validation, and flight qualification, thus leading to a future flight evaluation for the SCARLET technology.« less

On the tsunami wave-submerged breakwater interaction

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

Filianoti, P.; Piscopo, R.

The tsunami wave loads on a submerged rigid breakwater are inertial. It is the result arising from the simple calculation method here proposed, and it is confirmed by the comparison with results obtained by other researchers. The method is based on the estimate of the speed drop of the tsunami wave passing over the breakwater. The calculation is rigorous for a sinusoidal wave interacting with a rigid submerged obstacle, in the framework of the linear wave theory. This new approach gives a useful and simple tool for estimating tsunami loads on submerged breakwaters.An unexpected novelty come out from a workedmore » example: assuming the same wave height, storm waves are more dangerous than tsunami waves, for the safety against sliding of submerged breakwaters.« less

Dynamics of myosin II organization into contractile networks and fibers at the medial cell cortex

NASA Astrophysics Data System (ADS)

Nie, Wei

The cellular morphology of adhered cells depends crucially on the formation of a contractile meshwork of parallel and cross-linked stress fibers along the contacting surface. The motor activity and mini-filament assembly of non-muscle myosin II is an important component of cell-level cytoskeletal remodeling during mechanosensing. To monitor the dynamics of non-muscle myosin II, we used confocal microscopy to image cultured HeLa cells that stably express myosin regulatory light chain tagged with GFP (MRLC-GFP). MRLC-GFP was monitored in time-lapse movies at steady state and during the response of cells to varying concentrations of blebbistatin (which disrupts actomyosin stress fibers). Using image correlation spectroscopy analysis, we quantified the kinetics of disassembly and reassembly of actomyosin networks and compared to studies by other groups. This analysis suggested the following processes: myosin minifilament assembly and disassembly; aligning and contraction; myosin filament stabilization upon increasing contractile tension. Numerical simulations that include those processes capture some of the main features observed in the experiments. This study provides a framework to help interpret how different cortical myosin remodeling kinetics may contribute to different cell shape and rigidity depending on substrate stiffness. We discuss methods to monitor myosin reorganization using non-linear imaging methods.

Mechanistic insights into phosphoprotein-binding FHA domains.

PubMed

Liang, Xiangyang; Van Doren, Steven R

2008-08-01

[Structure: see text]. FHA domains are protein modules that switch signals in diverse biological pathways by monitoring the phosphorylation of threonine residues of target proteins. As part of the effort to gain insight into cellular avoidance of cancer, FHA domains involved in the cellular response to DNA damage have been especially well-characterized. The complete protein where the FHA domain resides and the interaction partners determine the nature of the signaling. Thus, a key biochemical question is how do FHA domains pick out their partners from among thousands of alternatives in the cell? This Account discusses the structure, affinity, and specificity of FHA domains and the formation of their functional structure. Although FHA domains share sequence identity at only five loop residues, they all fold into a beta-sandwich of two beta-sheets. The conserved arginine and serine of the recognition loops recognize the phosphorylation of the threonine targeted. Side chains emanating from loops that join beta-strand 4 with 5, 6 with 7, or 10 with 11 make specific contacts with amino acids of the ligand that tailor sequence preferences. Many FHA domains choose a partner in extended conformation, somewhat according to the residue three after the phosphothreonine in sequence (pT + 3 position). One group of FHA domains chooses a short carboxylate-containing side chain at pT + 3. Another group chooses a long, branched aliphatic side chain. A third group prefers other hydrophobic or uncharged polar side chains at pT + 3. However, another FHA domain instead chooses on the basis of pT - 2, pT - 3, and pT + 1 positions. An FHA domain from a marker of human cancer instead chooses a much longer protein fragment that adds a beta-strand to its beta-sheet and that presents hydrophobic residues from a novel helix to the usual recognition surface. This novel recognition site and more remote sites for the binding of other types of protein partners were predicted for the entire family of FHA domains by a bioinformatics approach. The phosphopeptide-dependent dynamics of an FHA domain, SH2 domain, and PTB domain suggest a common theme: rigid, preformed binding surfaces support van der Waals contacts that provide favorable binding enthalpy. Despite the lack of pronounced conformational changes in FHA domains linked to binding events, more subtle adjustments may be possible. In the one FHA domain tested, phosphothreonine peptide binding is accompanied by increased flexibility just outside the binding site and increased rigidity across the beta-sandwich. The folding of the same FHA domain progresses through near-native intermediates that stabilize the recognition loops in the center of the phosphoprotein-binding surface; this may promote rigidity in the interface and affinity for targets phosphorylated on threonine.

Contraception supply chain challenges: a review of evidence from low- and middle-income countries.

PubMed

Mukasa, Bakali; Ali, Moazzam; Farron, Madeline; Van de Weerdt, Renee

2017-10-01

To identify and assess factors determining the functioning of supply chain systems for modern contraception in low- and middle-income countries (LMICs), and to identify challenges contributing to contraception stockouts that may lead to unmet need. Scientific databases and grey literature were searched including Database of Abstracts of Reviews of Effectiveness (DARE), PubMed, MEDLINE, POPLINE, CINAHL, Academic Search Complete, Science Direct, Web of Science, Cochrane Central, Google Scholar, WHO databases and websites of key international organisations. Studies indicated that supply chain system inefficiencies significantly affect availability of modern FP and contraception commodities in LMICs, especially in rural public facilities where distribution barriers may be acute. Supply chain failures or bottlenecks may be attributed to: weak and poorly institutionalized logistic management information systems (LMIS), poor physical infrastructures in LMICs, lack of trained and dedicated staff for supply chain management, inadequate funding, and rigid government policies on task sharing. However, there is evidence that implementing effective LMISs and involving public and private providers will distribution channels resulted in reduction in medical commodities' stockout rates. Supply chain bottlenecks contribute significantly to persistent high stockout rates for modern contraceptives in LMICs. Interventions aimed at enhancing uptake of contraceptives to reduce the problem of unmet need in LMICs should make strong commitments towards strengthening these countries' health commodities supply chain management systems. Current evidence is limited and additional, and well-designed implementation research on contraception supply chain systems is warranted to gain further understanding and insights on the determinants of supply chain bottlenecks and their impact on stockouts of contraception commodities.

Multivariable control of the Space Shuttle Remote Manipulator System using linearization by state feedback

NASA Technical Reports Server (NTRS)

Gettman, Chang-Ching L.; Adams, Neil; Bedrossian, Nazareth; Valavani, Lena

1993-01-01

This paper demonstrates an approach to nonlinear control system design that uses linearization by state feedback to allow faster maneuvering of payloads by the Shuttle Remote Manipulator System (SRMS). A nonlinear feedback law is defined to cancel the nonlinear plant dynamics so that a linear controller can be designed for the SRMS. First a nonlinear design model was generated via SIMULINK. This design model included nonlinear arm dynamics derived from the Lagrangian approach, linearized servo model, and linearized gearbox model. The current SRMS position hold controller was implemented on this system. Next, a trajectory was defined using a rigid body kinematics SRMS tool, KRMS. The maneuver was simulated. Finally, higher bandwidth controllers were developed. Results of the new controllers were compared with the existing SRMS automatic control modes for the Space Station Freedom Mission Build 4 Payload extended on the SRMS.

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.

Savannah, Georgia: The Lasting Legacy of Colonial City Planning. Teaching with Historic Places.

ERIC Educational Resources Information Center

Kratzer, Judson

Strolling through the old city of Savannah, Georgia's rigid, grid pattern streets, down its linear brick walkways, past over 1,100 residential and public buildings of unparalleled architectural richness and diversity, visitors and residents come to appreciate the original plan that has existed intact since Savannah's founding in 1733. Twenty-four…

COUPLING THE ALKALINE-SURFACTANT-POLYMER TECHNOLOGY AND THE GELATION TECHNOLOGY TO MAXIMIZE OIL PRODUCTION

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

Malcolm Pitts; Jie Qi; Dan Wilson

2005-04-01

Gelation technologies have been developed to provide more efficient vertical sweep efficiencies for flooding naturally fractured oil reservoirs or more efficient areal sweep efficiency for those with high permeability contrast ''thief zones''. The field proven alkaline-surfactant-polymer technology economically recovers 15% to 25% OOIP more oil than waterflooding from swept pore space of an oil reservoir. However, alkaline-surfactant-polymer technology is not amenable to naturally fractured reservoirs or those with thief zones because much of injected solution bypasses target pore space containing oil. This work investigates whether combining these two technologies could broaden applicability of alkaline-surfactant-polymer flooding into these reservoirs. A priormore » fluid-fluid report discussed interaction of different gel chemical compositions and alkaline-surfactant-polymer solutions. Gel solutions under dynamic conditions of linear corefloods showed similar stability to alkaline-surfactant-polymer solutions as in the fluid-fluid analyses. Aluminum-polyacrylamide, flowing gels are not stable to alkaline-surfactant-polymer solutions of either pH 10.5 or 12.9. Chromium acetate-polyacrylamide flowing and rigid flowing gels are stable to subsequent alkaline-surfactant-polymer solution injection. Rigid flowing chromium acetate-polyacrylamide gels maintained permeability reduction better than flowing chromium acetate-polyacrylamide gels. Silicate-polyacrylamide gels are not stable with subsequent injection of either a pH 10.5 or a 12.9 alkaline-surfactant-polymer solution. Chromium acetate-xanthan gum rigid gels are not stable to subsequent alkaline-surfactant-polymer solution injection. Resorcinol-formaldehyde gels were stable to subsequent alkaline-surfactant-polymer solution injection. When evaluated in a dual core configuration, injected fluid flows into the core with the greatest effective permeability to the injected fluid. The same gel stability trends to subsequent alkaline-surfactant-polymer injected solution were observed. Aluminum citrate-polyacrylamide, resorcinol-formaldehyde, and the silicate-polyacrylamide gel systems did not produce significant incremental oil in linear corefloods. Both flowing and rigid flowing chromium acetate-polyacrylamide gels and the xanthan gum-chromium acetate gel system produced incremental oil with the rigid flowing gel producing the greatest amount. Higher oil recovery could have been due to higher differential pressures across cores. None of the gels tested appeared to alter alkaline-surfactant-polymer solution oil recovery. Total waterflood plus chemical flood oil recovery sequence recoveries were all similar.« less

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.

Electrokinetic transport of rigid macroions in the thin double layer limit: a boundary element approach.

PubMed

Allison, Stuart A; Xin, Yao

2005-08-15

A boundary element (BE) procedure is developed to numerically calculate the electrophoretic mobility of highly charged, rigid model macroions in the thin double layer regime based on the continuum primitive model. The procedure is based on that of O'Brien (R.W. O'Brien, J. Colloid Interface Sci. 92 (1983) 204). The advantage of the present procedure over existing BE methodologies that are applicable to rigid model macroions in general (S. Allison, Macromolecules 29 (1996) 7391) is that computationally time consuming integrations over a large number of volume elements that surround the model particle are completely avoided. The procedure is tested by comparing the mobilities derived from it with independent theory of the mobility of spheres of radius a in a salt solution with Debye-Huckel screening parameter, kappa. The procedure is shown to yield accurate mobilities provided (kappa)a exceeds approximately 50. The methodology is most relevant to model macroions of mean linear dimension, L, with 1000>(kappa)L>100 and reduced absolute zeta potential (q|zeta|/k(B)T) greater than 1.0. The procedure is then applied to the compact form of high molecular weight, duplex DNA that is formed in the presence of the trivalent counterion, spermidine, under low salt conditions. For T4 DNA (166,000 base pairs), the compact form is modeled as a sphere (diameter=600 nm) and as a toroid (largest linear dimension=600 nm). In order to reconcile experimental and model mobilities, approximately 95% of the DNA phosphates must be neutralized by bound counterions. This interpretation, based on electrokinetics, is consistent with independent studies.

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.

High transparent shape memory gel

NASA Astrophysics Data System (ADS)

Gong, Jin; Arai, Masanori; Kabir, M. H.; Makino, Masato; Furukawa, Hidemitsu

2014-03-01

Gels are a new material having three-dimensional network structures of macromolecules. They possess excellent properties as swellability, high permeability and biocompatibility, and have been applied in various fields of daily life, food, medicine, architecture, and chemistry. In this study, we tried to prepare new multi-functional and high-strength gels by using Meso-Decoration (Meso-Deco), one new method of structure design at intermediate mesoscale. High-performance rigid-rod aromatic polymorphic crystals, and the functional groups of thermoreversible Diels-Alder reaction were introduced into soft gels as crosslinkable pendent chains. The functionalization and strengthening of gels can be realized by meso-decorating the gels' structure using high-performance polymorphic crystals and thermoreversible pendent chains. New gels with good mechanical properties, novel optical properties and thermal properties are expected to be developed.

Meso-decorated self-healing gels: network structure and properties

NASA Astrophysics Data System (ADS)

Gong, Jin; Sawamura, Kensuke; Igarashi, Susumu; Furukawa, Hidemitsu

2013-04-01

Gels are a new material having three-dimensional network structures of macromolecules. They possess excellent properties as swellability, high permeability and biocompatibility, and have been applied in various fields of daily life, food, medicine, architecture, and chemistry. In this study, we tried to prepare new multi-functional and high-strength gels by using Meso-Decoration (Meso-Deco), one new method of structure design at intermediate mesoscale. High-performance rigid-rod aromatic polymorphic crystals, and the functional groups of thermoreversible Diels-Alder reaction were introduced into soft gels as crosslinkable pendent chains. The functionalization and strengthening of gels can be realized by meso-decorating the gels' structure using high-performance polymorphic crystals and thermoreversible pendent chains. New gels with good mechanical properties, novel optical properties and thermal properties are expected to be developed.

Ion-conduction and rigidity/flexibility of glasses

NASA Astrophysics Data System (ADS)

Novita, D. I.; Boolchand, P.; Malki, M.; Micoulaut, M.

2007-03-01

The (AgI)x(AgPO3)1-x solid electrolyte glass system has been examined extensively although a consensus on the increase of electrical conductivity with x data has been elusive. Here we show that the variability of the data is likely due to water contamination. Our work is on specifically prepared dry samples which display glass transition temperatures Tg(x) that are at least 50 to 100 C higher than those reported hitherto. In Raman scattering the frequency of the P-Ot bonds in PO4 tetrahedra of long chains is found to systematically red-shift with increasing x, and to display thresholds near x= xc(1) =0.095(3)(stress-transition) and x =xc(2) = 0.379(5)(rigidity transition). Calorimetric measurements show a reversibility window in the 0.09 < x < 0.38 range. Room temperature electrical conductivity, σ(x), increases with x to display thresholds near xc(1) and xc(2), and a logarithmic increase at x> xc(2) with a power-law μ = 1.78(10) that is in good agreement with theoretical predictions^1. Properties of flexibility and rigidity of backbones commonplace in covalent systems^2 is a concept that extends to solid electrolyte glasses as well. ^1Richard Zallen, Physics of Amorphous Solids ^2 P. Boolchand et al. Phil. Mag 85, 3823 (2005)

Synthesis and anti-HIV activity of novel N-1 side chain-modified analogs of 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT).

PubMed

Pontikis, R; Benhida, R; Aubertin, A M; Grierson, D S; Monneret, C

1997-06-06

A series of 33 N-1 side chain-modified analogs of 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (1, HEPT) were synthesized and evaluated for their anti-HIV-1 activity. In particular, the influence of substitution of the terminal hydroxy group of the acyclic structure of HEPT and the structural rigidity of this side chain were investigated. Halo (7, 8), azido (9), and amino (10-15) derivatives were synthesized from HEPT via the p-tosylate derivative 6. Acylation of the primary amine 15 afforded the amido analogs 16-20. The diaryl derivatives 26-29 were prepared by reaction of HEPT, or of the 6-(2-pyridylthio) analog 23, with diaryl disulfides in the presence of tri-n-butylphosphine. Compounds 39-41, in which the N-1 side chain is rigidified by incorporation of an E-configured double bond, were obtained by palladium(0)-catalyzed coupling of several different 6-(arylthio)uracil derivatives (37, 38) with allyl acetates 33. Compounds 13, 40a,c,d,f, and 41, incorporating an aromatic ring at the end of the acyclic side chain, were found to be more potent than the known diphenyl-substituted HEPT analog BPT (2), two of them, 40c,d, being 10-fold more active.

Polymer ultrapermeability from the inefficient packing of 2D chains

NASA Astrophysics Data System (ADS)

Rose, Ian; Bezzu, C. Grazia; Carta, Mariolino; Comesaña-Gándara, Bibiana; Lasseuguette, Elsa; Ferrari, M. Chiara; Bernardo, Paola; Clarizia, Gabriele; Fuoco, Alessio; Jansen, Johannes C.; Hart, Kyle E.; Liyana-Arachchi, Thilanga P.; Colina, Coray M.; McKeown, Neil B.

2017-09-01

The promise of ultrapermeable polymers, such as poly(trimethylsilylpropyne) (PTMSP), for reducing the size and increasing the efficiency of membranes for gas separations remains unfulfilled due to their poor selectivity. We report an ultrapermeable polymer of intrinsic microporosity (PIM-TMN-Trip) that is substantially more selective than PTMSP. From molecular simulations and experimental measurement we find that the inefficient packing of the two-dimensional (2D) chains of PIM-TMN-Trip generates a high concentration of both small (<0.7 nm) and large (0.7-1.0 nm) micropores, the former enhancing selectivity and the latter permeability. Gas permeability data for PIM-TMN-Trip surpass the 2008 Robeson upper bounds for O2/N2, H2/N2, CO2/N2, H2/CH4 and CO2/CH4, with the potential for biogas purification and carbon capture demonstrated for relevant gas mixtures. Comparisons between PIM-TMN-Trip and structurally similar polymers with three-dimensional (3D) contorted chains confirm that its additional intrinsic microporosity is generated from the awkward packing of its 2D polymer chains in a 3D amorphous solid. This strategy of shape-directed packing of chains of microporous polymers may be applied to other rigid polymers for gas separations.

An analysis of general chain systems

NASA Technical Reports Server (NTRS)

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

1972-01-01

A general analysis of dynamic systems consisting of connected rigid bodies is presented. The number of bodies and their manner of connection is arbitrary so long as no closed loops are formed. The analysis represents a dynamic finite element method, which is computer-oriented and designed so that nonworking, interval constraint forces are automatically eliminated. The method is based upon Lagrange's form of d'Alembert's principle. Shifter matrix transformations are used with the geometrical aspects of the analysis. The method is illustrated with a space manipulator.

Gaussian step-pressure loading of rigid viscoplastic plates. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Hayduk, R. J.; Durling, B. J.

1978-01-01

The response of a thin, rigid viscoplastic plate subjected to a spatially axisymmetric Gaussian step pressure impulse loading was studied analytically. A Gaussian pressure distribution in excess of the collapse load was applied to the plate, held constant for a length of time, and then suddenly removed. The plate deforms with monotonically increasing deflections until the dynamic energy is completely dissipated in plastic work. The simply supported plate of uniform thickness obeys the von Mises yield criterion and a generalized constitutive equation for rigid viscoplastic materials. For the small deflection bending response of the plate, the governing system of equations is essentially nonlinear. Transverse shear stress is neglected in the yield condition and rotary inertia in the equations of dynamic equilibrium. A proportional loading technique, known to give excellent approximations of the exact solution for the uniform load case, was used to linearize the problem and to obtain the analytical solutions in the form of eigenvalue expansions. The effects of load concentration, of an order of magnitude change in the viscosity of the plate material, and of load duration were examined while holding the total impulse constant.

Optimized Spectral Editing of 13C MAS NMR Spectra of Rigid Solids Using Cross-Polarization Methods

NASA Astrophysics Data System (ADS)

Sangill, R.; Rastrupandersen, N.; Bildsoe, H.; Jakobsen, H. J.; Nielsen, N. C.

Combinations of 13C magic-angle spinning (MAS) NMR experiments employing cross polarization (CP), cross polarization-depolarization (CPD), and cross polarization-depolarization-repolarization are analyzed quantitatively to derive simple and general procedures for optimized spectral editing of 13C CP/MAS NMR spectra of rigid solids by separation of the 13C resonances into CH n subspectra ( n = 0, 1, 2, and 3). Special attention is devoted to a differentiation by CPD/MAS of CH and CH 2 resonances since these groups behave quite similarly during spin lock under Hartmann-Hahn match and are therefore generally difficult to distinguish unambiguously. A general procedure for the design of subexperiments and linear combinations of their spectra to provide optimized signal-to-noise ratios for the edited subspectra is described. The technique is illustrated by a series of edited 13C CP/MAS spectra for a number of rigid solids ranging from simple organic compounds (sucrose and l-menthol) to complex pharmaceutical products (calcipotriol monohydrate and vitamin D 3) and polymers (polypropylene, polyvinyl alcohol, polyvinyl chloride, and polystyrene).

A model for rotorcraft flying qualities studies

NASA Technical Reports Server (NTRS)

Mittal, Manoj; Costello, Mark F.

1993-01-01

This paper outlines the development of a mathematical model that is expected to be useful for rotorcraft flying qualities research. A computer model is presented that can be applied to a range of different rotorcraft configurations. The algorithm computes vehicle trim and a linear state-space model of the aircraft. The trim algorithm uses non linear optimization theory to solve the nonlinear algebraic trim equations. The linear aircraft equations consist of an airframe model and a flight control system dynamic model. The airframe model includes coupled rotor and fuselage rigid body dynamics and aerodynamics. The aerodynamic model for the rotors utilizes blade element theory and a three state dynamic inflow model. Aerodynamics of the fuselage and fuselage empennages are included. The linear state-space description for the flight control system is developed using standard block diagram data.

Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility.

PubMed

Schueler-Furman, Ora; Wang, Chu; Baker, David

2005-08-01

RosettaDock uses real-space Monte Carlo minimization (MCM) on both rigid-body and side-chain degrees of freedom to identify the lowest free energy docked arrangement of 2 protein structures. An improved version of the method that uses gradient-based minimization for off-rotamer side-chain optimization and includes information from unbound structures was used to create predictions for Rounds 4 and 5 of CAPRI. First, large numbers of independent MCM trajectories were carried out and the lowest free energy docked configurations identified. Second, new trajectories were started from these lowest energy structures to thoroughly sample the surrounding conformation space, and the lowest energy configurations were submitted as predictions. For all cases in which there were no significant backbone conformational changes, a small number of very low-energy configurations were identified in the first, global search and subsequently found to be close to the center of the basin of attraction in the free energy landscape in the second, local search. Following the release of the experimental coordinates, it was found that the centers of these free energy minima were remarkably close to the native structures in not only the rigid-body orientation but also the detailed conformations of the side-chains. Out of 8 targets, the lowest energy models had interface root-mean-square deviations (RMSDs) less than 1.1 A from the correct structures for 6 targets, and interface RMSDs less than 0.4 A for 3 targets. The predictions were top submissions to CAPRI for Targets 11, 12, 14, 15, and 19. The close correspondence of the lowest free energy structures found in our searches to the experimental structures suggests that our free energy function is a reasonable representation of the physical chemistry, and that the real space search with full side-chain flexibility to some extent solves the protein-protein docking problem in the absence of significant backbone conformational changes. On the other hand, the approach fails when there are significant backbone conformational changes as the steric complementarity of the 2 proteins cannot be modeled without incorporating backbone flexibility, and this is the major goal of our current work.

Simulation of flexible appendage interactions with Mariner Venus/Mercury attitude control and science platform pointing

NASA Technical Reports Server (NTRS)

Fleischer, G. E.

1973-01-01

A new computer subroutine, which solves the attitude equations of motion for any vehicle idealized as a topological tree of hinge-connected rigid bodies, is used to simulate and analyze science instrument pointing control interaction with a flexible Mariner Venus/Mercury (MVM) spacecraft. The subroutine's user options include linearized or partially linearized hinge-connected models whose computational advantages are demonstrated for the MVM problem. Results of the pointing control/flexible vehicle interaction simulations, including imaging experiment pointing accuracy predictions and implications for MVM science sequence planning, are described in detail.

A class of parallel algorithms for computation of the manipulator inertia matrix

NASA Technical Reports Server (NTRS)

Fijany, Amir; Bejczy, Antal K.

1989-01-01

Parallel and parallel/pipeline algorithms for computation of the manipulator inertia matrix are presented. An algorithm based on composite rigid-body spatial inertia method, which provides better features for parallelization, is used for the computation of the inertia matrix. Two parallel algorithms are developed which achieve the time lower bound in computation. Also described is the mapping of these algorithms with topological variation on a two-dimensional processor array, with nearest-neighbor connection, and with cardinality variation on a linear processor array. An efficient parallel/pipeline algorithm for the linear array was also developed, but at significantly higher efficiency.

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

A new description of Earth's wobble modes using Clairaut coordinates: 1. Theory

NASA Astrophysics Data System (ADS)

Rochester, M. G.; Crossley, D. J.; Zhang, Y. L.

2014-09-01

This paper presents a novel mathematical reformulation of the theory of the free wobble/nutation of an axisymmetric reference earth model in hydrostatic equilibrium, using the linear momentum description. The new features of this work consist in the use of (i) Clairaut coordinates (rather than spherical polars), (ii) standard spherical harmonics (rather than generalized spherical surface harmonics), (iii) linear operators (rather than J-square symbols) to represent the effects of rotational and ellipticity coupling between dependent variables of different harmonic degree and (iv) a set of dependent variables all of which are continuous across material boundaries. The resulting infinite system of coupled ordinary differential equations is given explicitly, for an elastic solid mantle and inner core, an inviscid outer core and no magnetic field. The formulation is done to second order in the Earth's ellipticity. To this order it is shown that for wobble modes (in which the lowest harmonic in the displacement field is degree 1 toroidal, with azimuthal order m = ±1), it is sufficient to truncate the chain of coupled displacement fields at the toroidal harmonic of degree 5 in the solid parts of the earth model. In the liquid core, however, the harmonic expansion of displacement can in principle continue to indefinitely high degree at this order of accuracy. The full equations are shown to yield correct results in three simple cases amenable to analytic solution: a general earth model in rigid rotation, the tiltover mode in a homogeneous solid earth model and the tiltover and Chandler periods for an incompressible homogeneous solid earth model. Numerical results, from programmes based on this formulation, are presented in part II of this paper.

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.

Generation of wavy structure on lipid membrane by peripheral proteins: a linear elastic analysis.

PubMed

Mahata, Paritosh; Das, Sovan Lal

2017-05-01

We carry out a linear elastic analysis to study wavy structure generation on lipid membrane by peripheral membrane proteins. We model the lipid membrane as linearly elastic and anisotropic material. The hydrophobic insertion by proteins into the lipid membrane has been idealized as penetration of rigid rod-like inclusions into the membrane and the electrostatic interaction between protein and membrane has been modeled by a distributed surface traction acting on the membrane surface. With the proposed model we study curvature generation by several binding domains of peripheral membrane proteins containing BAR domains and amphipathic alpha-helices. It is observed that electrostatic interaction is essential for curvature generation by the BAR domains. © 2017 Federation of European Biochemical Societies.

Estimation of regions of attraction and ultimate boundedness for multiloop LQ regulators. [Linear Quadratic

NASA Technical Reports Server (NTRS)

Joshi, S. M.

1984-01-01

Closed-loop stability is investigated for multivariable linear time-invariant systems controlled by optimal full state feedback linear quadratic (LQ) regulators, with nonlinear gains present in the feedback channels. Estimates are obtained for the region of attraction when the nonlinearities escape the (0.5, infinity) sector in regions away from the origin and for the region of ultimate boundedness when the nonlinearities escape the sector near the origin. The expressions for these regions also provide methods for selecting the performance function parameters in order to obtain LQ designs with better tolerance for nonlinearities. The analytical results are illustrated by applying them to the problem of controlling the rigid-body pitch angle and elastic motion of a large, flexible space antenna.

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.

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.

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.

Perioperative Brain Shift and Deep Brain Stimulating Electrode Deformation Analysis: Implications for rigid and non-rigid devices

PubMed Central

Sillay, Karl A.; Kumbier, L. M.; Ross, C.; Brady, M.; Alexander, A.; Gupta, A.; Adluru, N.; Miranpuri, G. S.; Williams, J. C.

2016-01-01

Deep brain stimulation (DBS) efficacy is related to optimal electrode placement. Several authors have quantified brain shift related to surgical targeting; yet, few reports document and discuss the effects of brain shift after insertion. Objective: To quantify brain shift and electrode displacement after device insertion. Twelve patients were retrospectively reviewed, and one post-operative MRI and one time-delayed CT were obtained for each patient and their implanted electrodes modeled in 3D. Two competing methods were employed to measure the electrode tip location and deviation from the prototypical linear implant after the resolution of acute surgical changes, such as brain shift and pneumocephalus. In the interim between surgery and a pneumocephalus free postoperative scan, electrode deviation was documented in all patients and all electrodes. Significant shift of the electrode tip was identified in rostral, anterior, and medial directions (p < 0.05). Shift was greatest in the rostral direction, measuring an average of 1.41 mm. Brain shift and subsequent electrode displacement occurs in patients after DBS surgery with the reversal of intraoperative brain shift. Rostral displacement is on the order of the height of one DBS contact. Further investigation into the time course of intraoperative brain shift and its potential effects on procedures performed with rigid and non-rigid devices in supine and semi-sitting surgical positions is needed. PMID:23010803

Sustainable thermoplastic elastomers derived from cellulose, fatty acid and furfural via ATRP and click chemistry.

PubMed

Yu, Juan; Lu, Chuanwei; Wang, Chunpeng; Wang, Jifu; Fan, Yimin; Chu, Fuxiang

2017-11-15

Cellulose-based thermoplastic elastomers (TPEs) have attracted considerable attention because of their rigid backbone, good mechanical properties, renewable nature and abundance. In the present study, sustainable TPEs based on ethyl cellulose (EC), fatty acid and furfural were generated by the combination of ATRP and "click chemistry". To fabricate sustainable TPEs with higher toughness, a range of polymers, including mono random-copolymer poly(tetrahydrofurfuryl methacrylate-co-lauryl methacrylate) (P(THFMA-co-LMA), dual polymer side chains PTHFMA and PLMA, and mono-block copolymer PTHFMA-b-PLMA, were designed as side chains to fabricate EC brush copolymers with random, dual or block side chain architectures using the "grafting from" and "grafting onto" methods. The multi-armed structures, chemical compositions and phase separation of these EC brush copolymers were confirmed by FT-IR, 1 H NMR, GPC, DSC, TEM and SEM. Overall, three types of EC brush copolymers all exhibited the desired mechanical properties of TPEs. In addition, the EC brush copolymers with dual/block side chain architectures showed higher tensile strength than that of the random polymers with similar compositions. Copyright © 2017. Published by Elsevier Ltd.

Surface Modification and Nanojunction Fabrication with Molecular Metal Wires

DTIC Science & Technology

2014-02-17

Title: Transition Metal Complexes of a Super Rigid Anthyridine Ligand: Structural, Magnetic and DFT Studies. Transition metal complexes of iron ( II ...Compounds with Masked Diazonium Capping Groups (J. Organomet. Chem. 2013, 745, 93). (3) New Diruthenium( II ,III) Compounds Bearing Terminal Olefin Groups...2012, 36, 2340). (2) Synthesis , Structure, Magnetism, and Single Molecular Conductance of Linear Trinickel String Complexes with Sulfur-Containing

Investigation of Periodic-Disturbance Identification and Rejection in Spacecraft

DTIC Science & Technology

2006-08-01

linear theory. Therefore, it is of interest to examine its efficacy on the current nonlinear spacecraft model. In addition, the robustness of the...School, Monterey, California 93943 Spacecraft periodic-disturbance rejection using a realistic spacecraft hardware simulator and its associated models...is investigated. The effectiveness of the dipole-type disturbance rejection filter on the current realistic nonlinear rigid-body spacecraft model is

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.

Neuromechanic: a computational platform for simulation and analysis of the neural control of movement

PubMed Central

Bunderson, Nathan E.; Bingham, Jeffrey T.; Sohn, M. Hongchul; Ting, Lena H.; Burkholder, Thomas J.

2015-01-01

Neuromusculoskeletal models solve the basic problem of determining how the body moves under the influence of external and internal forces. Existing biomechanical modeling programs often emphasize dynamics with the goal of finding a feed-forward neural program to replicate experimental data or of estimating force contributions or individual muscles. The computation of rigid-body dynamics, muscle forces, and activation of the muscles are often performed separately. We have developed an intrinsically forward computational platform (Neuromechanic, www.neuromechanic.com) that explicitly represents the interdependencies among rigid body dynamics, frictional contact, muscle mechanics, and neural control modules. This formulation has significant advantages for optimization and forward simulation, particularly with application to neural controllers with feedback or regulatory features. Explicit inclusion of all state dependencies allows calculation of system derivatives with respect to kinematic states as well as muscle and neural control states, thus affording a wealth of analytical tools, including linearization, stability analyses and calculation of initial conditions for forward simulations. In this review, we describe our algorithm for generating state equations and explain how they may be used in integration, linearization and stability analysis tools to provide structural insights into the neural control of movement. PMID:23027632

Neuromechanic: a computational platform for simulation and analysis of the neural control of movement.

PubMed

Bunderson, Nathan E; Bingham, Jeffrey T; Sohn, M Hongchul; Ting, Lena H; Burkholder, Thomas J

2012-10-01

Neuromusculoskeletal models solve the basic problem of determining how the body moves under the influence of external and internal forces. Existing biomechanical modeling programs often emphasize dynamics with the goal of finding a feed-forward neural program to replicate experimental data or of estimating force contributions or individual muscles. The computation of rigid-body dynamics, muscle forces, and activation of the muscles are often performed separately. We have developed an intrinsically forward computational platform (Neuromechanic, www.neuromechanic.com) that explicitly represents the interdependencies among rigid body dynamics, frictional contact, muscle mechanics, and neural control modules. This formulation has significant advantages for optimization and forward simulation, particularly with application to neural controllers with feedback or regulatory features. Explicit inclusion of all state dependencies allows calculation of system derivatives with respect to kinematic states and muscle and neural control states, thus affording a wealth of analytical tools, including linearization, stability analyses and calculation of initial conditions for forward simulations. In this review, we describe our algorithm for generating state equations and explain how they may be used in integration, linearization, and stability analysis tools to provide structural insights into the neural control of movement. Copyright © 2012 John Wiley & Sons, Ltd.

The extended Fourier pseudospectral time-domain method for atmospheric sound propagation.

PubMed

Hornikx, Maarten; Waxler, Roger; Forssén, Jens

2010-10-01

An extended Fourier pseudospectral time-domain (PSTD) method is presented to model atmospheric sound propagation by solving the linearized Euler equations. In this method, evaluation of spatial derivatives is based on an eigenfunction expansion. Evaluation on a spatial grid requires only two spatial points per wavelength. Time iteration is done using a low-storage optimized six-stage Runge-Kutta method. This method is applied to two-dimensional non-moving media models, one with screens and one for an urban canyon, with generally high accuracy in both amplitude and phase. For a moving atmosphere, accurate results have been obtained in models with both a uniform and a logarithmic wind velocity profile over a rigid ground surface and in the presence of a screen. The method has also been validated for three-dimensional sound propagation over a screen. For that application, the developed method is in the order of 100 times faster than the second-order-accurate FDTD solution to the linearized Euler equations. The method is found to be well suited for atmospheric sound propagation simulations where effects of complex meteorology and straight rigid boundary surfaces are to be investigated.

Influence of anisotropy on percolation and jamming of linear k-mers on square lattice with defects

NASA Astrophysics Data System (ADS)

Tarasevich, Yu Yu; Laptev, V. V.; Burmistrov, A. S.; Shinyaeva, T. S.

2015-09-01

By means of the Monte Carlo simulation, we study the layers produced by the random sequential adsorption of the linear rigid objects (k-mers also known as rigid or stiff rods, sticks, needles) onto the square lattice with defects in the presence of an external field. The value of k varies from 2 to 32. The point defects randomly and uniformly placed on the substrate hinder adsorption of the elongated objects. The external field affects isotropic deposition of the particles, consequently the deposited layers are anisotropic. We study the influence of the defect concentration, the length of the objects, and the external field on the percolation threshold and the jamming concentration. Our main findings are (i) the critical defect concentration at which the percolation never occurs even at jammed state decreases for short k-mers (k < 16) and increases for long k-mers (k > 16) as anisotropy increases, (ii) the corresponding critical k-mer concentration decreases with anisotropy growth, (iii) the jamming concentration decreases drastically with growth of k-mer length for any anisotropy, (iv) for short k-mers, the percolation threshold is almost insensitive to the defect concentration for any anisotropy.

The effect of bottom boundary condition type on the behavior of adhesive contact of spherical probe on an elastic film

NASA Astrophysics Data System (ADS)

Zhu, X.; Xu, W.

2017-11-01

This study presents an investigation on the behavior of adhesive contact between a rigid sphere and an elastic film which is either perfectly bonded (case I) or in frictionless contact (case II) with a rigid substrate. By using linear fracture mechanics, we formulate an convenient semi-analytical approach to develop relations between the applied force, penetration depth and contact radius. Finite element analysis (FEA) is used to verify the relationships. Our results reveal that the interfacial boundary conditions between the film and substrate have distinct effects on the adhesive contact behavior between the sphere and the film. The aim of the present study is to provide an instructive inspiration for controlling adhesion strength of the thin film subject to adhesive contact.

Aeroelastic Analysis of a Trimmed Generic Hypersonic Vehicle

NASA Technical Reports Server (NTRS)

Nydick, I.; Friedmann, P. P.

1999-01-01

The aeroelastic equations of motion governing a hypersonic vehicle in free flight are derived. The equations of motion for a translating and rotating flexible body using Lagrange's equations in terms of quasi-coordinates are presented. These equations are simplified for the case of a vehicle with pitch and plunge rigid body degrees of freedom and small elastic displacements. The displacements are approximated by a truncated series of the unrestrained mode shapes, which are obtained using equivalent plate theory. Subsequently, the nonlinear equations of motion are linearized about the trim state, which is obtained using a rigid body trim model and steady hypersonic aerodynamics. The appropriate flutter derivatives are calculated from piston theory. Results describing mode shapes, trim behavior, and aeroelastic stability of a generic hypersonic vehicle are presented.

Magnetoimpedance effect in the FeNi/Ti-based multilayered structure: A pressure sensor prototype

NASA Astrophysics Data System (ADS)

Chlenova, A. A.; Melnikov, G. Yu.; Svalov, A. V.; Kurlyandskaya, G. V.

2016-09-01

Magnetically soft [Ti/FeNi]5/Ti/Cu/Ti/[FeNi/Ti]4 multilayered structures were obtained by magnetron sputtering. Based on them sensitive elements have been investigated with focus on the design of the giant magnetoimpedance (MI) pressure sensors. Magnetic properties and MI of fabricated sensitive elements were comparatively analyzed for both multilayers deposited both onto rigid and flexible polymer substrates. Structures on a rigid substrate had the highest MI ratio of 140 %. They showed the sensitivity of 0.70 %/Ba suitable for possible applications in pressure sensing. Structures deposited onto flexible Cyclo Olefin Copolymer substrates had slightly lower sensitivity of 0.55 %/Ba. That structures showing linear dependence of MI ratio in the pressure range of 0 to 360 Ba are promising for microfluidic and biosensor applications.

Damageable contact between an elastic body and a rigid foundation

NASA Astrophysics Data System (ADS)

Campo, M.; Fernández, J. R.; Silva, A.

2009-02-01

In this work, the contact problem between an elastic body and a rigid obstacle is studied, including the development of material damage which results from internal compression or tension. The variational problem is formulated as a first-kind variational inequality for the displacements coupled with a parabolic partial differential equation for the damage field. The existence of a unique local weak solution is stated. Then, a fully discrete scheme is introduced using the finite element method to approximate the spatial variable and an Euler scheme to discretize the time derivatives. Error estimates are derived on the approximate solutions, from which the linear convergence of the algorithm is deduced under suitable regularity conditions. Finally, three two-dimensional numerical simulations are performed to demonstrate the accuracy and the behaviour of the scheme.

Flexible single-crystal silicon nanomembrane photonic crystal cavity.

PubMed

Xu, Xiaochuan; Subbaraman, Harish; Chakravarty, Swapnajit; Hosseini, Amir; Covey, John; Yu, Yalin; Kwong, David; Zhang, Yang; Lai, Wei-Cheng; Zou, Yi; Lu, Nanshu; Chen, Ray T

2014-12-23

Flexible inorganic electronic devices promise numerous applications, especially in fields that could not be covered satisfactorily by conventional rigid devices. Benefits on a similar scale are also foreseeable for silicon photonic components. However, the difficulty in transferring intricate silicon photonic devices has deterred widespread development. In this paper, we demonstrate a flexible single-crystal silicon nanomembrane photonic crystal microcavity through a bonding and substrate removal approach. The transferred cavity shows a quality factor of 2.2×10(4) and could be bent to a curvature of 5 mm radius without deteriorating the performance compared to its counterparts on rigid substrates. A thorough characterization of the device reveals that the resonant wavelength is a linear function of the bending-induced strain. The device also shows a curvature-independent sensitivity to the ambient index variation.

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.

Evaluation of 4-dimensional Computed Tomography to 4-dimensional Cone-Beam Computed Tomography Deformable Image Registration for Lung Cancer Adaptive Radiation Therapy

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

Balik, Salim; Weiss, Elisabeth; Jan, Nuzhat

2013-06-01

Purpose: To evaluate 2 deformable image registration (DIR) algorithms for the purpose of contour mapping to support image-guided adaptive radiation therapy with 4-dimensional cone-beam CT (4DCBCT). Methods and Materials: One planning 4D fan-beam CT (4DFBCT) and 7 weekly 4DCBCT scans were acquired for 10 locally advanced non-small cell lung cancer patients. The gross tumor volume was delineated by a physician in all 4D images. End-of-inspiration phase planning 4DFBCT was registered to the corresponding phase in weekly 4DCBCT images for day-to-day registrations. For phase-to-phase registration, the end-of-inspiration phase from each 4D image was registered to the end-of-expiration phase. Two DIR algorithms—smallmore » deformation inverse consistent linear elastic (SICLE) and Insight Toolkit diffeomorphic demons (DEMONS)—were evaluated. Physician-delineated contours were compared with the warped contours by using the Dice similarity coefficient (DSC), average symmetric distance, and false-positive and false-negative indices. The DIR results are compared with rigid registration of tumor. Results: For day-to-day registrations, the mean DSC was 0.75 ± 0.09 with SICLE, 0.70 ± 0.12 with DEMONS, 0.66 ± 0.12 with rigid-tumor registration, and 0.60 ± 0.14 with rigid-bone registration. Results were comparable to intraobserver variability calculated from phase-to-phase registrations as well as measured interobserver variation for 1 patient. SICLE and DEMONS, when compared with rigid-bone (4.1 mm) and rigid-tumor (3.6 mm) registration, respectively reduced the average symmetric distance to 2.6 and 3.3 mm. On average, SICLE and DEMONS increased the DSC to 0.80 and 0.79, respectively, compared with rigid-tumor (0.78) registrations for 4DCBCT phase-to-phase registrations. Conclusions: Deformable image registration achieved comparable accuracy to reported interobserver delineation variability and higher accuracy than rigid-tumor registration. Deformable image registration performance varied with the algorithm and the patient.« less

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.

Parallel O(log n) algorithms for open- and closed-chain rigid multibody systems based on a new mass matrix factorization technique

NASA Technical Reports Server (NTRS)

Fijany, Amir

1993-01-01

In this paper, parallel O(log n) algorithms for computation of rigid multibody dynamics are developed. These parallel algorithms are derived by parallelization of new O(n) algorithms for the problem. The underlying feature of these O(n) algorithms is a drastically different strategy for decomposition of interbody force which leads to a new factorization of the mass matrix (M). Specifically, it is shown that a factorization of the inverse of the mass matrix in the form of the Schur Complement is derived as M(exp -1) = C - B(exp *)A(exp -1)B, wherein matrices C, A, and B are block tridiagonal matrices. The new O(n) algorithm is then derived as a recursive implementation of this factorization of M(exp -1). For the closed-chain systems, similar factorizations and O(n) algorithms for computation of Operational Space Mass Matrix lambda and its inverse lambda(exp -1) are also derived. It is shown that these O(n) algorithms are strictly parallel, that is, they are less efficient than other algorithms for serial computation of the problem. But, to our knowledge, they are the only known algorithms that can be parallelized and that lead to both time- and processor-optimal parallel algorithms for the problem, i.e., parallel O(log n) algorithms with O(n) processors. The developed parallel algorithms, in addition to their theoretical significance, are also practical from an implementation point of view due to their simple architectural requirements.

Object matching using a locally affine invariant and linear programming techniques.

PubMed

Li, Hongsheng; Huang, Xiaolei; He, Lei

2013-02-01

In this paper, we introduce a new matching method based on a novel locally affine-invariant geometric constraint and linear programming techniques. To model and solve the matching problem in a linear programming formulation, all geometric constraints should be able to be exactly or approximately reformulated into a linear form. This is a major difficulty for this kind of matching algorithm. We propose a novel locally affine-invariant constraint which can be exactly linearized and requires a lot fewer auxiliary variables than other linear programming-based methods do. The key idea behind it is that each point in the template point set can be exactly represented by an affine combination of its neighboring points, whose weights can be solved easily by least squares. Errors of reconstructing each matched point using such weights are used to penalize the disagreement of geometric relationships between the template points and the matched points. The resulting overall objective function can be solved efficiently by linear programming techniques. Our experimental results on both rigid and nonrigid object matching show the effectiveness of the proposed algorithm.

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.

Mechanical transduction via a single soft polymer

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

The effect of thermal history on crystalline structure and mechanical properties of β-nucleated isotactic polypropylene

NASA Astrophysics Data System (ADS)

Tian, Yefei; Zhou, Jian; Feng, Jiachun

2018-04-01

The effect of thermal history on β-nucleated iPP was systematically investigated by comparing the variance of crystalline microstructures and mechanical property of stepwise crystallized sample and annealed sample, which experienced different thermal history. The mechanical property tests exhibit that that the toughness of stepwise crystallized sample and annealed sample were both decreased compared to control sample, while the tensile strength of the stepwise crystallized sample increased slightly. Structure investigation showed that the α-relaxation peak, which is related to the assignment of chains in rigid amorphous phase, moved to the high temperature region for stepwise crystallized sample, while it moved to the low temperature region for annealed sample. The results indicated the weakening in rigid amorphous fraction (RAF) and the increase in lamellar thickness of β-iPP after stepwise crystallization treatment. For annealed sample, the RAF strengthened and lamellar thickness decreased slightly after thermal treatment. A mechanism of crystalline microstructures evolution of restricted area between the main lamellar under different treatments was proposed.

On the limited recognition of inorganic surfaces by short peptides compared with antibodies.

PubMed

Artzy-Schnirman, Arbel; Abu-Shah, Enas; Dishon, Matan; Soifer, Hadas; Sivan, Yotam; Reiter, Yoram; Benhar, Itai; Sivan, Uri

2014-06-01

The vast potential applications of biomolecules that bind inorganic surfaces led mostly to the isolation of short peptides that target selectively specific materials. The demonstrated differential affinity toward certain surfaces created the impression that the recognition capacity of short peptides may match that of rigid biomolecules. In the following, we challenge this view by comparing the capacity of antibody molecules to discriminate between the (100) and (111A) facets of a gallium arsenide semiconductor crystal with the capacity of short peptides to do the same. Applying selection from several peptide and single chain phage display libraries, we find a number of antibody molecules that bind preferentially a given crystal facet but fail to isolate, in dozens of attempts, a single peptide capable of such recognition. The experiments underscore the importance of rigidity to the recognition of inorganic flat targets and therefore set limitations on potential applications of short peptides in biomimetics. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.

Structure-Based Druggability Assessment of the Mammalian Structural Proteome with Inclusion of Light Protein Flexibility

PubMed Central

Loving, Kathryn A.; Lin, Andy; Cheng, Alan C.

2014-01-01

Advances reported over the last few years and the increasing availability of protein crystal structure data have greatly improved structure-based druggability approaches. However, in practice, nearly all druggability estimation methods are applied to protein crystal structures as rigid proteins, with protein flexibility often not directly addressed. The inclusion of protein flexibility is important in correctly identifying the druggability of pockets that would be missed by methods based solely on the rigid crystal structure. These include cryptic pockets and flexible pockets often found at protein-protein interaction interfaces. Here, we apply an approach that uses protein modeling in concert with druggability estimation to account for light protein backbone movement and protein side-chain flexibility in protein binding sites. We assess the advantages and limitations of this approach on widely-used protein druggability sets. Applying the approach to all mammalian protein crystal structures in the PDB results in identification of 69 proteins with potential druggable cryptic pockets. PMID:25079060

Anomalous temperature dependence of layer spacing of de Vries liquid crystals: Compensation model

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

Merkel, K.; Kocot, A.; Vij, J. K., E-mail: jvij@tcd.ie

Smectic liquid crystals that exhibit temperature independent layer thickness offer technological advantages for their use in displays and photonic devices. The dependence of the layer spacing in SmA and SmC phases of de Vries liquid crystals is found to exhibit distinct features. On entering the SmC phase, the layer thickness initially decreases below SmA to SmC (T{sub A–C}) transition temperature but increases anomalously with reducing temperature despite the molecular tilt increasing. This anomalous observation is being explained quantitatively. Results of IR spectroscopy show that layer shrinkage is caused by tilt of the mesogen's rigid core, whereas the expansion is causedmore » by the chains getting more ordered with reducing temperature. This mutual compensation arising from molecular fragments contributing to the layer thickness differs from the previous models. The orientational order parameter of the rigid core of the mesogen provides direct evidence for de Vries cone model in the SmA phase for the two compounds investigated.« less

Synthesis, structure and magnetic property of a two-dimensional coordination polymer decorated with sine wave-like 1D double chain

NASA Astrophysics Data System (ADS)

Yao, Xiao-Qiang; Li, Dan-Yang; Xiao, Guo-Bin; Ma, Heng-Chang; Lei, Zi-Qiang; Liu, Jia-Cheng

2018-04-01

A new compound, {[Co(BPFI)(NDC)]H2O·0.5DMF}n (1) has been synthesized under hydrothermal condition by the self-assembly of V-shaped N-containing rigid ligand BPFI with Co(II) ions in the presence of H2NDC acid, where BPFI = 2,8-di(1H-imidazole-1-yl)dibenzo[b,d]furan, H2NDC = naphthalene-1,4-dicarboxylic acid. Compound 1 was characterized by elemental analysis, single crystal X-ray diffraction, FT-IR spectroscopy and UV-visible spectra. Structural analysis reveals that compound 1 is a unique dinuclear Co-based 2D (4,4) layer structure decorated with parallel double chains. In addition, magnetic study reveals the existence of antiferromagnetic coupling interactions between the Co(II) ions within the dinuclear unit of 1.

Closed-Loop System Identification Experience for Flight Control Law and Flying Qualities Evaluation of a High Performance Fighter Aircraft

NASA Technical Reports Server (NTRS)

Murphy, Patrick C.

1996-01-01

This paper highlights some of the results and issues associated with estimating models to evaluate control law design methods and design criteria for advanced high performance aircraft. Experimental fighter aircraft such as the NASA-High Alpha Research Vehicle (HARV) have the capability to maneuver at very high angles of attack where nonlinear aerodynamics often predominate. HARV is an experimental F/A-18, configured with thrust vectoring and conformal actuated nose strakes. Identifying closed-loop models for this type of aircraft can be made difficult by nonlinearities and high order characteristics of the system. In this paper, only lateral-directional axes are considered since the lateral-directional control law was specifically designed to produce classical airplane responses normally expected with low-order, rigid-body systems. Evaluation of the control design methodology was made using low-order equivalent systems determined from flight and simulation. This allowed comparison of the closed-loop rigid-body dynamics achieved in flight with that designed in simulation. In flight, the On Board Excitation System was used to apply optimal inputs to lateral stick and pedals at five angles at attack : 5, 20, 30, 45, and 60 degrees. Data analysis and closed-loop model identification were done using frequency domain maximum likelihood. The structure of identified models was a linear state-space model reflecting classical 4th-order airplane dynamics. Input time delays associated with the high-order controller and aircraft system were accounted for in data preprocessing. A comparison of flight estimated models with small perturbation linear design models highlighted nonlinearities in the system and indicated that the closed-loop rigid-body dynamics were sensitive to input amplitudes at 20 and 30 degrees angle of attack.

Closed-Loop System Identification Experience for Flight Control Law and Flying Qualities Evaluation of a High Performance Fighter Aircraft

NASA Technical Reports Server (NTRS)

Murphy, Patrick C.

1999-01-01

This paper highlights some of the results and issues associated with estimating models to evaluate control law design methods and design criteria for advanced high performance aircraft. Experimental fighter aircraft such as the NASA High Alpha Research Vehicle (HARV) have the capability to maneuver at very high angles of attack where nonlinear aerodynamics often predominate. HARV is an experimental F/A-18, configured with thrust vectoring and conformal actuated nose strakes. Identifying closed-loop models for this type of aircraft can be made difficult by nonlinearities and high-order characteristics of the system. In this paper only lateral-directional axes are considered since the lateral-directional control law was specifically designed to produce classical airplane responses normally expected with low-order, rigid-body systems. Evaluation of the control design methodology was made using low-order equivalent systems determined from flight and simulation. This allowed comparison of the closed-loop rigid-body dynamics achieved in flight with that designed in simulation. In flight, the On Board Excitation System was used to apply optimal inputs to lateral stick and pedals at five angles of attack: 5, 20, 30, 45, and 60 degrees. Data analysis and closed-loop model identification were done using frequency domain maximum likelihood. The structure of the identified models was a linear state-space model reflecting classical 4th-order airplane dynamics. Input time delays associated with the high-order controller and aircraft system were accounted for in data preprocessing. A comparison of flight estimated models with small perturbation linear design models highlighted nonlinearities in the system and indicated that the estimated closed-loop rigid-body dynamics were sensitive to input amplitudes at 20 and 30 degrees angle of attack.

3-D in vitro estimation of temperature using the change in backscattered ultrasonic energy.

PubMed

Arthur, R Martin; Basu, Debomita; Guo, Yuzheng; Trobaugh, Jason W; Moros, Eduardo G

2010-08-01

Temperature imaging with a non-invasive modality to monitor the heating of tumors during hyperthermia treatment is an attractive alternative to sparse invasive measurement. Previously, we predicted monotonic changes in backscattered energy (CBE) of ultrasound with temperature for certain sub-wavelength scatterers. We also measured CBE values similar to our predictions in bovine liver, turkey breast muscle, and pork rib muscle in 2-D in vitro studies and in nude mice during 2-D in vivo studies. To extend these studies to three dimensions, we compensated for motion and measured CBE in turkey breast muscle. 3-D data sets were assembled from images formed by a phased-array imager with a 7.5-MHz linear probe moved in 0.6-mm steps in elevation during uniform heating from 37 to 45 degrees C in 0.5 degrees C increments. We used cross-correlation as a similarity measure in RF signals to automatically track feature displacement as a function of temperature. Feature displacement was non-rigid. Envelopes of image regions, compensated for non-rigid motion, were found with the Hilbert transform then smoothed with a 3 x 3 running average filter before forming the backscattered energy at each pixel. CBE in 3-D motion-compensated images was nearly linear with an average sensitivity of 0.30 dB/ degrees C. 3-D estimation of temperature in separate tissue regions had errors with a maximum standard deviation of about 0.5 degrees C over 1-cm(3) volumes. Success of CBE temperature estimation based on 3-D non-rigid tracking and compensation for real and apparent motion of image features could serve as the foundation for the eventual generation of 3-D temperature maps in soft tissue in a non-invasive, convenient, and low-cost way in clinical hyperthermia.

Double Neimark Sacker bifurcation and torus bifurcation of a class of vibratory systems with symmetrical rigid stops

NASA Astrophysics Data System (ADS)

Luo, G. W.; Chu, Y. D.; Zhang, Y. L.; Zhang, J. G.

2006-11-01

A multidegree-of-freedom system having symmetrically placed rigid stops and subjected to periodic excitation is considered. The system consists of linear components, but the maximum displacement of one of the masses is limited to a threshold value by the symmetrical rigid stops. Repeated impacts usually occur in the vibratory system due to the rigid amplitude constraints. Such models play an important role in the studies of mechanical systems with clearances or gaps. Double Neimark-Sacker bifurcation of the system is analyzed by using the center manifold and normal form method of maps. The period-one double-impact symmetrical motion and homologous disturbed map of the system are derived analytically. A center manifold theorem technique is applied to reduce the Poincaré map to a four-dimensional one, and the normal form map associated with double Neimark-Sacker bifurcation is obtained. The bifurcation sets for the normal-form map are illustrated in detail. Local behavior of the vibratory systems with symmetrical rigid stops, near the points of double Neimark-Sacker bifurcations, is reported by the presentation of results for a three-degree-of-freedom vibratory system with symmetrical stops. The existence and stability of period-one double-impact symmetrical motion are analyzed explicitly. Also, local bifurcations at the points of change in stability are analyzed, thus giving some information on dynamical behavior near the points of double Neimark-Sacker bifurcations. Near the value of double Neimark-Sacker bifurcation there exist period-one double-impact symmetrical motion and quasi-periodic impact motions. The quasi-periodic impact motions are represented by the closed circle and "tire-like" attractor in projected Poincaré sections. With change of system parameters, the quasi-periodic impact motions usually lead to chaos via "tire-like" torus doubling.

Surface orientation effects on bending properties of surgical mesh are independent of tensile properties.

PubMed

Simon, David D; Andrews, Sharon M; Robinson-Zeigler, Rebecca; Valdes, Thelma; Woods, Terry O

2018-02-01

Current mechanical testing of surgical mesh focuses primarily on tensile properties even though implanted devices are not subjected to pure tensile loads. Our objective was to determine the flexural (bending) properties of surgical mesh and determine if they correlate with mesh tensile properties. The flexural rigidity values of 11 different surgical mesh designs were determined along three textile directions (machine, cross-machine, and 45° to machine; n = 5 for each) using ASTM D1388-14 while tracking surface orientation. Tensile testing was also performed on the same specimens using ASTM D882-12. Linear regressions were performed to compare mesh flexural rigidity to mesh thickness, areal mass density, filament diameter, ultimate tensile strength, and maximum extension. Of 33 mesh specimen groups, 30 had significant differences in flexural rigidity values when comparing surface orientations (top and bottom). Flexural rigidity and mesh tensile properties also varied with textile direction (machine and cross-machine). There was no strong correlation between the flexural and tensile properties, with mesh thickness having the best overall correlation with flexural rigidity. Currently, surface orientation is not indicated on marketed surgical mesh, and a single mesh may behave differently depending on the direction of loading. The lack of correlation between flexural stiffness and tensile properties indicates the need to examine mesh bending stiffness to provide a more comprehensive understanding of surgical mesh mechanical behaviors. Further investigation is needed to determine if these flexural properties result in the surgical mesh behaving mechanically different depending on implantation direction. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 854-862, 2018. © 2017 Wiley Periodicals, Inc.

Ontogenetic scaling of fore limb and hind limb joint posture and limb bone cross-sectional geometry in vervets and baboons.

PubMed

Burgess, M Loring; Schmitt, Daniel; Zeininger, Angel; McFarlin, Shannon C; Zihlman, Adrienne L; Polk, John D; Ruff, Christopher B

2016-09-01

Previous studies suggest that the postures habitually adopted by an animal influence the mechanical loading of its long bones. Relatively extended limb postures in larger animals should preferentially reduce anteroposterior (A-P) relative to mediolateral (M-L) bending of the limb bones and therefore decrease A-P/M-L rigidity. We test this hypothesis by examining growth-related changes in limb bone structure in two primate taxa that differ in ontogenetic patterns of joint posture. Knee and elbow angles of adult and immature vervets (Chlorocebus aethiops, n = 16) were compared to published data for baboons (Papio hamadryas ursinus, n = 33, Patel et al., ). Ontogenetic changes in ratios of A-P/M-L bending rigidity in the femur and humerus were compared in skeletal samples (C. aethiops, n = 28; P. cynocephalus, n = 39). Size changes were assessed with linear regression, and age group differences tested with ANOVA. Only the knee of baboons shows significant postural change, becoming more extended with age and mass. A-P/M-L bending rigidity of the femur decreases during ontogeny in immature and adult female baboons only. Trends in the humerus are less marked. Adult male baboons have higher A-P/M-L bending rigidity of the femur than females. The hypothesized relationship between more extended joints and reduced A-P/M-L bending rigidity is supported by our results for immature and adult female baboon hind limbs, and the lack of significant age changes in either parameter in forelimbs and vervets. Adult males of both species depart from general ontogenetic trends, possibly due to socially mediated behavioral differences between sexes. Am J Phys Anthropol 161:72-83, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

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

Li, Na; Huang, Rudan, E-mail: huangrd@bit.edu.cn

Six new inorganic–organic hybrids based on rigid triangular N-containing ligands, NaCu{sup I}{sub 2}(tib){sub 4}(H{sub 2}O){sub 4}[H{sub 2}PW{sup V}W{sup VI}{sub 11}O{sub 40}][H{sub 2}PW{sup VI}{sub 12}O{sub 40}]·6H{sub 2}O (1), Cu{sup II}{sub 3}(tib){sub 4}Cl{sub 4}[H{sub 2}PW{sup VI}{sub 12}O{sub 40}]{sub 2}·4H{sub 2}O (2), Co(tib){sub 2}[PW{sup V}{sub 3}W{sup VI}{sub 9}O{sub 38}]·5H{sub 2}O (3), Cu{sup II}{sub 3}(tib){sub 2}[P{sub 2}Mo{sup VI}{sub 5}O{sub 22}(O{sub 2})]·4H{sub 2}O (4), Mn(pytpy){sub 2}Mo{sup VI}{sub 4}O{sub 13} (5) and Co(pytpy){sub 2}Mo{sup VI}{sub 4}O{sub 13} (6) (tib=1,3,5-tris(1-imidazolyl)benzene, pytpy=4’-(4”-pyridyl)2,4’:6’,4”-terpyridine), have been hydrothermally synthesized. Single crystal X-ray diffraction studies revealed that compounds 1–4 display two-dimensional (2D) layered structures, and in compounds 1–3, the adjacent Keggin anionsmore » link with each other by W–O–W covalent interactions to form 1D inorganic chains. Compounds 5–6 are 3D “pillar-layer” frameworks based on bimetal–oxide layers pillared by the pytpy ligands. The compounds have been characterized by elemental analysis, powder X−ray diffraction, X-ray photoelectron spectroscopy and thermo gravimetric analyses. Moreover, the electrochemical and catalytic properties of compound 1 have been investigated as well. - Graphical abstract: Six new inorganic–organic hybrids based on rigid triangular N-containing ligands have been obtained under hydrothermal conditions and characterized by single-crystal X-ray diffraction analyses, elemental analyses, IR spectra, and thermogravimetric (TG) analyses. Compounds 1–4 display two-dimensional (2D) layers structure, and in compounds 1–3, the adjacent Keggin anions link with each other by W–O–W covalent interactions to form 1D inorganic Keggin anions chains. Compounds 5–6 are 3D “pillar-layer” frameworks based on bimetal–oxide layers pillared by the pytpy ligands. - Highlights: • MOFs based on POMs have been prepared. • Six new compounds based on rigid triangular N-containing ligands. • The adjacent POMs only share the oxygen atom to form a 1D inorganic Keggin chains.« less

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.

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

Fundamental investigations of clay/polymer nanocomposites and applications in co-extruded microlayered systems

NASA Astrophysics Data System (ADS)

Decker, Jeremy John

The second and fourth generations of hydroxylated dendritic polyesters (HBP2, HBP4) were combined with unmodified sodium montmorillonite clay (Na +MMT) in water to generate a broad range of polymer clay nanocomposites from 0 to 100% wt/wt Na+MMT. X-ray diffraction (XRD) and transmission electron microscopy (TEM) were used to investigate intercalation states of the clay galleries. It was shown that interlayer spacings were independent of generation number and changed over the composition range from 0.5 nm to 3.5 nm in 0.5 nm increments that corresponded to a flattened HBP conformation within the clay tactoids. The HBP4/Na+MMT systems were investigated to study the vitrified Rigid Amorphous Fraction (RAF) induced by the clay surfaces. Differential Scanning Calorimetry (DSC) showed changes in heat capacity, Delta Cp, at Tg, that decreased with clay content, until completely suppressed at 80 wt% Na+MMT due to confinement. RAF was quantified from these changes in heat capacity and verified by the analysis of orthopositronium lifetime temperature scans utilizing positron annihilation lifetime spectroscopy (PALS): verifying the glassy nature of the RAF at elevated temperatures. Mathematical relationships allowed for correlation of the interlayer spacings with DeltaC p. RAF formation correlated to intercalated HBP4, and external surfaces of the clay tactoids. The interdiffusion of a polymer pair in microlayers was exploited to increase the concentration of nanoclay particles. When microlayers of a nanocomposite composed of organically modified montmorillonite (M2(HT)2 ) inside maleic anhydride grafted linear low-density polyethylene (LLDPE-g-MA) and low-density polyethylene (LDPE) were taken into the melt, the greater mobility of the linear LLDPE-g-MA chains compared to the branched LDPE chains caused shrinkage of the nanocomposite microlayers, concentrating the M 2(HT)2 contained within. Analysis of the clay morphology within these layers demonstrated an increase in clay particle lengths and aspect ratios, which was attributed to the growth of skewed aggregates during concentration. The melt induced clay concentration and increased clay particle dimensions caused significant decreases in the permeability of the nanocomposite microlayers and reduced the overall permeability of the multilayered films. Morphology and transport behavior of these microlayered films were compared to a series of bulk nanocomposites using a second LLDPE-g-MA containing M 2(HT)2 with varying clay content.

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.

Influence of fast and slow alkali myosin light chain isoforms on the kinetics of stretch-induced force transients of fast-twitch type IIA fibres of rat.

PubMed

Andruchov, Oleg; Galler, Stefan

2008-03-01

This study contributes to understand the physiological role of slow myosin light chain isoforms in fast-twitch type IIA fibres of skeletal muscle. These isoforms are often attached to the myosin necks of rat type IIA fibres, whereby the slow alkali myosin light chain isoform MLC1s is much more frequent and abundant than the slow regulatory myosin light chain isoform MLC2s. In the present study, single-skinned rat type IIA fibres were maximally Ca(2+) activated and subjected to stepwise stretches for causing a perturbation of myosin head pulling cycles. From the time course of the resulting force transients, myosin head kinetics was deduced. Fibres containing MLC1s exhibited slower kinetics independently of the presence or absence of MLC2s. At the maximal MLC1s concentration of about 75%, the slowing was about 40%. The slowing effect of MLC1s is possibly due to differences in the myosin heavy chain binding sites of the fast and slow alkali MLC isoforms, which changes the rigidity of the myosin neck. Compared with the impact of myosin heavy chain isoforms in various fast-twitch fibre types, the influence of MLC1s on myosin head kinetics of type IIA fibres is much smaller. In conclusion, the physiological role of fast and slow MLC isoforms in type IIA fibres is a fine-tuning of the myosin head kinetics.

Rigid microenvironments promote cardiac differentiation of mouse and human embryonic stem cells

NASA Astrophysics Data System (ADS)

Arshi, Armin; Nakashima, Yasuhiro; Nakano, Haruko; Eaimkhong, Sarayoot; Evseenko, Denis; Reed, Jason; Stieg, Adam Z.; Gimzewski, James K.; Nakano, Atsushi

2013-04-01

While adult heart muscle is the least regenerative of tissues, embryonic cardiomyocytes are proliferative, with embryonic stem (ES) cells providing an endless reservoir. In addition to secreted factors and cell-cell interactions, the extracellular microenvironment has been shown to play an important role in stem cell lineage specification, and understanding how scaffold elasticity influences cardiac differentiation is crucial to cardiac tissue engineering. Though previous studies have analyzed the role of matrix elasticity on the function of differentiated cardiomyocytes, whether it affects the induction of cardiomyocytes from pluripotent stem cells is poorly understood. Here, we examine the role of matrix rigidity on cardiac differentiation using mouse and human ES cells. Culture on polydimethylsiloxane (PDMS) substrates of varied monomer-to-crosslinker ratios revealed that rigid extracellular matrices promote a higher yield of de novo cardiomyocytes from undifferentiated ES cells. Using a genetically modified ES system that allows us to purify differentiated cardiomyocytes by drug selection, we demonstrate that rigid environments induce higher cardiac troponin T expression, beating rate of foci, and expression ratio of adult α- to fetal β- myosin heavy chain in a purified cardiac population. M-mode and mechanical interferometry image analyses demonstrate that these ES-derived cardiomyocytes display functional maturity and synchronization of beating when co-cultured with neonatal cardiomyocytes harvested from a developing embryo. Together, these data identify matrix stiffness as an independent factor that instructs not only the maturation of already differentiated cardiomyocytes but also the induction and proliferation of cardiomyocytes from undifferentiated progenitors. Manipulation of the stiffness will help direct the production of functional cardiomyocytes en masse from stem cells for regenerative medicine purposes.

Using a novel rigid-fluoride polymer to control the interfacial thickness of graphene and tailor the dielectric behavior of poly(vinylidene fluoride-trifluoroethylene-chlorotrifluoroethylene) nanocomposites.

PubMed

Han, Xianghui; Chen, Sheng; Lv, Xuguang; Luo, Hang; Zhang, Dou; Bowen, Chris R

2018-01-24

Polymer nanocomposites based on conductive fillers for high performance dielectrics have attracted increasing attention in recent years. However, a number of physical issues are unclear, such as the effect of interfacial thickness on the dielectric properties of the polymer nanocomposites, which limits the enhancement of permittivity. In this research, two core-shell structured reduced graphene oxide (rGO)@rigid-fluoro-polymer conducting fillers with different shell thicknesses are prepared using a surface-initiated reversible-addition-fragmentation chain transfer polymerization method, which are denoted as rGO@PTFMS-1 with a thin shell and rGO@PTFMS-2 with a thick shell. A rigid liquid crystalline fluoride-polymer poly{5-bis[(4-trifluoro-methoxyphenyl)oxycarbonyl]styrene} (PTFMS) is chosen for the first time to tailor the shell thicknesses of rGO via tailoring the degree of polymerization. The effect of interfacial thickness on the dielectric behavior of the P(VDF-TrFE-CTFE) nanocomposites with rGO and modified rGO is studied in detail. The results demonstrate that the percolation threshold of the nanocomposites increased from 0.68 vol% to 1.69 vol% with an increase in shell thickness. Compared to the rGO@PTFMS-1/P(VDF-TrFE-CTFE) composites, the rGO@PTFMS-2/P(VDF-TrFE-CTFE) composites exhibited a higher breakdown strength and a lower dielectric constant, which can be interpreted by interfacial polarization and the micro-capacitor model, resulting from the insulating nature of the rigid-polymer shell and the change of rGO's morphology. The findings provide an innovative approach to tailor dielectric composites, and promote a deeper understanding of the influence of interfacial region thickness on the dielectric performance.

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.

Geometric somersaults of a polymer chain through cyclic twisting motions

NASA Astrophysics Data System (ADS)

Yanao, Tomohiro; Hino, Taiko

2017-01-01

This study explores the significance of geometric angle shifts, which we call geometric somersaults, arising from cyclic twisting motions of a polymer chain. A five-bead polymer chain serves as a concise and minimal model of a molecular shaft throughout this study. We first show that this polymer chain can change its orientation about its longitudinal axis largely, e.g., 120∘, under conditions of zero total angular momentum by changing the two dihedral angles in a cyclic manner. This phenomenon is an example of the so-called "falling cat" phenomenon, where a falling cat undergoes a geometric somersault by changing its body shape under conditions of zero total angular momentum. We then extend the geometric somersault of the polymer chain to a noisy and viscous environment, where the polymer chain is steered by external driving forces. This extension shows that the polymer chain can achieve an orientation change keeping its total angular momentum and total external torque fluctuating around zero in a noisy and viscous environment. As an application, we argue that the geometric somersault of the polymer chain by 120∘ may serve as a prototypical and coarse-grained model for the rotary motion of the central shaft of ATP synthase (FOF1 -ATPase). This geometric somersault is in clear contrast to the standard picture for the rotary motion of the central shaft as a rigid body, which generally incurs nonzero total angular momentum and nonzero total external torque. The power profile of the geometric somersault implies a preliminary mechanism for elastic power transmission. The results of this study may be of fundamental interest in twisting and rotary motions of biomolecules.

Interlocking Molecular Gear Chains Built on Surfaces.

PubMed

Zhao, Rundong; Qi, Fei; Zhao, Yan-Ling; Hermann, Klaus E; Zhang, Rui-Qin; Van Hove, Michel A

2018-05-17

Periodic chains of molecular gears in which molecules couple with each other and rotate on surfaces have been previously explored by us theoretically using ab initio simulation tools. On the basis of the knowledge and experience gained about the interactions between neighboring molecular gears, we here explore the transmission of rotational motion and energy over larger distances, namely, through a longer chain of gear-like passive "slave" molecules. Such microscopic gears exhibit quite different behaviors compared to rigid cogwheels in the macroscopic world due to their structural flexibility affecting intermolecular interaction. Here, we investigate the capabilities of such gear chains and reveal the mechanisms of the transmission process in terms of both quantum-level density functional theory (DFT) and simple classical mechanics. We find that the transmission of rotation along gear chains depends strongly on the gear-gear distance: short distances can cause tilting of gears and even irregular "creep-then-jump" (or "stick-slip") motion or expulsion of gears; long gear-gear distances cause weak coupling between gears, slipping and skipping. More importantly, for transmission of rotation at intermediate gear-gear distances, our modeling clearly exhibits the relative roles of several important factors: flexibility of gear arms, axles, and supports, as well as resulting rotational delays, slippages, and thermal and other effects. These studies therefore allow better informed design of future molecular machine components involving motors, gears, axles, etc.

Degradation studies on highly oriented poly(glycolic acid) fibres with different lamellar structures.

PubMed

de Oca, Horacio Montes; Farrar, David F; Ward, Ian M

2011-04-01

Highly oriented poly(glycolic acid) (PGA) fibres with an initial tensile strength of 1.1 GPa and different lamellar morphologies were prepared and studied during degradation in aqueous media at 37°C. A combination of small- and wide-angle X-ray scattering was used to study the structural changes during degradation and to generate two structural models of highly oriented PGA fibres with different lamellar morphologies. It is shown that as a result of crystallisation during degradation PGA crystals grow preferentially along the (110) and (020) directions of the crystal lattice or perpendicular to the orientation direction of the fibres. (1)H nuclear magnetic resonance measurements revealed three phases within the fibres with different relaxation times: (1) a mobile amorphous phase with a short relaxation time; (2) a semi-rigid phase with an intermediate relaxation time; (3) a rigid crystalline phase with a longer relaxation time. It is shown that the mobile amorphous phase degrades very rapidly and that it plays only a small role in the tensile mechanical behaviour of the fibres during degradation. It is shown that semi-rigid chains connecting crystalline domains are responsible for transferring the stress between crystalline domains and carrying the tensile deformation. It is proposed that once these tie molecules degrade considerably the oriented fibres very rapidly lose their strength retention. Copyright © 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

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

PubMed

Abraham, Alex; Chatterji, Apratim

2018-04-21

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

Self assembled linear polymeric chains with tuneable semiflexibility using isotropic interactions

NASA Astrophysics Data System (ADS)

Abraham, Alex; Chatterji, Apratim

2018-04-01

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

Automatic Mrf-Based Registration of High Resolution Satellite Video Data

NASA Astrophysics Data System (ADS)

Platias, C.; Vakalopoulou, M.; Karantzalos, K.

2016-06-01

In this paper we propose a deformable registration framework for high resolution satellite video data able to automatically and accurately co-register satellite video frames and/or register them to a reference map/image. The proposed approach performs non-rigid registration, formulates a Markov Random Fields (MRF) model, while efficient linear programming is employed for reaching the lowest potential of the cost function. The developed approach has been applied and validated on satellite video sequences from Skybox Imaging and compared with a rigid, descriptor-based registration method. Regarding the computational performance, both the MRF-based and the descriptor-based methods were quite efficient, with the first one converging in some minutes and the second in some seconds. Regarding the registration accuracy the proposed MRF-based method significantly outperformed the descriptor-based one in all the performing experiments.

A theoretical evaluation of rigid baffles in suppression of combustion instability

NASA Technical Reports Server (NTRS)

Baer, M. R.; Mitchell, C. E.

1976-01-01

An analytical technique for the prediction of the effects of rigid baffles on the stability of liquid propellant combustors is presented. A three dimensional combustor model characterized by a concentrated combustion source at the chamber injector and a constant Mach number nozzle is used. The linearized partial differential equations describing the unsteady flow field are solved by an eigenfunction matching method. Boundary layer corrections to this unsteady flow are used to evaluate viscous and turbulence effects within the flow. An integral stability relationship is then employed to predict the decay rate of the oscillations. Results show that sufficient dissipation exists to indicate that the proper mechanism of baffle damping is a fluid dynamic loss. The response of the dissipation model to varying baffle blade length, mean flow Mach number and oscillation amplitude is examined.

Nonlinear oscillation of a rigid body over high- Tc superconductors supported by electro-magnetic forces

NASA Astrophysics Data System (ADS)

Sugiura, T.; Ogawa, S.; Ura, H.

2005-10-01

Characteristics of high- Tc superconducting levitation systems are no contact support and stable levitation without control. They can be applied to supporting mechanisms in machines, such as linear-drives and magnetically levitated trains. But small damping due to noncontact support and nonlinearity in the magnetic force can easily cause complicated phenomena of nonlinear dynamics. This research deals with nonlinear oscillation of a rigid bar supported at its both ends by electro-magnetic forces between superconductors and permanent magnets as a simple modeling of the above application. Deriving the equation of motion, we discussed an effect of nonlinearity in the magnetic force on dynamics of the levitated body: occurrence of combination resonance in the asymmetrical system. Numerical analyses and experiments were also carried out, and their results confirmed the above theoretical prediction.

Assessment of Multiaxial Mechanical Response of Rigid Polyurethane Foams

NASA Astrophysics Data System (ADS)

Pettarin, Valeria; Fasce, Laura A.; Frontini, Patricia M.

2014-02-01

Multiaxial deformation behavior and failure surface of rigid polyurethane foams were determined using standard experimental facilities. Two commercial foams of different densities were assayed under uniaxial, biaxial, and triaxial stress states. These different stress states were reached in a uniaxial universal testing machine using suitable testing configurations which imply the use of special grips and lateral restricted samples. Actual strains were monitored with a video extensometer. Polyurethane foams exhibited typical isotropic brittle behavior, except under compressive loads where the response turned out to be ductile. A general failure surface in the stress space which accounts for density effects could be successfully generated. All of failure data, determined at the loss of linear elasticity point, collapsed in a single locus defined as the combination of a brittle crushing of closed-cell cellular materials criterion capped by an elastic buckling criterion.

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.

Optimizing the way kinematical feed chains with great distance between slides are chosen for CNC machine tools

NASA Astrophysics Data System (ADS)

Lucian, P.; Gheorghe, S.

2017-08-01

This paper presents a new method, based on FRISCO formula, for optimizing the choice of the best control system for kinematical feed chains with great distance between slides used in computer numerical controlled machine tools. Such machines are usually, but not limited to, used for machining large and complex parts (mostly in the aviation industry) or complex casting molds. For such machine tools the kinematic feed chains are arranged in a dual-parallel drive structure that allows the mobile element to be moved by the two kinematical branches and their related control systems. Such an arrangement allows for high speed and high rigidity (a critical requirement for precision machining) during the machining process. A significant issue for such an arrangement it’s the ability of the two parallel control systems to follow the same trajectory accurately in order to address this issue it is necessary to achieve synchronous motion control for the two kinematical branches ensuring that the correct perpendicular position it’s kept by the mobile element during its motion on the two slides.

Polyurethane foams based on crude glycerol-derived biopolyols: One-pot preparation of biopolyols with branched fatty acid ester chains and its effects on foam formation and properties

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

Li, Cong; Luo, Xiaolan; Li, Tao

2014-01-01

Environmentally friendly biopolyols have been produced with crude glycerol as the sole feedstock using a one-pot thermochemical conversion process without the addition of extra catalysts and reagents. Structural features of these biopolyols were characterized by rheology analysis. Rigid polyurethane (PU) foams were obtained from these crude glycerol-based biopolyols and the foaming mechanism was explored. Investigations revealed that partial carbonyl groups hydrogen-bonded with NeH were replaced by aromatic rings after the introduction of branched fatty acid ester chains in the “urea rich” phase, and that distinct microphases had formed in the foams. Studies showed that branched fatty acid ester chains inmore » the biopolyols played an important role in reducing the degree of microphase separation and stabilizing bubbles during foaming processes. PU foams with thermal conductivity comparable to commercial products made from petroleum-based polyols were obtained. These studies show the potential for development of PU foams based on crude glycerol, a renewable resource.« less

Adjusting membrane lipids under salt stress: the case of the moderate halophilic organism Halobacillus halophilus.

PubMed

Lopalco, Patrizia; Angelini, Roberto; Lobasso, Simona; Köcher, Saskia; Thompson, Melanie; Müller, Volker; Corcelli, Angela

2013-04-01

The lipid composition of Halobacillus halophilus was investigated by combined thin-layer chromatography and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analyses of the total lipid extract. Main polar lipids were found to be sulfoquinovosyldiacylglycerol and phosphatidylglycerol, while cardiolipin was a minor lipid together with phosphatidic acid, alanyl-phosphatidylglycerol and two not yet fully identified lipid components. In addition the analyses of residual lipids, associated with denatured proteins after the lipid extraction, revealed the presence of significant amounts of cardiolipin, indicating that it is a not readily extractable phospholipid. Post decay source mass spectrometry analyses allowed the determination of acyl chains of main lipid components. On increasing the culture medium salinity, an increase in the shorter chains and the presence of chain unsaturations were observed. These changes in the lipid core structures might compensate for the increase in packing and rigidity of phospholipid and sulfoglycolipid polar heads in high-salt medium, therefore contributing to the homeostasis of membrane fluidity and permeability in salt stress conditions. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Can 5-methylcytosine analogues with extended alkyl side chains guide DNA methylation?

PubMed

Kotandeniya, D; Seiler, C L; Fernandez, J; Pujari, S S; Curwick, L; Murphy, K; Wickramaratne, S; Yan, S; Murphy, D; Sham, Yuk Y; Tretyakova, N Y

2018-01-25

5-Methylcytosine ( Me C) is an endogenous modification of DNA that plays a crucial role in DNA-protein interactions, chromatin structure, epigenetic regulation, and DNA repair. Me C is produced via enzymatic methylation of the C-5 position of cytosine by DNA-methyltransferases (DNMT) which use S-adenosylmethionine (SAM) as a cofactor. Hemimethylated CG dinucleotides generated as a result of DNA replication are specifically recognized and methylated by maintenance DNA methyltransferase 1 (DNMT1). The accuracy of DNMT1-mediated methylation is essential for preserving tissue-specific DNA methylation and thus gene expression patterns. In the present study, we synthesized DNA duplexes containing MeC analogues with modified C-5 side chains and examined their ability to guide cytosine methylation by the human DNMT1 protein. We found that the ability of 5-alkylcytosines to direct cytosine methylation decreased with increased alkyl chain length and rigidity (methyl > ethyl > propyl ∼ vinyl). Molecular modeling studies indicated that this loss of activity may be caused by the distorted geometry of the DNA-protein complex in the presence of unnatural alkylcytosines.

Design of a dynamic sensor inspired by bat ears

NASA Astrophysics Data System (ADS)

Müller, Rolf; Pannala, Mittu; Reddy, O. Praveen K.; Meymand, Sajjad Z.

2012-09-01

In bats, the outer ear shapes act as beamforming baffles that create a spatial sensitivity pattern for the reception of the biosonar signals. Whereas technical receivers for wave-based signals usually have rigid geometries, the outer ears of some bat species, such as horseshoe bats, can undergo non-rigid deformations as a result of muscular actuation. It is hypothesized that these deformations provide the animals with a mechanism to adapt their spatial hearing sensitivity on short, sub-second time scales. This biological approach could be of interest to engineering as an inspiration for the design of beamforming devices that combine flexibility with parsimonious implementation. To explore this possibility, a biomimetic dynamic baffle was designed based on a simple shape overall geometry based on an average bat ear. This shape was augmented with three different biomimetic local shape features, a ridge on its exposed surface as well as a flap and an incision along its rim. Dynamic non-rigid deformations of the shape were accomplished through a simple actuation mechanism based on linear actuation inserted at a single point. Despite its simplicity, the prototype device was able to reproduce the dynamic functional characteristics that have been predicted for its biological paragon in a qualitative fashion.

Distributed-Lagrange-Multiplier-based computational method for particulate flow with collisions

NASA Astrophysics Data System (ADS)

Ardekani, Arezoo; Rangel, Roger

2006-11-01

A Distributed-Lagrange-Multiplier-based computational method is developed for colliding particles in a solid-fluid system. A numerical simulation is conducted in two dimensions using the finite volume method. The entire domain is treated as a fluid but the fluid in the particle domains satisfies a rigidity constraint. We present an efficient method for predicting the collision between particles. In earlier methods, a repulsive force was applied to the particles when their distance was less than a critical value. In this method, an impulsive force is computed. During the frictionless collision process between two particles, linear momentum is conserved while the tangential forces are zero. Thus, instead of satisfying a condition of rigid body motion for each particle separately, as done when particles are not in contact, both particles are rigidified together along their line of centers. Particles separate from each other when the impulsive force is less than zero and after this time, a rigidity constraint is satisfied for each particle separately. Grid independency is implemented to ensure the accuracy of the numerical simulation. A comparison between this method and previous collision strategies is presented and discussed.

On oscillatory magnetoconvection in a nanofluid layer in the presence of internal heat source and Soret effect

NASA Astrophysics Data System (ADS)

Khalid, Izzati Khalidah; Mokhtar, Nor Fadzillah Mohd; Bakri, Nur Amirah; Siri, Zailan; Ibrahim, Zarina Bibi; Gani, Siti Salwa Abd

2017-11-01

The onset of oscillatory magnetoconvection for an infinite horizontal nanofluid layer subjected to Soret effect and internal heat source heated from below is examined theoretically with the implementation of linear stability theory. Two important properties that are thermophoresis and Brownian motion are included in the model and three types of lower-upper bounding systems of the model: rigid-rigid, rigid-free as well as free-free boundaries are examined. Eigenvalue equations are gained from a normal mode analysis and executed using Galerkin technique. Magnetic field effect, internal heat source effect, Soret effect and other nanofluid parameters on the oscillatory convection are presented graphically. For oscillatory mode, it is found that the effect of internal heat source is quite significant for small values of the non-dimensional parameter and elevating the internal heat source speed up the onset of convection. Meanwhile, the increasing of the strength of magnetic field in a nanofluid layer reduced the rate of thermal instability and sustain the stabilization of the system. For the Soret effect, the onset of convection in the system is accelerated when the values of the Soret effect is increased.

Molecular simulation of gas adsorption and diffusion in a breathing MOF using a rigid force field.

PubMed

García-Pérez, E; Serra-Crespo, P; Hamad, S; Kapteijn, F; Gascon, J

2014-08-14

Simulation of gas adsorption in flexible porous materials is still limited by the slow progress in the development of flexible force fields. Moreover, the high computational cost of such flexible force fields may be a drawback even when they are fully developed. In this work, molecular simulations of gas adsorption and diffusion of carbon dioxide and methane in NH2-MIL-53(Al) are carried out using a linear combination of two crystallographic structures with rigid force fields. Once the interactions of carbon dioxide molecules and the bridging hydroxyls groups of the framework are optimized, an excellent match is found for simulations and experimental data for the adsorption of methane and carbon dioxide, including the stepwise uptake due to the breathing effect. In addition, diffusivities of pure components are calculated. The pore expansion by the breathing effect influences the self-diffusion mechanism and much higher diffusivities are observed at relatively high adsorbate loadings. This work demonstrates that using a rigid force field combined with a minimum number of experiments, reproduces adsorption and simulates diffusion of carbon dioxide and methane in the flexible metal-organic framework NH2-MIL-53(Al).

Doping-induced spectral shifts in two-dimensional metal oxides

NASA Astrophysics Data System (ADS)

Ylvisaker, E. R.; Pickett, W. E.

2013-03-01

Doping of strongly layered ionic oxides is an established paradigm for creating novel electronic behavior. This is nowhere more apparent than in superconductivity, where doping gives rise to high-temperature superconductivity in cuprates (hole doped) and to surprisingly high Tc in HfNCl (Tc = 25.5 K, electron doped). First-principles calculations of hole doping of the layered delafossite CuAlO2 reveal unexpectedly large doping-induced shifts in spectral density, strongly in opposition to the rigid-band picture that is widely used as an accepted guideline. These spectral shifts, of similar origin as the charge transfer used to produce negative electron affinity surfaces and adjust Schottky barrier heights, drastically alter the character of the Fermi level carriers, leading in this material to an O-Cu-O molecule-based carrier (or polaron, at low doping) rather than a nearly pure-Cu hole as in a rigid-band picture. First-principles linear response electron-phonon coupling (EPC) calculations reveal, as a consequence, net weak EPC and no superconductivity rather than the high Tc obtained previously using rigid-band expectations. These specifically two-dimensional dipole-layer-driven spectral shifts provide new insights into materials design in layered materials for functionalities besides superconductivity.

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